Starting phenix.real_space_refine on Wed Apr 10 16:23:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rau_24386/04_2024/7rau_24386_updated.pdb" } resolution = 3.99 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= 0.003 sd= 0.021 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 116 5.16 5 C 13072 2.51 5 N 3272 2.21 5 O 3540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 118": "NH1" <-> "NH2" Residue "A ARG 122": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 337": "NH1" <-> "NH2" Residue "A ARG 363": "NH1" <-> "NH2" Residue "A ARG 416": "NH1" <-> "NH2" Residue "A ARG 462": "NH1" <-> "NH2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A ARG 698": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "B ARG 118": "NH1" <-> "NH2" Residue "B ARG 122": "NH1" <-> "NH2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B ARG 188": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B ARG 337": "NH1" <-> "NH2" Residue "B ARG 363": "NH1" <-> "NH2" Residue "B ARG 416": "NH1" <-> "NH2" Residue "B ARG 462": "NH1" <-> "NH2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 693": "NH1" <-> "NH2" Residue "B ARG 698": "NH1" <-> "NH2" Residue "B ARG 716": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "C ARG 118": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 225": "NH1" <-> "NH2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "C ARG 363": "NH1" <-> "NH2" Residue "C ARG 416": "NH1" <-> "NH2" Residue "C ARG 462": "NH1" <-> "NH2" Residue "C TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 693": "NH1" <-> "NH2" Residue "C ARG 698": "NH1" <-> "NH2" Residue "C ARG 716": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "D ARG 118": "NH1" <-> "NH2" Residue "D ARG 122": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 202": "NH1" <-> "NH2" Residue "D ARG 225": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D ARG 363": "NH1" <-> "NH2" Residue "D ARG 416": "NH1" <-> "NH2" Residue "D ARG 462": "NH1" <-> "NH2" Residue "D TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 693": "NH1" <-> "NH2" Residue "D ARG 698": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 20000 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 4964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4964 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 596} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {'A0O': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 10.32, per 1000 atoms: 0.52 Number of scatterers: 20000 At special positions: 0 Unit cell: (144.1, 144.1, 118.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 116 16.00 O 3540 8.00 N 3272 7.00 C 13072 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: 7.12 Conformation dependent library (CDL) restraints added in 3.6 seconds 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4664 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 116 helices and 4 sheets defined 58.3% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.64 Creating SS restraints... Processing helix chain 'A' and resid 116 through 128 Processing helix chain 'A' and resid 132 through 148 removed outlier: 3.529A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 183 through 197 removed outlier: 4.014A pdb=" N GLU A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 228 through 237 Processing helix chain 'A' and resid 265 through 271 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 316 through 328 removed outlier: 3.877A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.752A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.820A pdb=" N THR A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 435 removed outlier: 3.783A pdb=" N LEU A 428 " --> pdb=" O PRO A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 457 removed outlier: 3.614A pdb=" N PHE A 442 " --> pdb=" O LYS A 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 453 " --> pdb=" O PHE A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 507 removed outlier: 3.647A pdb=" N TRP A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 495 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N CYS A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 541 removed outlier: 3.514A pdb=" N VAL A 533 " --> pdb=" O GLN A 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 537 " --> pdb=" O VAL A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 564 removed outlier: 3.618A pdb=" N LEU A 548 " --> pdb=" O LYS A 545 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS A 550 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 553 " --> pdb=" O CYS A 550 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 557 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN A 561 " --> pdb=" O GLY A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 568 No H-bonds generated for 'chain 'A' and resid 566 through 568' Processing helix chain 'A' and resid 574 through 607 removed outlier: 3.581A pdb=" N MET A 578 " --> pdb=" O MET A 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE A 579 " --> pdb=" O TYR A 575 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 582 " --> pdb=" O MET A 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS A 585 " --> pdb=" O LYS A 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE A 601 " --> pdb=" O PHE A 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 637 removed outlier: 3.618A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 636 " --> pdb=" O LEU A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 680 removed outlier: 3.594A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 661 " --> pdb=" O LEU A 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 670 " --> pdb=" O PHE A 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 704 removed outlier: 4.626A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU A 701 " --> pdb=" O ALA A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'B' and resid 116 through 128 Processing helix chain 'B' and resid 132 through 148 removed outlier: 3.529A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 183 through 197 removed outlier: 4.014A pdb=" N GLU B 196 " --> pdb=" O ALA B 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 197 " --> pdb=" O PHE B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 228 through 237 Processing helix chain 'B' and resid 265 through 271 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 299 through 305 Processing helix chain 'B' and resid 316 through 328 removed outlier: 3.878A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 351 Processing helix chain 'B' and resid 354 through 361 removed outlier: 3.752A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 416 through 421 removed outlier: 3.820A pdb=" N THR B 421 " --> pdb=" O HIS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 435 removed