Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 16 15:32:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1f_40962/08_2023/8t1f_40962_updated.pdb" } resolution = 3.49 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= 0.002 sd= 0.024 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 104 5.16 5 C 13566 2.51 5 N 3414 2.21 5 O 3690 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 271": "NH1" <-> "NH2" Residue "A PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A ARG 616": "NH1" <-> "NH2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 757": "NH1" <-> "NH2" Residue "A ARG 779": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 391": "NH1" <-> "NH2" Residue "B ARG 464": "NH1" <-> "NH2" Residue "B ARG 616": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B ARG 746": "NH1" <-> "NH2" Residue "B ARG 757": "NH1" <-> "NH2" Residue "B ARG 779": "NH1" <-> "NH2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 271": "NH1" <-> "NH2" Residue "C PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 391": "NH1" <-> "NH2" Residue "C ARG 464": "NH1" <-> "NH2" Residue "C ARG 616": "NH1" <-> "NH2" Residue "C ARG 661": "NH1" <-> "NH2" Residue "C ARG 746": "NH1" <-> "NH2" Residue "C ARG 757": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 269": "NH1" <-> "NH2" Residue "D ARG 271": "NH1" <-> "NH2" Residue "D PHE 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 391": "NH1" <-> "NH2" Residue "D ARG 464": "NH1" <-> "NH2" Residue "D ARG 616": "NH1" <-> "NH2" Residue "D ARG 661": "NH1" <-> "NH2" Residue "D ARG 746": "NH1" <-> "NH2" Residue "D ARG 757": "NH1" <-> "NH2" Residue "D ARG 779": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 20790 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5107 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 24, 'TRANS': 610} Chain breaks: 1 Chain: "B" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5116 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 24, 'TRANS': 611} Chain breaks: 1 Chain: "C" Number of atoms: 5107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5107 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 24, 'TRANS': 610} Chain breaks: 1 Chain: "D" Number of atoms: 5116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5116 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 24, 'TRANS': 611} Chain breaks: 1 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'POV': 1, 'X7N': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.35, per 1000 atoms: 0.50 Number of scatterers: 20790 At special positions: 0 Unit cell: (151.06, 147.74, 120.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 104 16.00 P 4 15.00 F 12 9.00 O 3690 8.00 N 3414 7.00 C 13566 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: 8.17 Conformation dependent library (CDL) restraints added in 2.8 seconds 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 118 helices and 4 sheets defined 50.7% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.55 Creating SS restraints... Processing helix chain 'A' and resid 151 through 160 removed outlier: 3.568A pdb=" N SER A 159 " --> pdb=" O PHE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 removed outlier: 4.135A pdb=" N LEU A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 194 through 200 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.689A pdb=" N ALA A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A 218 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.702A pdb=" N LEU A 256 " --> pdb=" O HIS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 278 No H-bonds generated for 'chain 'A' and resid 276 through 278' Processing helix chain 'A' and resid 288 through 292 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.804A pdb=" N LEU A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 355 removed outlier: 4.313A pdb=" N PHE A 341 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 removed outlier: 3.608A pdb=" N ALA A 377 " --> pdb=" O PRO A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 391 removed outlier: 3.838A pdb=" N HIS A 388 " --> pdb=" O GLY A 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG A 391 " --> pdb=" O GLN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 433 through 439 Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 454 through 464 Processing helix chain 'A' and resid 466 through 490 removed outlier: 3.839A pdb=" N ASN A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N CYS A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE A 485 " --> pdb=" O ALA A 481 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 532 removed outlier: 3.757A pdb=" N LEU A 523 " --> pdb=" O PHE A 519 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP A 531 " --> pdb=" O THR A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 569 removed outlier: 4.054A pdb=" N PHE A 554 " --> pdb=" O GLN A 550 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 557 " --> pdb=" O TYR A 553 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 560 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 561 " --> pdb=" O SER A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 585 removed outlier: 3.813A pdb=" N LEU A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 579 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 582 " --> pdb=" O VAL A 579 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 583 " --> pdb=" O PHE A 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 584 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 585 " --> pdb=" O LEU A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.581A pdb=" N LEU A 590 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR A 591 " --> pdb=" O ASN A 588 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR A 593 " --> pdb=" O LEU A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 612 removed outlier: 3.640A pdb=" N MET A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 625 removed outlier: 3.855A pdb=" N PHE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 666 through 678 removed outlier: 3.799A pdb=" N LEU A 671 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 674 " --> pdb=" O LEU A 670 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 678 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 719 removed outlier: 3.647A pdb=" N ILE A 704 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 710 " --> pdb=" O THR A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 745 removed outlier: 3.651A pdb=" N LYS A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS A 734 " --> pdb=" O LYS A 730 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 735 " --> pdb=" O HIS A 731 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 739 " --> pdb=" O LEU A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 755 Processing helix chain 'B' and resid 151 through 159 removed outlier: 3.547A pdb=" N PHE B 155 " --> pdb=" O ARG B 151 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 209 through 220 Processing helix chain 'B' and resid 241 through 247 Processing helix chain 'B' and resid 251 through 259 removed outlier: 3.745A pdb=" N LEU B 256 " --> pdb=" O HIS B 252 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 257 " --> pdb=" O TYR B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 Processing helix chain 'B' and resid 298 through 304 Processing helix chain 'B' and resid 326 through 330 Processing helix chain 'B' and resid 338 through 356 removed outlier: 3.688A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 385 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 433 through 439 Processing helix chain 'B' and resid 446 through 449 No H-bonds generated for 'chain 'B' and resid 446 through 449' Processing helix chain 'B' and resid 453 through 465 removed outlier: 4.146A pdb=" N GLU B 457 " --> pdb=" O GLU B 453 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 460 " --> pdb=" O ASN B 456 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 465 " --> pdb=" O ASP B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 481 removed outlier: 4.025A pdb=" N ASN B 474 " --> pdb=" O SER B 470 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 479 " --> pdb=" O VAL B 475 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS B 480 " --> pdb=" O VAL B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 505 through 534 removed outlier: 3.646A pdb=" N LEU B 509 " --> pdb=" O THR B 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 510 " --> pdb=" O VAL B 506 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 515 " --> pdb=" O LEU B 511 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN B 528 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE B 529 " --> pdb=" O PHE B 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 534 " --> pdb=" O LYS B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 567 removed outlier: 3.507A pdb=" N PHE B 554 " --> pdb=" O GLN B 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL B 560 " --> pdb=" O TYR B 556 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE B 561 " --> pdb=" O SER B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 593 removed outlier: 3.582A pdb=" N ALA B 576 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N VAL B 577 " --> pdb=" O TYR B 574 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET B 578 " --> pdb=" O LEU B 575 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 582 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL B 583 " --> pdb=" O PHE B 580 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY B 585 " --> pdb=" O LEU B 582 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP B 586 " --> pdb=" O VAL B 583 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN B 588 " --> pdb=" O GLY B 585 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 589 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR B 591 " --> pdb=" O ASN B 588 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 592 " --> pdb=" O ALA B 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR B 593 " --> pdb=" O LEU B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 611 removed outlier: 4.432A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 removed outlier: 3.516A pdb=" N VAL B 620 " --> pdb=" O ARG B 616 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 666 through 677 removed outlier: 3.603A pdb=" N PHE B 674 " --> pdb=" O LEU B 670 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 720 removed outlier: 3.510A pdb=" N ILE B 696 " --> pdb=" O PRO B 692 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 708 " --> pdb=" O ILE B 704 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 714 " --> pdb=" O LEU B 710 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 717 " --> pdb=" O MET B 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 747 removed outlier: 4.956A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N HIS B 731 " --> pdb=" O LYS B 727 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 753 No H-bonds generated for 'chain 'B' and resid 750 through 753' Processing helix chain 'C' and resid 151 through 160 removed outlier: 3.569A pdb=" N SER C 159 " --> pdb=" O PHE C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 4.135A pdb=" N LEU C 174 " --> pdb=" O LEU C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 210 through 220 removed outlier: 3.690A pdb=" N ALA C 217 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU C 218 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 247 Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.702A pdb=" N LEU C 256 " --> pdb=" O HIS C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 276 through 278 No H-bonds generated for 'chain 'C' and resid 276 through 278' Processing helix chain 'C' and resid 288 through 292 Processing helix chain 'C' and resid 298 through 305 Processing helix chain 'C' and resid 324 through 330 removed outlier: 3.805A pdb=" N LEU C 328 " --> pdb=" O VAL C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 355 removed outlier: 4.313A pdb=" N PHE C 341 " --> pdb=" O GLU C 337 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LYS C 344 " --> pdb=" O LYS C 340 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS C 352 " --> pdb=" O LEU C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.609A pdb=" N ALA C 377 " --> pdb=" O PRO C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.837A pdb=" N HIS C 388 " --> pdb=" O GLY C 384 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 391 " --> pdb=" O GLN C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 399 No H-bonds generated for 'chain 'C' and resid 397 through 399' Processing helix chain 'C' and resid 433 through 439 Processing helix chain 'C' and resid 446 through 449 No H-bonds generated for 'chain 'C' and resid 446 through 449' Processing helix chain 'C' and resid 454 through 464 Processing helix chain 'C' and resid 466 through 490 removed outlier: 3.840A pdb=" N ASN C 474 " --> pdb=" O SER C 470 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N CYS C 480 " --> pdb=" O VAL C 476 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 485 " --> pdb=" O ALA C 481 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA C 489 " --> pdb=" O PHE C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 508 through 532 removed outlier: 3.757A pdb=" N LEU C 523 " --> pdb=" O PHE C 519 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP C 531 " --> pdb=" O THR C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 569 removed outlier: 4.054A pdb=" N PHE C 554 " --> pdb=" O GLN C 550 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER C 557 " --> pdb=" O TYR C 553 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 560 " --> pdb=" O TYR C 556 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE C 561 " --> pdb=" O SER C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 572 through 585 removed outlier: 3.814A pdb=" N LEU C 575 " --> pdb=" O GLU C 572 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 579 " --> pdb=" O ALA C 576 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 582 " --> pdb=" O VAL C 579 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 583 " --> pdb=" O PHE C 580 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU C 584 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY C 585 " --> pdb=" O LEU C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 593 removed outlier: 3.582A pdb=" N LEU C 590 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N TYR C 591 " --> pdb=" O ASN C 588 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR C 593 " --> pdb=" O LEU C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 612 removed outlier: 3.640A pdb=" N MET C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE C 606 " --> pdb=" O TYR C 602 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 607 " --> pdb=" O SER C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 625 removed outlier: 3.855A pdb=" N PHE C 624 " --> pdb=" O VAL C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 632 Processing helix chain 'C' and resid 666 through 678 removed outlier: 3.799A pdb=" N LEU C 671 " --> pdb=" O SER C 667 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 674 " --> pdb=" O