outlier: 3.782A pdb=" N LEU B 428 " --> pdb=" O PRO B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 457 removed outlier: 3.614A pdb=" N PHE B 442 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE B 453 " --> pdb=" O PHE B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 507 removed outlier: 3.646A pdb=" N TRP B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR B 495 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 541 removed outlier: 3.514A pdb=" N VAL B 533 " --> pdb=" O GLN B 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 537 " --> pdb=" O VAL B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 564 removed outlier: 3.617A pdb=" N LEU B 548 " --> pdb=" O LYS B 545 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS B 550 " --> pdb=" O TYR B 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 553 " --> pdb=" O CYS B 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 557 " --> pdb=" O ALA B 554 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN B 561 " --> pdb=" O GLY B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 574 through 607 removed outlier: 3.582A pdb=" N MET B 578 " --> pdb=" O MET B 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 579 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL B 582 " --> pdb=" O MET B 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS B 585 " --> pdb=" O LYS B 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 588 " --> pdb=" O LEU B 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 601 " --> pdb=" O PHE B 597 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 637 removed outlier: 3.618A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 636 " --> pdb=" O LEU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 680 removed outlier: 3.593A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 661 " --> pdb=" O LEU B 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU B 670 " --> pdb=" O PHE B 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 704 removed outlier: 4.626A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 697 " --> pdb=" O ARG B 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU B 701 " --> pdb=" O ALA B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'C' and resid 116 through 127 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.529A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 183 through 197 removed outlier: 4.013A pdb=" N GLU C 196 " --> pdb=" O ALA C 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN C 197 " --> pdb=" O PHE C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 265 through 271 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 299 through 305 Processing helix chain 'C' and resid 316 through 328 removed outlier: 3.877A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 351 Processing helix chain 'C' and resid 354 through 361 removed outlier: 3.752A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 370 No H-bonds generated for 'chain 'C' and resid 368 through 370' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 416 through 421 removed outlier: 3.819A pdb=" N THR C 421 " --> pdb=" O HIS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 435 removed outlier: 3.783A pdb=" N LEU C 428 " --> pdb=" O PRO C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 removed outlier: 3.614A pdb=" N PHE C 442 " --> pdb=" O LYS C 438 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 507 removed outlier: 3.647A pdb=" N TRP C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR C 495 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 541 removed outlier: 3.514A pdb=" N VAL C 533 " --> pdb=" O GLN C 529 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL C 537 " --> pdb=" O VAL C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 564 removed outlier: 3.617A pdb=" N LEU C 548 " --> pdb=" O LYS C 545 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS C 550 " --> pdb=" O TYR C 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 553 " --> pdb=" O CYS C 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 557 " --> pdb=" O ALA C 554 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN C 561 " --> pdb=" O GLY C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 566 through 568 No H-bonds generated for 'chain 'C' and resid 566 through 568' Processing helix chain 'C' and resid 574 through 607 removed outlier: 3.581A pdb=" N MET C 578 " --> pdb=" O MET C 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 579 " --> pdb=" O TYR C 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL C 582 " --> pdb=" O MET C 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 585 " --> pdb=" O LYS C 581 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU C 588 " --> pdb=" O LEU C 584 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE C 601 " --> pdb=" O PHE C 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 removed outlier: 3.618A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR C 636 " --> pdb=" O LEU C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 680 removed outlier: 3.593A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE C 659 " --> pdb=" O LEU C 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 661 " --> pdb=" O LEU C 657 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU C 670 " --> pdb=" O PHE C 666 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N MET C 677 " --> pdb=" O LEU C 673 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 704 removed outlier: 4.626A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 697 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU C 701 " --> pdb=" O ALA C 697 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'D' and resid 116 through 128 Processing helix chain 'D' and resid 132 through 148 removed outlier: 3.529A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 161 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 183 through 197 removed outlier: 4.014A pdb=" N GLU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN D 197 " --> pdb=" O PHE D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 228 through 237 Processing helix chain 'D' and resid 265 through 271 Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 294 through 296 No H-bonds generated for 'chain 'D' and resid 294 through 296' Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 316 through 328 removed outlier: 3.878A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 351 Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.752A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 370 No H-bonds generated for 'chain 'D' and resid 368 through 370' Processing helix chain 'D' and resid 403 through 408 Processing helix chain 'D' and resid 416 through 421 removed outlier: 3.819A pdb=" N THR D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 