LEU C 670 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU C 676 " --> pdb=" O ASP C 672 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE C 678 " --> pdb=" O PHE C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 719 removed outlier: 3.648A pdb=" N ILE C 704 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 710 " --> pdb=" O THR C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 745 removed outlier: 3.651A pdb=" N LYS C 730 " --> pdb=" O SER C 726 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS C 734 " --> pdb=" O LYS C 730 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 739 " --> pdb=" O LEU C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 755 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.548A pdb=" N PHE D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 156 " --> pdb=" O PRO D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 175 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 194 through 200 Processing helix chain 'D' and resid 209 through 220 Processing helix chain 'D' and resid 241 through 247 Processing helix chain 'D' and resid 251 through 259 removed outlier: 3.746A pdb=" N LEU D 256 " --> pdb=" O HIS D 252 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D 257 " --> pdb=" O TYR D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 294 Processing helix chain 'D' and resid 298 through 304 Processing helix chain 'D' and resid 326 through 330 Processing helix chain 'D' and resid 338 through 356 removed outlier: 3.688A pdb=" N THR D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 Processing helix chain 'D' and resid 385 through 390 Processing helix chain 'D' and resid 400 through 402 No H-bonds generated for 'chain 'D' and resid 400 through 402' Processing helix chain 'D' and resid 433 through 439 Processing helix chain 'D' and resid 446 through 449 No H-bonds generated for 'chain 'D' and resid 446 through 449' Processing helix chain 'D' and resid 453 through 465 removed outlier: 4.146A pdb=" N GLU D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG D 460 " --> pdb=" O ASN D 456 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS D 465 " --> pdb=" O ASP D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 481 removed outlier: 4.024A pdb=" N ASN D 474 " --> pdb=" O SER D 470 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU D 479 " --> pdb=" O VAL D 475 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N CYS D 480 " --> pdb=" O VAL D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 490 Processing helix chain 'D' and resid 505 through 534 removed outlier: 3.645A pdb=" N LEU D 509 " --> pdb=" O THR D 505 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG D 510 " --> pdb=" O VAL D 506 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 515 " --> pdb=" O LEU D 511 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN D 528 " --> pdb=" O PHE D 524 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 529 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 534 " --> pdb=" O LYS D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 567 removed outlier: 3.507A pdb=" N PHE D 554 " --> pdb=" O GLN D 550 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL D 560 " --> pdb=" O TYR D 556 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE D 561 " --> pdb=" O SER D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 593 removed outlier: 3.582A pdb=" N ALA D 576 " --> pdb=" O ALA D 573 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VAL D 577 " --> pdb=" O TYR D 574 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET D 578 " --> pdb=" O LEU D 575 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 582 " --> pdb=" O VAL D 579 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL D 583 " --> pdb=" O PHE D 580 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLY D 585 " --> pdb=" O LEU D 582 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TRP D 586 " --> pdb=" O VAL D 583 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN D 588 " --> pdb=" O GLY D 585 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA D 589 " --> pdb=" O TRP D 586 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR D 591 " --> pdb=" O ASN D 588 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE D 592 " --> pdb=" O ALA D 589 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 593 " --> pdb=" O LEU D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 611 removed outlier: 4.432A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN D 607 " --> pdb=" O SER D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 624 removed outlier: 3.516A pdb=" N VAL D 620 " --> pdb=" O ARG D 616 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 622 " --> pdb=" O LEU D 618 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 632 Processing helix chain 'D' and resid 666 through 677 removed outlier: 3.603A pdb=" N PHE D 674 " --> pdb=" O LEU D 670 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 692 through 720 removed outlier: 3.511A pdb=" N ILE D 696 " --> pdb=" O PRO D 692 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL D 708 " --> pdb=" O ILE D 704 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 714 " --> pdb=" O LEU D 710 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 717 " --> pdb=" O MET D 713 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N MET D 718 " --> pdb=" O LEU D 714 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 747 removed outlier: 4.955A pdb=" N LYS D 730 " --> pdb=" O SER D 726 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N HIS D 731 " --> pdb=" O LYS D 727 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 747 " --> pdb=" O ASP D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 753 No H-bonds generated for 'chain 'D' and resid 750 through 753' Processing sheet with id= A, first strand: chain 'A' and resid 405 through 407 Processing sheet with id= B, first strand: chain 'B' and resid 778 through 782 removed outlier: 3.790A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= D, first strand: chain 'D' and resid 778 through 782 removed outlier: 3.791A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) 671 hydrogen bonds defined for protein. 1917 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: 5.98 Time building geometry restraints manager: 8.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3485 1.32 - 1.45: 5674 1.45 - 1.57: 11927 1.57 - 1.69: 12 1.69 - 1.82: 172 Bond restraints: 21270 Sorted by residual: bond pdb=" C4 X7N A1201 " pdb=" N5 X7N A1201 " ideal model delta sigma weight residual 1.456 1.367 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C ILE B 210 " pdb=" N PRO B 211 " ideal model delta sigma weight residual 1.336 1.389 -0.054 1.23e-02 6.61e+03 1.91e+01 bond pdb=" C4 X7N C1201 " pdb=" N5 X7N C1201 " ideal model delta sigma weight residual 1.456 1.369 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C ILE D 210 " pdb=" N PRO D 211 " ideal model delta sigma weight residual 1.336 1.389 -0.053 1.23e-02 6.61e+03 1.88e+01 bond pdb=" C ARG A 151 " pdb=" N PRO A 152 " ideal model delta sigma weight residual 1.337 1.384 -0.048 1.11e-02 8.12e+03 1.85e+01 ... (remaining 21265 not shown) Histogram of bond angle deviations from ideal: 97.75 - 105.52: 423 105.52 - 113.29: 11247 113.29 - 121.06: 11233 121.06 - 128.83: 5710 128.83 - 136.60: 187 Bond angle restraints: 28800 Sorted by residual: angle pdb=" C THR A 721 " pdb=" N VAL A 722 " pdb=" CA VAL A 722 " ideal model delta sigma weight residual 121.97 133.98 -12.01 1.80e+00 3.09e-01 4.45e+01 angle pdb=" C THR C 721 " pdb=" N VAL C 722 " pdb=" CA VAL C 722 " ideal model delta sigma weight residual 121.97 133.95 -11.98 1.80e+00 3.09e-01 4.43e+01 angle pdb=" N ALA B 364 " pdb=" CA ALA B 364 " pdb=" C ALA B 364 " ideal model delta sigma weight residual 114.75 106.74 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" N ALA D 364 " pdb=" CA ALA D 364 " pdb=" C ALA D 364 " ideal model delta sigma weight residual 114.75 106.74 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" C SER A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta sigma weight residual 121.54 133.38 -11.84 1.91e+00 2.74e-01 3.84e+01 ... (remaining 28795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 12433 35.58 - 71.15: 164 71.15 - 106.73: 12 106.73 - 142.30: 9 142.30 - 177.88: 6 Dihedral angle restraints: 12624 sinusoidal: 5190 harmonic: 7434 Sorted by residual: dihedral pdb=" CA VAL C 722 " pdb=" C VAL C 722 " pdb=" N GLY C 723 " pdb=" CA GLY C 723 " ideal model delta harmonic sigma weight residual -180.00 -112.53 -67.47 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA VAL A 722 " pdb=" C VAL A 722 " pdb=" N GLY A 723 " pdb=" CA GLY A 723 " ideal model delta harmonic sigma weight residual -180.00 -112.54 -67.46 0 5.00e+00 4.00e-02 1.82e+02 dihedral pdb=" CA SER A 189 " pdb=" C SER A 189 " pdb=" N THR A 190 " pdb=" CA THR A 190 " ideal model delta harmonic sigma weight residual -180.00 -132.57 -47.43 0 5.00e+00 4.00e-02 9.00e+01 ... (remaining 12621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2703 0.072 - 0.145: 470 0.145 - 0.217: 47 0.217 - 0.290: 16 0.290 - 0.362: 2 Chirality restraints: 3238 Sorted by residual: chirality pdb=" CB VAL C 722 " pdb=" CA VAL C 722 " pdb=" CG1 VAL C 722 " pdb=" CG2 VAL C 722 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CB VAL A 722 " pdb=" CA VAL A 722 " pdb=" CG1 VAL A 722 " pdb=" CG2 VAL A 722 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" CG LEU B 551 " pdb=" CB LEU B 551 " pdb=" CD1 LEU B 551 " pdb=" CD2 LEU B 551 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 3235 not shown) Planarity restraints: 3584 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 X7N B1201 " -0.084 2.00e-02 2.50e+03 5.36e-02 6.47e+01 pdb=" C17 X7N B1201 " 0.002 2.00e-02 2.50e+03 pdb=" C18 X7N B1201 " -0.013 2.00e-02 2.50e+03 pdb=" C19 X7N B1201 " -0.046 2.00e-02 2.50e+03 pdb=" C2 X7N B1201 " -0.015 2.00e-02 2.50e+03 pdb=" C26 X7N B1201 " 0.111 2.00e-02 2.50e+03 pdb=" C3 X7N B1201 " 0.003 2.00e-02 2.50e+03 pdb=" C4 X7N B1201 " 0.060 2.00e-02 2.50e+03 pdb=" N25 X7N B1201 