435 removed outlier: 3.782A pdb=" N LEU D 428 " --> pdb=" O PRO D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 457 removed outlier: 3.614A pdb=" N PHE D 442 " --> pdb=" O LYS D 438 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 453 " --> pdb=" O PHE D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 481 through 507 removed outlier: 3.646A pdb=" N TRP D 493 " --> pdb=" O PHE D 489 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR D 495 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N CYS D 496 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 541 removed outlier: 3.515A pdb=" N VAL D 533 " --> pdb=" O GLN D 529 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL D 537 " --> pdb=" O VAL D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 564 removed outlier: 3.617A pdb=" N LEU D 548 " --> pdb=" O LYS D 545 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS D 550 " --> pdb=" O TYR D 547 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 553 " --> pdb=" O CYS D 550 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 557 " --> pdb=" O ALA D 554 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN D 561 " --> pdb=" O GLY D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 566 through 568 No H-bonds generated for 'chain 'D' and resid 566 through 568' Processing helix chain 'D' and resid 574 through 607 removed outlier: 3.581A pdb=" N MET D 578 " --> pdb=" O MET D 574 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE D 579 " --> pdb=" O TYR D 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL D 582 " --> pdb=" O MET D 578 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS D 585 " --> pdb=" O LYS D 581 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE D 601 " --> pdb=" O PHE D 597 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 637 removed outlier: 3.617A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR D 636 " --> pdb=" O LEU D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 680 removed outlier: 3.594A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE D 659 " --> pdb=" O LEU D 655 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 661 " --> pdb=" O LEU D 657 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU D 670 " --> pdb=" O PHE D 666 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET D 677 " --> pdb=" O LEU D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 704 removed outlier: 4.626A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 697 " --> pdb=" O ARG D 693 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 701 " --> pdb=" O ALA D 697 " (cutoff:3.500A) Processing helix chain 'D' and resid 709 through 714 Processing sheet with id= A, first strand: chain 'A' and resid 719 through 721 removed outlier: 3.506A pdb=" N VAL A 385 " --> pdb=" O TYR A 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP A 380 " --> pdb=" O SER A 387 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU A 389 " --> pdb=" O THR A 378 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR A 378 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 719 through 721 removed outlier: 3.506A pdb=" N VAL B 385 " --> pdb=" O TYR B 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP B 380 " --> pdb=" O SER B 387 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU B 389 " --> pdb=" O THR B 378 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR B 378 " --> pdb=" O LEU B 389 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 719 through 721 removed outlier: 3.505A pdb=" N VAL C 385 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP C 380 " --> pdb=" O SER C 387 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU C 389 " --> pdb=" O THR C 378 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR C 378 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 719 through 721 removed outlier: 3.505A pdb=" N VAL D 385 " --> pdb=" O TYR D 382 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TRP D 380 " --> pdb=" O SER D 387 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LEU D 389 " --> pdb=" O THR D 378 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N THR D 378 " --> pdb=" O LEU D 389 " (cutoff:3.500A) 871 hydrogen bonds defined for protein. 2445 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: 5.57 Time building geometry restraints manager: 7.82 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: 3386 1.32 - 1.44: 5383 1.44 - 1.57: 11451 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 20424 Sorted by residual: bond pdb=" C07 A0O D 901 " pdb=" C12 A0O D 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O D 902 " pdb=" C12 A0O D 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C07 A0O C 902 " pdb=" C12 A0O C 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O C 901 " pdb=" C12 A0O C 901 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C07 A0O B 902 " pdb=" C12 A0O B 902 " ideal model delta sigma weight residual 1.430 1.644 -0.214 2.00e-02 2.50e+03 1.14e+02 ... (remaining 20419 not shown) Histogram of bond angle deviations from ideal: 99.34 - 108.39: 761 108.39 - 117.43: 14328 117.43 - 126.48: 12207 126.48 - 135.52: 316 135.52 - 144.57: 8 Bond angle restraints: 27620 Sorted by residual: angle pdb=" C04 A0O A 902 " pdb=" C06 A0O A 902 " pdb=" O01 A0O A 902 " ideal model delta sigma weight residual 117.13 144.57 -27.44 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O C 902 " pdb=" C06 A0O C 902 " pdb=" O01 A0O C 902 " ideal model delta sigma weight residual 117.13 144.56 -27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" C04 A0O B 902 " pdb=" C06 A0O B 902 " pdb=" O01 A0O B 902 " ideal model delta sigma weight residual 117.13 144.44 -27.31 3.00e+00 1.11e-01 8.29e+01 angle pdb=" C04 A0O D 902 " pdb=" C06 A0O D 902 " pdb=" O01 A0O D 902 " ideal model delta sigma weight residual 117.13 144.43 -27.30 3.00e+00 1.11e-01 8.28e+01 angle pdb=" C04 A0O A 901 " pdb=" C06 A0O A 901 " pdb=" O01 A0O A 901 " ideal model delta sigma weight residual 117.13 144.26 -27.13 3.00e+00 1.11e-01 8.18e+01 ... (remaining 27615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.20: 11032 15.20 - 30.39: 792 30.39 - 45.59: 252 45.59 - 60.79: 44 60.79 - 75.99: 20 Dihedral angle restraints: 12140 sinusoidal: 4964 harmonic: 7176 Sorted by residual: dihedral pdb=" CA ASP C 414 " pdb=" C ASP C 414 " pdb=" N ASN C 415 " pdb=" CA ASN C 415 " ideal model delta harmonic sigma weight residual 180.00 137.21 42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP D 414 " pdb=" C ASP D 414 " pdb=" N ASN D 415 " pdb=" CA ASN D 415 " ideal model delta harmonic sigma weight residual 180.00 137.23 42.77 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA ASP A 414 " pdb=" C ASP A 414 " pdb=" N ASN A 415 " pdb=" CA ASN A 415 " ideal model delta harmonic