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X7N C1201 " -0.056 2.00e-02 2.50e+03 5.35e-02 6.45e+01 pdb=" C17 X7N C1201 " 0.054 2.00e-02 2.50e+03 pdb=" C18 X7N C1201 " 0.043 2.00e-02 2.50e+03 pdb=" C19 X7N C1201 " -0.101 2.00e-02 2.50e+03 pdb=" C2 X7N C1201 " 0.030 2.00e-02 2.50e+03 pdb=" C26 X7N C1201 " 0.013 2.00e-02 2.50e+03 pdb=" C3 X7N C1201 " 0.045 2.00e-02 2.50e+03 pdb=" C4 X7N C1201 " -0.060 2.00e-02 2.50e+03 pdb=" N25 X7N C1201 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 X7N D1201 " 0.074 2.00e-02 2.50e+03 4.90e-02 5.41e+01 pdb=" C17 X7N D1201 " 0.003 2.00e-02 2.50e+03 pdb=" C18 X7N D1201 " 0.015 2.00e-02 2.50e+03 pdb=" C19 X7N D1201 " 0.036 2.00e-02 2.50e+03 pdb=" C2 X7N D1201 " 0.015 2.00e-02 2.50e+03 pdb=" C26 X7N D1201 " -0.102 2.00e-02 2.50e+03 pdb=" C3 X7N D1201 " 0.001 2.00e-02 2.50e+03 pdb=" C4 X7N D1201 " -0.061 2.00e-02 2.50e+03 pdb=" N25 X7N D1201 " 0.018 2.00e-02 2.50e+03 ... (remaining 3581 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1138 2.72 - 3.26: 20341 3.26 - 3.81: 33221 3.81 - 4.35: 42696 4.35 - 4.90: 70195 Nonbonded interactions: 167591 Sorted by model distance: nonbonded pdb=" OH TYR A 235 " pdb=" O GLY D 800 " model vdw 2.171 2.440 nonbonded pdb=" O LEU D 686 " pdb=" OG1 THR D 689 " model vdw 2.263 2.440 nonbonded pdb=" O LEU B 686 " pdb=" OG1 THR B 689 " model vdw 2.264 2.440 nonbonded pdb=" O ARG A 206 " pdb=" OH TYR A 253 " model vdw 2.289 2.440 nonbonded pdb=" O ARG C 206 " pdb=" OH TYR C 253 " model vdw 2.290 2.440 ... (remaining 167586 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' and (resid 148 through 802 or resid 1201 through 1202)) selection = chain 'C' selection = (chain 'D' and (resid 148 through 802 or resid 1201 through 1202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.020 Extract box with map and model: 8.640 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 50.160 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.089 21270 Z= 0.431 Angle : 1.372 20.302 28800 Z= 0.765 Chirality : 0.058 0.362 3238 Planarity : 0.007 0.065 3584 Dihedral : 14.053 177.877 7836 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.64 % Favored : 87.73 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.41 % 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: -5.59 (0.12), residues: 2526 helix: -3.95 (0.08), residues: 1402 sheet: -3.48 (0.42), residues: 116 loop : -3.12 (0.17), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 664 time to evaluate : 2.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 1 residues processed: 672 average time/residue: 0.3468 time to fit residues: 348.3527 Evaluate side-chains 399 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 398 time to evaluate : 2.335 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1820 time to fit residues: 3.5607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.7980 chunk 191 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 197 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 228 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 HIS A 207 ASN A 228 ASN A 265 HIS A 338 ASN A 361 ASN A 474 ASN ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN A 541 ASN A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 637 ASN A 784 ASN B 176 HIS B 204 ASN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 326 HIS B 338 ASN B 361 ASN B 492 GLN B 550 GLN B 588 ASN B 789 ASN C 176 HIS C 222 ASN C 228 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 361 ASN C 474 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 550 GLN C 637 ASN ** C 712 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 784 ASN D 176 HIS D 204 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN D 326 HIS D 492 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 789 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 21270 Z= 0.273 Angle : 0.798 11.010 28800 Z= 0.399 Chirality : 0.044 0.238 3238 Planarity : 0.005 0.048 3584 Dihedral : 13.190 164.782 2982 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.55 % Allowed : 10.53 % Favored : 88.92 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.91 (0.14), residues: 2526 helix: -2.28 (0.11), residues: 1426 sheet: -2.83 (0.50), residues: 98 loop : -2.87 (0.18), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 454 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 37 residues processed: 493 average time/residue: 0.3102 time to fit residues: 238.6469 Evaluate side-chains 414 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 377 time to evaluate : 2.841 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 0 residues processed: 37 average time/residue: 0.2362 time to fit residues: 18.3370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 0.3980 chunk 71 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 229 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 204 optimal weight: 0.9990 chunk 227 optimal weight: 9.9990 chunk 78 optimal weight: 0.1980 chunk 183 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN B 228 ASN ** B 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN C 712 ASN D 204 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 21270 Z= 0.186 Angle : 0.716 11.336 28800 Z= 0.355 Chirality : 0.041 0.242 3238 Planarity : 0.004 0.046 3584 Dihedral : 12.181 149.504 2982 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.45 % Favored : 89.07 % Rotamer Outliers : 2.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.93 (0.16), residues: 2526 helix: -1.34 (0.13), residues: 1404 sheet: -2.55 (0.53), residues: 98 loop : -2.67 (0.18), residues: 1024 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 426 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 18 residues processed: 466 average time/residue: 0.3019 time to fit residues: 225.0371 Evaluate side-chains 378 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 360 time to evaluate : 2.508 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1954 time to fit residues: 9.9821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 118 optimal weight: 9.9990 chunk 25 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 243 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN B 338 ASN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS ** D 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 791 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 21270 Z= 0.238 Angle : 0.723 13.487 28800 Z= 0.358 Chirality : 0.042 0.243 3238 Planarity : 0.004 0.056 3584 Dihedral : 11.475 127.344 2982 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.44 % Allowed : 10.81 % Favored : 88.76 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.52 (0.16), residues: 2526 helix: -0.94 (0.13), residues: 1440 sheet: -2.41 (0.52), residues: 98 loop : -2.64 (0.19), residues: 988 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 391 time to evaluate : 2.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 33 residues processed: 436 average time/residue: 0.3077 time to fit residues: 212.9662 Evaluate side-chains 380 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 347 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.2081 time to fit residues: 15.6680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 181 optimal weight: 0.4980 chunk 100 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 168 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 492 GLN C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 21270 Z= 0.253 Angle : 0.713 11.835 28800 Z= 0.354 Chirality : 0.043 0.245 3238 Planarity : 0.004 0.057 3584 Dihedral : 11.163 120.985 2982 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.40 % Allowed : 10.89 % Favored : 88.72 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.31 (0.16), residues: 2526 helix: -0.67 (0.13), residues: 1436 sheet: -2.37 (0.52), residues: 98 loop : -2.71 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 379 time to evaluate : 2.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 27 residues processed: 407 average time/residue: 0.3010 time to fit residues: 194.6133 Evaluate side-chains 376 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 349 time to evaluate : 2.383 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1880 time to fit residues: 12.8663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 143 optimal weight: 0.0670 chunk 60 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN C 207 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 21270 Z= 0.179 Angle : 0.682 11.986 28800 Z= 0.337 Chirality : 0.041 0.243 3238 Planarity : 0.004 0.059 3584 Dihedral : 10.910 118.866 2982 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.29 % Favored : 89.35 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.04 (0.16), residues: 2526 helix: -0.43 (0.14), residues: 1426 sheet: -2.34 (0.53), residues: 98 loop : -2.60 (0.19), residues: 1002 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 386 time to evaluate : 2.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 11 residues processed: 404 average time/residue: 0.3024 time to fit residues: 194.7108 Evaluate side-chains 351 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 340 time to evaluate : 2.167 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1905 time to fit residues: 6.9076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 9.9990 chunk 137 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 152 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 112 optimal weight: 0.0170 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN B 252 HIS ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 21270 Z= 0.191 Angle : 0.690 12.702 28800 Z= 0.342 Chirality : 0.041 0.229 3238 Planarity : 0.004 0.059 3584 Dihedral : 10.715 115.660 2982 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.36 % Allowed : 10.37 % Favored : 89.27 % Rotamer Outliers : 1.