sigma weight residual 180.00 137.25 42.75 0 5.00e+00 4.00e-02 7.31e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2454 0.056 - 0.112: 621 0.112 - 0.167: 57 0.167 - 0.223: 12 0.223 - 0.279: 8 Chirality restraints: 3152 Sorted by residual: chirality pdb=" CG LEU B 673 " pdb=" CB LEU B 673 " pdb=" CD1 LEU B 673 " pdb=" CD2 LEU B 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU D 673 " pdb=" CB LEU D 673 " pdb=" CD1 LEU D 673 " pdb=" CD2 LEU D 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CG LEU C 673 " pdb=" CB LEU C 673 " pdb=" CD1 LEU C 673 " pdb=" CD2 LEU C 673 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 3149 not shown) Planarity restraints: 3420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 314 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.98e+00 pdb=" C ASN C 314 " 0.046 2.00e-02 2.50e+03 pdb=" O ASN C 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP C 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 314 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C ASN B 314 " 0.045 2.00e-02 2.50e+03 pdb=" O ASN B 314 " -0.017 2.00e-02 2.50e+03 pdb=" N ASP B 315 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 314 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C ASN D 314 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN D 314 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP D 315 " 0.015 2.00e-02 2.50e+03 ... (remaining 3417 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6224 2.82 - 3.34: 19845 3.34 - 3.86: 32170 3.86 - 4.38: 37555 4.38 - 4.90: 59319 Nonbonded interactions: 155113 Sorted by model distance: nonbonded pdb=" OD1 ASN D 180 " pdb=" OG1 THR D 183 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASN B 180 " pdb=" OG1 THR B 183 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASN C 180 " pdb=" OG1 THR C 183 " model vdw 2.300 2.440 nonbonded pdb=" OD1 ASN A 180 " pdb=" OG1 THR A 183 " model vdw 2.300 2.440 nonbonded pdb=" O ALA A 604 " pdb=" OG SER A 607 " model vdw 2.310 2.440 ... (remaining 155108 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' selection = chain 'C' selection = chain 'D' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.700 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 52.490 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.120 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:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 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 : 0.009 0.214 20424 Z= 0.565 Angle : 1.259 27.437 27620 Z= 0.624 Chirality : 0.048 0.279 3152 Planarity : 0.005 0.046 3420 Dihedral : 12.741 75.985 7476 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.31 % Favored : 93.52 % Rotamer: Outliers : 1.11 % Allowed : 6.67 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % 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: -4.28 (0.12), residues: 2408 helix: -3.15 (0.08), residues: 1424 sheet: 2.30 (0.57), residues: 64 loop : -2.43 (0.16), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 559 HIS 0.006 0.002 HIS B 523 PHE 0.021 0.002 PHE D 526 TYR 0.024 0.003 TYR D 213 ARG 0.006 0.001 ARG D 416 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 656 time to evaluate : 2.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 MET cc_start: 0.9224 (mmp) cc_final: 0.8446 (mmm) REVERT: A 174 LYS cc_start: 0.9484 (tttp) cc_final: 0.8688 (ttpt) REVERT: A 178 ASN cc_start: 0.9478 (m110) cc_final: 0.8902 (p0) REVERT: A 257 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8714 (mt-10) REVERT: A 268 LEU cc_start: 0.9781 (tp) cc_final: 0.9566 (tt) REVERT: A 284 ASN cc_start: 0.9266 (t0) cc_final: 0.9001 (t0) REVERT: A 308 GLU cc_start: 0.9224 (mm-30) cc_final: 0.8817 (tt0) REVERT: A 323 MET cc_start: 0.9138 (tpp) cc_final: 0.8783 (tpp) REVERT: A 333 LEU cc_start: 0.9284 (tp) cc_final: 0.8410 (tp) REVERT: A 355 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8853 (tp30) REVERT: A 364 GLU cc_start: 0.9010 (pp20) cc_final: 0.8723 (tm-30) REVERT: A 392 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9333 (mm) REVERT: A 396 ASP cc_start: 0.8539 (t70) cc_final: 0.8212 (t70) REVERT: A 405 GLU cc_start: 0.9457 (tt0) cc_final: 0.9109 (pt0) REVERT: A 414 ASP cc_start: 0.9122 (t0) cc_final: 0.8879 (p0) REVERT: A 415 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.7803 (t0) REVERT: A 418 GLU cc_start: 0.9556 (tp30) cc_final: 0.9341 (mp0) REVERT: A 419 MET cc_start: 0.9526 (mtm) cc_final: 0.9216 (mtm) REVERT: A 423 GLU cc_start: 0.8199 (tp30) cc_final: 0.7845 (tp30) REVERT: A 438 LYS cc_start: 0.8927 (ptmm) cc_final: 0.8586 (tptt) REVERT: A 440 MET cc_start: 0.9135 (mmp) cc_final: 0.8668 (mmp) REVERT: A 448 TYR cc_start: 0.7606 (t80) cc_final: 0.6368 (t80) REVERT: A 479 MET cc_start: 0.5935 (tpt) cc_final: 0.4912 (tmm) REVERT: A 489 PHE cc_start: 0.9419 (t80) cc_final: 0.9023 (t80) REVERT: A 538 PHE cc_start: 0.8695 (m-10) cc_final: 0.8477 (t80) REVERT: A 547 TYR cc_start: 0.7774 (p90) cc_final: 0.7409 (p90) REVERT: A 562 MET cc_start: 0.9199 (tpt) cc_final: 0.8408 (tpp) REVERT: A 572 MET cc_start: 0.8723 (ppp) cc_final: 0.7956 (tpt) REVERT: A 575 TYR cc_start: 0.8340 (p90) cc_final: 0.7886 (p90) REVERT: A 578 MET cc_start: 0.8717 (mmm) cc_final: 0.8445 (mmm) REVERT: A 597 PHE cc_start: 0.8037 (t80) cc_final: 0.7577 (t80) REVERT: A 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8400 (mt-10) REVERT: A 704 GLU cc_start: 0.9259 (tp30) cc_final: 0.8604 (tp30) REVERT: A 734 ILE cc_start: 0.9160 (mt) cc_final: 0.8835 (mm) REVERT: B 159 MET cc_start: 0.9169 (mmp) cc_final: 0.8419 (mmm) REVERT: B 174 LYS cc_start: 0.9430 (tttp) cc_final: 0.8439 (ttpt) REVERT: B 178 ASN cc_start: 0.9270 (m110) cc_final: 0.8573 (p0) REVERT: B 257 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8605 (mt-10) REVERT: B 261 PHE cc_start: 0.9289 (p90) cc_final: 0.8799 (p90) REVERT: B 284 ASN cc_start: 0.9223 (t0) cc_final: 0.8998 (t0) REVERT: B 308 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8697 (tt0) REVERT: B 320 MET cc_start: 0.9023 (mmp) cc_final: 0.8792 (mmt) REVERT: B 323 MET cc_start: 0.9132 (tpp) cc_final: 0.8878 (tpt) REVERT: B 333 LEU cc_start: 0.9134 (tp) cc_final: 0.8283 (tp) REVERT: B 350 LYS cc_start: 0.9451 (tttt) cc_final: 0.9209 (ttmm) REVERT: B 392 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9327 (mm) REVERT: B 396 ASP cc_start: 0.8383 (t70) cc_final: 0.7992 (t70) REVERT: B 405 GLU cc_start: 0.9449 (tt0) cc_final: 0.9095 (pt0) REVERT: B 412 ASN cc_start: 0.9578 (p0) cc_final: 0.9367 (p0) REVERT: B 414 ASP cc_start: 0.9072 (t0) cc_final: 0.8742 (p0) REVERT: B 415 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.7401 (t0) REVERT: B 418 GLU cc_start: 0.9609 (tp30) cc_final: 0.9268 (mp0) REVERT: B 419 MET cc_start: 0.9549 (mtm) cc_final: 0.9304 (mtm) REVERT: B 423 GLU cc_start: 0.8493 (tp30) cc_final: 0.8082 (tp30) REVERT: B 438 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8686 (tptt) REVERT: B 440 MET cc_start: 0.9126 (mmp) cc_final: 0.8695 (mmp) REVERT: B 448 TYR cc_start: 0.7683 (t80) cc_final: 0.6425 (t80) REVERT: B 479 MET cc_start: 0.6227 (tpt) cc_final: 0.5653 (tmm) REVERT: B 489 PHE cc_start: 0.9373 (t80) cc_final: 0.9008 (t80) REVERT: B 562 MET cc_start: 0.9144 (tpt) cc_final: 0.8256 (tpp) REVERT: B 572 MET cc_start: 0.8786 (ppp) cc_final: 0.8056 (tpt) REVERT: B 575 TYR cc_start: 0.8406 (p90) cc_final: 0.7852 (p90) REVERT: B 578 MET cc_start: 0.8551 (mmm) cc_final: 0.8290 (mmm) REVERT: B 597 PHE cc_start: 0.8075 (t80) cc_final: 0.7608 (t80) REVERT: B 695 GLN cc_start: 0.9422 (mt0) cc_final: 0.8489 (tt0) REVERT: B 702 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8501 (mt-10) REVERT: B 704 GLU cc_start: 0.9221 (tp30) cc_final: 0.8962 (tp30) REVERT: C 159 MET cc_start: 0.9175 (mmp) cc_final: 0.8378 (mmm) REVERT: C 174 LYS cc_start: 0.9463 (tttp) cc_final: 0.9067 (tptt) REVERT: C 177 LEU cc_start: 0.9825 (mm) cc_final: 0.9514 (mt) REVERT: C 178 ASN cc_start: 0.9381 (m110) cc_final: 0.8635 (p0) REVERT: C 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8600 (mt-10) REVERT: C 261 PHE cc_start: 0.9334 (p90) cc_final: 0.8799 (p90) REVERT: C 268 LEU cc_start: 0.9774 (tp) cc_final: 0.9527 (tt) REVERT: C 284 ASN cc_start: 0.9261 (t0) cc_final: 0.9013 (t0) REVERT: C 290 THR cc_start: 0.9365 (p) cc_final: 0.9150 (t) REVERT: C 308 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8728 (tt0) REVERT: C 320 MET cc_start: 0.9176 (mmp) cc_final: 0.8952 (mmt) REVERT: C 323 MET cc_start: 0.9160 (tpp) cc_final: 0.8956 (tpt) REVERT: C 333 LEU cc_start: 0.9163 (tp) cc_final: 0.8293 (tp) REVERT: C 364 GLU cc_start: 0.9043 (pp20) cc_final: 0.8774 (tm-30) REVERT: C 371 ARG cc_start: 0.8970 (mtp-110) cc_final: 0.8348 (ttm110) REVERT: C 396 ASP cc_start: 0.8467 (t70) cc_final: 0.8136 (t70) REVERT: C 405 GLU cc_start: 0.9448 (tt0) cc_final: 0.9076 (pt0) REVERT: C 414 ASP cc_start: 0.9144 (t0) cc_final: 0.8738 (p0) REVERT: C 415 ASN cc_start: 0.9163 (OUTLIER) cc_final: 0.7935 (t0) REVERT: C 418 GLU cc_start: 0.9597 (tp30) cc_final: 0.9363 (mp0) REVERT: C 419 MET cc_start: 0.9530 (mtm) cc_final: 0.9318 (mtm) REVERT: C 438 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8719 (tptt) REVERT: C 440 MET cc_start: 0.9044 (mmp) cc_final: 0.8563 (mmp) REVERT: C 448 TYR cc_start: 0.7658 (t80) cc_final: 0.7237 (t80) REVERT: C 479 MET cc_start: 0.6170 (tpt) cc_final: 0.5356 (tmm) REVERT: C 489 PHE cc_start: 0.9369 (t80) cc_final: 0.9068 (t80) REVERT: C 572 MET cc_start: 0.8794 (ppp) cc_final: 0.8026 (tpt) REVERT: C 575 TYR cc_start: 0.8304 (p90) cc_final: 0.7876 (p90) REVERT: C 578 MET cc_start: 0.8628 (mmm) cc_final: 0.8324 (mmm) REVERT: C 597 PHE cc_start: 0.8030 (t80) cc_final: 0.7557 (t80) REVERT: C 702 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 704 GLU cc_start: 0.9231 (tp30) cc_final: 0.8978 (tp30) REVERT: D 159 MET cc_start: 0.9068 (mmp) cc_final: 0.8258 (mmm) REVERT: D 174 LYS cc_start: 0.9375 (tttp) cc_final: 0.8983 (tptt) REVERT: D 177 LEU cc_start: 0.9809 (mm) cc_final: 0.9435 (mt) REVERT: D 178 ASN cc_start: 0.9336 (m110) cc_final: 0.8592 (p0) REVERT: D 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8632 (mt-10) REVERT: D 261 PHE cc_start: 0.9318 (p90) cc_final: 0.8810 (p90) REVERT: D 268 LEU cc_start: 0.9764 (tp) cc_final: 0.9502 (tt) REVERT: D 284 ASN cc_start: 0.9221 (t0) cc_final: 0.8959 (t0) REVERT: D 290 THR cc_start: 0.9312 (p) cc_final: 0.9104 (t) REVERT: D 308 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8725 (tt0) REVERT: D 320 MET cc_start: 0.9205 (mmp) cc_final: 0.8971 (mmt) REVERT: D 323 MET cc_start: 0.9201 (tpp) cc_final: 0.8844 (tpt) REVERT: D 333 LEU cc_start: 0.9201 (tp) cc_final: 0.8289 (tp) REVERT: D 364 GLU cc_start: 0.9052 (pp20) cc_final: 0.8771 (tm-30) REVERT: D 396 ASP cc_start: 0.8479 (t70) cc_final: 0.8151 (t70) REVERT: D 405 GLU cc_start: 0.9454 (tt0) cc_final: 0.9073 (pt0) REVERT: D 414 ASP cc_start: 0.9191 (t0) cc_final: 0.8758 (p0) REVERT: D 415 ASN cc_start: 0.9157 (OUTLIER) cc_final: 0.7912 (t0) REVERT: D 418 GLU cc_start: 0.9598 (tp30) cc_final: 0.9362 (mp0) REVERT: D 419 MET cc_start: 0.9551 (mtm) cc_final: 0.9333 (mtm) REVERT: D 438 LYS cc_start: 0.8939 (ptmm) cc_final: 0.8634 (tptt) REVERT: D 440 MET cc_start: 0.9093 (mmp) cc_final: 0.8618 (mmp) REVERT: D 448 TYR cc_start: 0.7547 (t80) cc_final: 0.6749 (t80) REVERT: D 479 MET cc_start: 0.5880 (tpt) cc_final: 0.5266 (tmm) REVERT: D 489 PHE cc_start: 0.9381 (t80) cc_final: 0.9052 (t80) REVERT: D 550 CYS cc_start: 0.9324 (m) cc_final: 0.9106 (t) REVERT: D 562 MET cc_start: 0.9161 (tpt) cc_final: 0.8232 (tpp) REVERT: D 572 MET cc_start: 0.8824 (ppp) cc_final: 0.8078 (tpt) REVERT: D 575 TYR cc_start: 0.8302 (p90) cc_final: 0.7763 (p90) REVERT: D 578 MET cc_start: 0.8627 (mmm) cc_final: 0.8296 (mmm) REVERT: D 597 PHE cc_start: 0.7924 (t80) cc_final: 0.7468 (t80) REVERT: D 702 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8368 (mt-10) REVERT: D 704 GLU cc_start: 0.9283 (tp30) cc_final: 0.8699 (tp30) outliers start: 24 outliers final: 0 residues processed: 672 average time/residue: 0.2841 time to fit residues: 300.6739 Evaluate side-chains 473 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 467 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 415 ASN Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 415 ASN Chi-restraints excluded: chain C residue 415 ASN Chi-restraints excluded: chain D residue 415 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 206 optimal weight: 0.9980 chunk 184 optimal weight: 9.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 98 optimal weight: 9.9990 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 221 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 160 HIS A 244 HIS A 330 ASN A 339 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 ASN A 735 ASN B 160 HIS B 244 HIS B 330 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN B 483 GLN B 671 ASN B 735 ASN C 160 HIS C 244 HIS C 330 ASN ** C 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 ASN C 671 ASN C 735 ASN D 160 HIS D 244 HIS D 330 ASN ** D 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN D 483 GLN D 671 ASN D 735 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20424 Z= 0.224 Angle : 0.706 9.778 27620 Z= 0.365 Chirality : 0.039 0.158 3152 Planarity : 0.004 0.031 3420 Dihedral : 6.646 39.106 2720 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.33 % Allowed : 15.93 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.54 (0.15), residues: 2408 helix: -0.65 (0.12), residues: 1496 sheet: 2.24 (0.63), residues: 68 loop : -1.83 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 521 HIS 0.004 0.001 HIS A 426 PHE 0.015 0.001 PHE B 524 TYR 0.016 0.001 TYR A 213 ARG 0.003 0.000 ARG B 716 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 490 time to evaluate : 2.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9737 (mt) cc_final: 0.9401 (pp) REVERT: A 174 LYS cc_start: 0.9544 (tttp) cc_final: 0.8763 (ttpt) REVERT: A 178 ASN cc_start: 0.9464 (m110) cc_final: 0.8791 (p0) REVERT: A 257 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8734 (mt-10) REVERT: A 261 PHE cc_start: 0.9423 (p90) cc_final: 0.9079 (p90) REVERT: A 284 ASN cc_start: 0.9189 (t0) cc_final: 0.8939 (t0) REVERT: A 308 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8822 (tt0) REVERT: A 320 MET cc_start: 0.9255 (mmp) cc_final: 0.8939 (mmt) REVERT: A 355 GLU cc_start: 0.9290 (mm-30) cc_final: 0.8990 (tp30) REVERT: A 364 GLU cc_start: 0.9018 (pp20) cc_final: 0.8700 (tm-30) REVERT: A 405 GLU cc_start: 0.9586 (tt0) cc_final: 0.9143 (pt0) REVERT: A 410 ASN cc_start: 0.8750 (OUTLIER) cc_final: 0.8549 (t0) REVERT: A 414 ASP cc_start: 0.9104 (t0) cc_final: 0.8719 (p0) REVERT: A 438 LYS cc_start: 0.8954 (ptmm) cc_final: 0.8570 (tptt) REVERT: A 448 TYR cc_start: 0.7089 (t80) cc_final: 0.6127 (t80) REVERT: A 479 MET cc_start: 0.5782 (tpt) cc_final: 0.5043 (tmm) REVERT: A 488 MET cc_start: 0.8633 (mtp) cc_final: 0.8201 (ptp) REVERT: A 542 PHE cc_start: 0.6338 (m-10) cc_final: 0.5875 (m-10) REVERT: A 555 MET cc_start: 0.9213 (mtm) cc_final: 0.8686 (mmm) REVERT: A 562 MET cc_start: 0.9086 (tpt) cc_final: 0.8312 (tpt) REVERT: A 572 MET cc_start: 0.8675 (ppp) cc_final: 0.8086 (tpt) REVERT: A 575 TYR cc_start: 0.8153 (p90) cc_final: 0.7415 (p90) REVERT: A 597 PHE cc_start: 0.7751 (t80) cc_final: 0.6653 (t80) REVERT: A 661 TYR cc_start: 0.8908 (t80) cc_final: 0.8617 (t80) REVERT: A 674 ILE cc_start: 0.9458 (mm) cc_final: 0.8977 (mm) REVERT: A 677 MET cc_start: 0.8980 (ttt) cc_final: 0.8776 (mtp) REVERT: A 702 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 704 GLU cc_start: 0.9163 (tp30) cc_final: 0.8616 (tm-30) REVERT: A 706 MET cc_start: 0.9227 (mmp) cc_final: 0.9008 (mmm) REVERT: B 139 LEU cc_start: 0.9739 (mt) cc_final: 0.9472 (pp) REVERT: B 174 LYS cc_start: 0.9480 (tttp) cc_final: 0.8587 (ttpt) REVERT: B 178 ASN cc_start: 0.9340 (m110) cc_final: 0.8673 (p0) REVERT: B 214 GLU cc_start: 0.9575 (tm-30) cc_final: 0.8780 (tm-30) REVERT: B 257 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8578 (mt-10) REVERT: B 261 PHE cc_start: 0.9304 (p90) cc_final: 0.8976 (p90) REVERT: B 308 GLU cc_start: 0.9205 (mm-30) cc_final: 0.8735 (tt0) REVERT: B 323 MET cc_start: 0.9216 (tpp) cc_final: 0.9003 (tpt) REVERT: B 405 GLU cc_start: 0.9584 (tt0) cc_final: 0.9134 (pt0) REVERT: B 414 ASP cc_start: 0.9023 (t0) cc_final: 0.8582 (p0) REVERT: B 419 MET cc_start: 0.9389 (mtm) cc_final: 0.9048 (mtm) REVERT: B 438 LYS cc_start: 0.9069 (ptmm) cc_final: 0.8552 (tptt) REVERT: B 448 TYR cc_start: 0.7219 (t80) cc_final: 0.6776 (t80) REVERT: B 479 MET cc_start: 0.5856 (tpt) cc_final: 0.5074 (tmm) REVERT: B 488 MET cc_start: 0.8597 (mtp) cc_final: 0.8366 (ptp) REVERT: B 555 MET cc_start: 0.9019 (mtm) cc_final: 0.8368 (mmm) REVERT: B 572 MET cc_start: 0.8860 (ppp) cc_final: 0.8184 (tpt) REVERT: B 575 TYR cc_start: 0.8116 (p90) cc_final: 0.7238 (p90) REVERT: B 578 MET cc_start: 0.8615 (mmm) cc_final: 0.8319 (mmm) REVERT: B 597 PHE cc_start: 0.7749 (t80) cc_final: 0.6595 (t80) REVERT: B 661 TYR cc_start: 0.8773 (t80) cc_final: 0.8476 (t80) REVERT: B 677 MET cc_start: 0.8978 (mmm) cc_final: 0.8539 (mmm) REVERT: B 702 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8627 (mt-10) REVERT: B 704 GLU cc_start: 0.9186 (tp30) cc_final: 0.8647 (tm-30) REVERT: C 139 LEU cc_start: 0.9729 (mt) cc_final: 0.9428 (pp) REVERT: C 174 LYS cc_start: 0.9537 (tttp) cc_final: 0.8660 (ttpt) REVERT: C 178 ASN cc_start: 0.9384 (m110) cc_final: 0.8764 (p0) REVERT: C 214 GLU cc_start: 0.9559 (tm-30) cc_final: 0.8703 (tm-30) REVERT: C 257 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8655 (mt-10) REVERT: C 261 PHE cc_start: 0.9375 (p90) cc_final: 0.8972 (p90) REVERT: C 284 ASN cc_start: 0.9128 (t0) cc_final: 0.8898 (t0) REVERT: C 290 THR cc_start: 0.9424 (p) cc_final: 0.9179 (t) REVERT: C 308 GLU cc_start: 0.9264 (mm-30) cc_final: 0.8726 (tt0) REVERT: C 364 GLU cc_start: 0.9036 (pp20) cc_final: 0.8810 (tm-30) REVERT: C 405 GLU cc_start: 0.9557 (tt0) cc_final: 0.9132 (pt0) REVERT: C 410 ASN cc_start: 0.8687 (OUTLIER) cc_final: 0.8479 (t0) REVERT: C 414 ASP cc_start: 0.9117 (t0) cc_final: 0.8622 (p0) REVERT: C 419 MET cc_start: 0.9411 (mtm) cc_final: 0.9073 (mtm) REVERT: C 438 LYS cc_start: 0.9080 (ptmm) cc_final: 0.8599 (tptt) REVERT: C 448 TYR cc_start: 0.7745 (t80) cc_final: 0.7353 (t80) REVERT: C 479 MET cc_start: 0.6026 (tpt) cc_final: 0.5258 (tmm) REVERT: C 488 MET cc_start: 0.8561 (mtp) cc_final: 0.8343 (ptp) REVERT: C 493 TRP cc_start: 0.8523 (t60) cc_final: 0.7958 (t60) REVERT: C 572 MET cc_start: 0.8732 (ppp) cc_final: 0.8321 (tpt) REVERT: C 574 MET cc_start: 0.8673 (mmt) cc_final: 0.8293 (mmm) REVERT: C 578 MET cc_start: 0.8573 (mmm) cc_final: 0.8250 (mmm) REVERT: C 597 PHE cc_start: 0.7729 (t80) cc_final: 0.6726 (t80) REVERT: C 634 LYS cc_start: 0.8628 (pttt) cc_final: 0.8287 (ptpp) REVERT: C 702 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8555 (mt-10) REVERT: C 704 GLU cc_start: 0.9185 (tp30) cc_final: 0.8675 (tm-30) REVERT: D 139 LEU cc_start: 0.9750 (mt) cc_final: 0.9471 (pp) REVERT: D 159 MET cc_start: 0.9141 (mmp) cc_final: 0.8877 (mmm) REVERT: D 174 LYS cc_start: 0.9505 (tttp) cc_final: 0.8633 (ttpt) REVERT: D 178 ASN cc_start: 0.9327 (m110) cc_final: 0.8628 (p0) REVERT: D 214 GLU cc_start: 0.9564 (tm-30) cc_final: 0.8741 (tm-30) REVERT: D 257 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8652 (mt-10) REVERT: D 261 PHE cc_start: 0.9366 (p90) cc_final: 0.8999 (p90) REVERT: D 284 ASN cc_start: 0.9171 (t0) cc_final: 0.8925 (t0) REVERT: D 290 THR cc_start: 0.9401 (p) cc_final: 0.9145 (t) REVERT: D 308 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8740 (tt0) REVERT: D 364 GLU cc_start: 0.9056 (pp20) cc_final: 0.8820 (tm-30) REVERT: D 405 GLU cc_start: 0.9556 (tt0) cc_final: 0.9143 (pt0) REVERT: D 410 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8500 (t0) REVERT: D 414 ASP cc_start: 0.9155 (t0) cc_final: 0.8638 (p0) REVERT: D 419 MET cc_start: 0.9425 (mtm) cc_final: 0.9077 (mtm) REVERT: D 438 LYS cc_start: 0.9050 (ptmm) cc_final: 0.8576 (tptt) REVERT: D 448 TYR cc_start: 0.7709 (t80) cc_final: 0.7329 (t80) REVERT: D 479 MET cc_start: 0.6034 (tpt) cc_final: 0.5307 (tmm) REVERT: D 488 MET cc_start: 0.8532 (mtp) cc_final: 0.8322 (ptp) REVERT: D 493 TRP cc_start: 0.8484 (t60) cc_final: 0.7669 (t60) REVERT: D 532 LEU cc_start: 0.9168 (mt) cc_final: 0.8756 (tp) REVERT: D 550 CYS cc_start: 0.9141 (m) cc_final: 0.8842 (p) REVERT: D 555 MET cc_start: 0.9010 (mtm) cc_final: 0.8579 (mmm) REVERT: D 572 MET cc_start: 0.8775 (ppp) cc_final: 0.8313 (tpt) REVERT: D 575 TYR cc_start: 0.8211 (p90) cc_final: 0.7900 (p90) REVERT: D 578 MET cc_start: 0.8609 (mmm) cc_final: 0.8329 (mmm) REVERT: D 597 PHE cc_start: 0.7646 (t80) cc_final: 0.6629 (t80) REVERT: D 661 TYR cc_start: 0.8802 (t80) cc_final: 0.8596 (t80) REVERT: D 704 GLU cc_start: 0.9218 (tp30) cc_final: 0.8704 (tm-30) outliers start: 72 outliers final: 31 residues processed: 543 average time/residue: 0.2659 time to fit residues: 233.8090 Evaluate side-chains 460 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 426 time to evaluate : 2.