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.83 (0.17), residues: 2526 helix: -0.25 (0.14), residues: 1422 sheet: -1.96 (0.59), residues: 88 loop : -2.56 (0.19), residues: 1016 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 358 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 375 average time/residue: 0.3114 time to fit residues: 188.5188 Evaluate side-chains 346 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 330 time to evaluate : 2.414 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1990 time to fit residues: 9.2341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 0.0980 chunk 96 optimal weight: 0.9990 chunk 145 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 190 optimal weight: 0.0470 chunk 220 optimal weight: 0.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN C 588 ASN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.053 21270 Z= 0.159 Angle : 0.678 12.229 28800 Z= 0.335 Chirality : 0.041 0.351 3238 Planarity : 0.004 0.060 3584 Dihedral : 10.468 113.076 2982 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.36 % Allowed : 9.74 % Favored : 89.90 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.63 (0.17), residues: 2526 helix: -0.09 (0.14), residues: 1416 sheet: -1.94 (0.59), residues: 88 loop : -2.43 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 366 time to evaluate : 2.803 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 9 residues processed: 381 average time/residue: 0.2919 time to fit residues: 178.4917 Evaluate side-chains 349 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 340 time to evaluate : 2.278 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1888 time to fit residues: 6.3896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 0.9980 chunk 212 optimal weight: 0.5980 chunk 226 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 98 optimal weight: 0.0010 chunk 177 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 214 optimal weight: 0.8980 chunk 225 optimal weight: 10.0000 chunk 148 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN A 588 ASN ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 21270 Z= 0.176 Angle : 0.697 13.449 28800 Z= 0.343 Chirality : 0.041 0.221 3238 Planarity : 0.004 0.060 3584 Dihedral : 10.362 111.088 2982 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.13 % Favored : 89.55 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.58 (0.17), residues: 2526 helix: -0.05 (0.14), residues: 1440 sheet: -1.52 (0.63), residues: 78 loop : -2.51 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 356 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 364 average time/residue: 0.3130 time to fit residues: 180.0051 Evaluate side-chains 339 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 333 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3354 time to fit residues: 6.3505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 154 optimal weight: 0.0770 chunk 122 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 overall best weight: 0.7540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 550 GLN ** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 21270 Z= 0.184 Angle : 0.709 12.765 28800 Z= 0.350 Chirality : 0.041 0.230 3238 Planarity : 0.004 0.061 3584 Dihedral : 10.253 109.737 2982 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.32 % Allowed : 10.45 % Favored : 89.23 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.59 (0.17), residues: 2526 helix: -0.03 (0.14), residues: 1444 sheet: -1.50 (0.63), residues: 78 loop : -2.55 (0.19), residues: 1004 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5052 Ramachandran restraints generated. 2526 Oldfield, 0 Emsley, 2526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 349 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 354 average time/residue: 0.3018 time to fit residues: 169.7771 Evaluate side-chains 331 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 2.577 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1920 time to fit residues: 3.7954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 0.1980 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 29 optimal weight: 0.0370 chunk 55 optimal weight: 0.9990 chunk 200 optimal weight: 5.9990 chunk 83 optimal weight: 0.9990 chunk 205 optimal weight: 0.3980 chunk 25 optimal weight: 0.0770 chunk 36 optimal weight: 10.0000 chunk 175 optimal weight: 0.2980 overall best weight: 0.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 550 GLN A 588 ASN ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 550 GLN ** D 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.168188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.135071 restraints weight = 29593.860| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.12 r_work: 0.3310 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 21270 Z= 0.154 Angle : 0.688 12.690 28800 Z= 0.340 Chirality : 0.040 0.203 3238 Planarity : 0.004 0.063 3584 Dihedral : 10.056 107.744 2982 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.50 % Favored : 90.26 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -1.34 (0.17), residues: 2526 helix: 0.21 (0.14), residues: 1430 sheet: -1.73 (0.63), residues: 74 loop : -2.45 (0.19), residues: 1022 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4647.23 seconds wall clock time: 85 minutes 8.12 seconds (5108.12 seconds total)