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASP Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 201 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 547 TYR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 410 ASN Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 547 TYR Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 410 ASN Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 547 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 585 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 184 optimal weight: 4.9990 chunk 150 optimal weight: 0.2980 chunk 61 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 239 optimal weight: 0.6980 chunk 197 optimal weight: 9.9990 chunk 220 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 410 ASN C 483 GLN D 410 ASN D 483 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20424 Z= 0.151 Angle : 0.656 10.344 27620 Z= 0.318 Chirality : 0.039 0.240 3152 Planarity : 0.003 0.025 3420 Dihedral : 5.888 37.680 2708 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.33 % Allowed : 19.07 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.52 (0.16), residues: 2408 helix: 0.38 (0.13), residues: 1516 sheet: 2.34 (0.61), residues: 68 loop : -1.91 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 521 HIS 0.004 0.001 HIS B 426 PHE 0.014 0.001 PHE A 524 TYR 0.020 0.001 TYR C 575 ARG 0.003 0.000 ARG A 487 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 493 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9688 (mt) cc_final: 0.9462 (pp) REVERT: A 178 ASN cc_start: 0.9440 (m110) cc_final: 0.8834 (p0) REVERT: A 214 GLU cc_start: 0.9527 (tm-30) cc_final: 0.9221 (tp30) REVERT: A 244 HIS cc_start: 0.8893 (m90) cc_final: 0.8243 (m90) REVERT: A 261 PHE cc_start: 0.9255 (p90) cc_final: 0.8814 (p90) REVERT: A 284 ASN cc_start: 0.9163 (t0) cc_final: 0.8928 (t0) REVERT: A 308 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8747 (tt0) REVERT: A 320 MET cc_start: 0.9199 (mmp) cc_final: 0.8855 (mmt) REVERT: A 355 GLU cc_start: 0.9259 (mm-30) cc_final: 0.8935 (tp30) REVERT: A 371 ARG cc_start: 0.8962 (mtp-110) cc_final: 0.8254 (ttm110) REVERT: A 405 GLU cc_start: 0.9574 (tt0) cc_final: 0.9120 (pt0) REVERT: A 414 ASP cc_start: 0.8987 (t0) cc_final: 0.8748 (p0) REVERT: A 448 TYR cc_start: 0.7264 (t80) cc_final: 0.6279 (t80) REVERT: A 479 MET cc_start: 0.5446 (tpt) cc_final: 0.4752 (tmm) REVERT: A 508 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.5872 (tp) REVERT: A 527 PHE cc_start: 0.9404 (t80) cc_final: 0.9163 (t80) REVERT: A 562 MET cc_start: 0.9129 (tpt) cc_final: 0.8498 (tpt) REVERT: A 572 MET cc_start: 0.8735 (ppp) cc_final: 0.8105 (tpt) REVERT: A 575 TYR cc_start: 0.8044 (p90) cc_final: 0.7673 (p90) REVERT: A 597 PHE cc_start: 0.7725 (t80) cc_final: 0.7283 (t80) REVERT: A 672 MET cc_start: 0.8970 (tpp) cc_final: 0.8444 (tpt) REVERT: A 674 ILE cc_start: 0.9466 (mm) cc_final: 0.8995 (mm) REVERT: A 704 GLU cc_start: 0.9140 (tp30) cc_final: 0.8612 (tp30) REVERT: B 139 LEU cc_start: 0.9763 (mt) cc_final: 0.9542 (pp) REVERT: B 174 LYS cc_start: 0.9459 (tttp) cc_final: 0.8593 (ttpt) REVERT: B 178 ASN cc_start: 0.9346 (m110) cc_final: 0.8722 (p0) REVERT: B 214 GLU cc_start: 0.9524 (tm-30) cc_final: 0.8675 (tm-30) REVERT: B 225 ARG cc_start: 0.9370 (mmt180) cc_final: 0.8682 (mmm-85) REVERT: B 257 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8619 (mt-10) REVERT: B 261 PHE cc_start: 0.9088 (p90) cc_final: 0.8713 (p90) REVERT: B 290 THR cc_start: 0.9394 (p) cc_final: 0.9158 (t) REVERT: B 308 GLU cc_start: 0.9214 (mm-30) cc_final: 0.8723 (tt0) REVERT: B 405 GLU cc_start: 0.9578 (tt0) cc_final: 0.9131 (pt0) REVERT: B 414 ASP cc_start: 0.8936 (t0) cc_final: 0.8672 (p0) REVERT: B 438 LYS cc_start: 0.9046 (ptmm) cc_final: 0.8641 (tptt) REVERT: B 448 TYR cc_start: 0.7370 (t80) cc_final: 0.6227 (t80) REVERT: B 479 MET cc_start: 0.5836 (tpt) cc_final: 0.5040 (tmm) REVERT: B 488 MET cc_start: 0.8517 (mtp) cc_final: 0.8281 (ptp) REVERT: B 508 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.5950 (tp) REVERT: B 562 MET cc_start: 0.9183 (tpt) cc_final: 0.8414 (tpt) REVERT: B 572 MET cc_start: 0.8808 (ppp) cc_final: 0.8499 (tmm) REVERT: B 574 MET cc_start: 0.8371 (mmt) cc_final: 0.7618 (mmm) REVERT: B 575 TYR cc_start: 0.8299 (p90) cc_final: 0.8037 (p90) REVERT: B 578 MET cc_start: 0.8608 (mmm) cc_final: 0.8311 (mmm) REVERT: B 597 PHE cc_start: 0.7852 (t80) cc_final: 0.6787 (t80) REVERT: B 661 TYR cc_start: 0.8732 (t80) cc_final: 0.8489 (t80) REVERT: B 677 MET cc_start: 0.8941 (mmm) cc_final: 0.8525 (mmm) REVERT: B 702 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8619 (mt-10) REVERT: B 704 GLU cc_start: 0.9175 (tp30) cc_final: 0.8653 (tm-30) REVERT: C 139 LEU cc_start: 0.9712 (mt) cc_final: 0.9448 (pp) REVERT: C 174 LYS cc_start: 0.9507 (tttp) cc_final: 0.8612 (ttpt) REVERT: C 178 ASN cc_start: 0.9362 (m110) cc_final: 0.8722 (p0) REVERT: C 214 GLU cc_start: 0.9520 (tm-30) cc_final: 0.9170 (tp30) REVERT: C 257 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8646 (mt-10) REVERT: C 261 PHE cc_start: 0.9199 (p90) cc_final: 0.8779 (p90) REVERT: C 284 ASN cc_start: 0.9134 (t0) cc_final: 0.8854 (t0) REVERT: C 290 THR cc_start: 0.9382 (p) cc_final: 0.9150 (t) REVERT: C 293 ASP cc_start: 0.8693 (p0) cc_final: 0.7996 (p0) REVERT: C 308 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8719 (tt0) REVERT: C 405 GLU cc_start: 0.9567 (tt0) cc_final: 0.9141 (pt0) REVERT: C 414 ASP cc_start: 0.9019 (t0) cc_final: 0.8683 (p0) REVERT: C 448 TYR cc_start: 0.7885 (t80) cc_final: 0.7194 (t80) REVERT: C 479 MET cc_start: 0.5908 (tpt) cc_final: 0.5188 (tmm) REVERT: C 488 MET cc_start: 0.8491 (mtp) cc_final: 0.8244 (ptp) REVERT: C 508 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.5740 (tt) REVERT: C 559 TRP cc_start: 0.9355 (m100) cc_final: 0.8584 (m100) REVERT: C 562 MET cc_start: 0.9127 (tpt) cc_final: 0.8686 (tpp) REVERT: C 574 MET cc_start: 0.8682 (mmt) cc_final: 0.8411 (mmt) REVERT: C 672 MET cc_start: 0.8990 (tpp) cc_final: 0.8531 (tpt) REVERT: C 692 TRP cc_start: 0.8772 (t60) cc_final: 0.8227 (t60) REVERT: C 702 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8585 (mt-10) REVERT: C 704 GLU cc_start: 0.9182 (tp30) cc_final: 0.8674 (tm-30) REVERT: D 139 LEU cc_start: 0.9747 (mt) cc_final: 0.9508 (pp) REVERT: D 159 MET cc_start: 0.9182 (mmp) cc_final: 0.8964 (mmm) REVERT: D 174 LYS cc_start: 0.9491 (tttp) cc_final: 0.8617 (ttpt) REVERT: D 178 ASN cc_start: 0.9298 (m110) cc_final: 0.8775 (p0) REVERT: D 214 GLU cc_start: 0.9516 (tm-30) cc_final: 0.8608 (tm-30) REVERT: D 257 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8644 (mt-10) REVERT: D 261 PHE cc_start: 0.9200 (p90) cc_final: 0.8805 (p90) REVERT: D 284 ASN cc_start: 0.9155 (t0) cc_final: 0.8877 (t0) REVERT: D 290 THR cc_start: 0.9359 (p) cc_final: 0.9108 (t) REVERT: D 293 ASP cc_start: 0.8719 (p0) cc_final: 0.8085 (p0) REVERT: D 308 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8704 (tt0) REVERT: D 405 GLU cc_start: 0.9574 (tt0) cc_final: 0.9126 (pt0) REVERT: D 414 ASP cc_start: 0.9067 (t0) cc_final: 0.8704 (p0) REVERT: D 448 TYR cc_start: 0.7893 (t80) cc_final: 0.7216 (t80) REVERT: D 479 MET cc_start: 0.5538 (tpt) cc_final: 0.4940 (tmm) REVERT: D 488 MET cc_start: 0.8604 (mtp) cc_final: 0.8393 (ptp) REVERT: D 508 LEU cc_start: 0.6405 (OUTLIER) cc_final: 0.5839 (tp) REVERT: D 532 LEU cc_start: 0.9330 (mt) cc_final: 0.8981 (tp) REVERT: D 550 CYS cc_start: 0.9016 (m) cc_final: 0.8804 (m) REVERT: D 562 MET cc_start: 0.9148 (tpt) cc_final: 0.8714 (tpp) REVERT: D 572 MET cc_start: 0.8841 (ppp) cc_final: 0.8449 (tpt) REVERT: D 574 MET cc_start: 0.8508 (mmt) cc_final: 0.8271 (mmm) REVERT: D 578 MET cc_start: 0.8647 (mmm) cc_final: 0.8420 (mmm) REVERT: D 672 MET cc_start: 0.9009 (tpp) cc_final: 0.8794 (tpt) REVERT: D 677 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8815 (mmm) REVERT: D 704 GLU cc_start: 0.9154 (tp30) cc_final: 0.8734 (tp30) outliers start: 72 outliers final: 31 residues processed: 536 average time/residue: 0.2688 time to fit residues: 233.9678 Evaluate side-chains 463 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 427 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 445 PHE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 677 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 9.9990 chunk 166 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 7.9990 chunk 149 optimal weight: 9.9990 chunk 222 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 211 optimal weight: 0.0050 chunk 63 optimal weight: 8.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 483 GLN ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN C 483 GLN D 483 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20424 Z= 0.169 Angle : 0.653 9.547 27620 Z= 0.319 Chirality : 0.040 0.267 3152 Planarity : 0.003 0.021 3420 Dihedral : 5.660 38.232 2708 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.33 % Allowed : 21.44 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -0.04 (0.17), residues: 2408 helix: 0.88 (0.13), residues: 1524 sheet: 2.73 (0.58), residues: 64 loop : -2.01 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 493 HIS 0.003 0.001 HIS C 426 PHE 0.025 0.001 PHE A 449 TYR 0.017 0.001 TYR C 575 ARG 0.002 0.000 ARG A 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 445 time to evaluate : 2.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9736 (mt) cc_final: 0.9525 (pp) REVERT: A 178 ASN cc_start: 0.9434 (m110) cc_final: 0.8926 (p0) REVERT: A 214 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9253 (tp30) REVERT: A 244 HIS cc_start: 0.8884 (m90) cc_final: 0.8193 (m90) REVERT: A 261 PHE cc_start: 0.9264 (p90) cc_final: 0.8692 (p90) REVERT: A 284 ASN cc_start: 0.9080 (t0) cc_final: 0.8838 (t0) REVERT: A 290 THR cc_start: 0.9380 (OUTLIER) cc_final: 0.9173 (t) REVERT: A 308 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8734 (tt0) REVERT: A 371 ARG cc_start: 0.9082 (mtp-110) cc_final: 0.8263 (ttm-80) REVERT: A 405 GLU cc_start: 0.9624 (tt0) cc_final: 0.8734 (tp30) REVERT: A 448 TYR cc_start: 0.7401 (t80) cc_final: 0.7052 (t80) REVERT: A 479 MET cc_start: 0.5356 (tpt) cc_final: 0.4713 (tmm) REVERT: A 508 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5760 (tp) REVERT: A 527 PHE cc_start: 0.9384 (t80) cc_final: 0.9173 (t80) REVERT: A 672 MET cc_start: 0.8990 (tpp) cc_final: 0.8764 (tpt) REVERT: A 704 GLU cc_start: 0.9149 (tp30) cc_final: 0.8744 (tp30) REVERT: B 139 LEU cc_start: 0.9771 (mt) cc_final: 0.9488 (pp) REVERT: B 174 LYS cc_start: 0.9472 (tttp) cc_final: 0.8653 (ttpt) REVERT: B 178 ASN cc_start: 0.9345 (m110) cc_final: 0.8808 (p0) REVERT: B 214 GLU cc_start: 0.9533 (tm-30) cc_final: 0.9208 (tp30) REVERT: B 225 ARG cc_start: 0.9360 (mmt180) cc_final: 0.8676 (mmm-85) REVERT: B 257 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8629 (mt-10) REVERT: B 290 THR cc_start: 0.9412 (p) cc_final: 0.9165 (t) REVERT: B 308 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8739 (tt0) REVERT: B 448 TYR cc_start: 0.7472 (t80) cc_final: 0.6335 (t80) REVERT: B 479 MET cc_start: 0.5717 (tpt) cc_final: 0.4917 (ttp) REVERT: B 488 MET cc_start: 0.8514 (mtp) cc_final: 0.8276 (ptp) REVERT: B 508 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.5831 (tt) REVERT: B 562 MET cc_start: 0.9207 (tpt) cc_final: 0.8460 (tpt) REVERT: B 572 MET cc_start: 0.8785 (ppp) cc_final: 0.8446 (tmm) REVERT: B 574 MET cc_start: 0.8301 (mmt) cc_final: 0.7429 (mmt) REVERT: B 575 TYR cc_start: 0.8416 (p90) cc_final: 0.8129 (p90) REVERT: B 578 MET cc_start: 0.8620 (mmm) cc_final: 0.8361 (mmm) REVERT: B 672 MET cc_start: 0.8979 (tpp) cc_final: 0.8696 (tpt) REVERT: B 702 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8667 (mt-10) REVERT: B 704 GLU cc_start: 0.9165 (tp30) cc_final: 0.8649 (tm-30) REVERT: C 174 LYS cc_start: 0.9521 (tttp) cc_final: 0.8693 (ttpt) REVERT: C 178 ASN cc_start: 0.9461 (m110) cc_final: 0.8744 (p0) REVERT: C 214 GLU cc_start: 0.9524 (tm-30) cc_final: 0.9219 (tp30) REVERT: C 257 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8658 (mt-10) REVERT: C 261 PHE cc_start: 0.9187 (p90) cc_final: 0.8734 (p90) REVERT: C 290 THR cc_start: 0.9400 (p) cc_final: 0.9151 (t) REVERT: C 308 GLU cc_start: 0.9284 (mm-30) cc_final: 0.8695 (tt0) REVERT: C 405 GLU cc_start: 0.9597 (tt0) cc_final: 0.9370 (tt0) REVERT: C 447 PHE cc_start: 0.9137 (t80) cc_final: 0.8605 (t80) REVERT: C 448 TYR cc_start: 0.8072 (t80) cc_final: 0.7500 (t80) REVERT: C 479 MET cc_start: 0.5792 (tpt) cc_final: 0.5153 (tmm) REVERT: C 488 MET cc_start: 0.8494 (mtp) cc_final: 0.8242 (ptp) REVERT: C 508 LEU cc_start: 0.6486 (OUTLIER) cc_final: 0.5890 (tp) REVERT: C 555 MET cc_start: 0.8768 (mtp) cc_final: 0.8507 (mmm) REVERT: C 562 MET cc_start: 0.9139 (tpt) cc_final: 0.8923 (tpp) REVERT: C 634 LYS cc_start: 0.8588 (pttt) cc_final: 0.8178 (ptpt) REVERT: C 702 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8577 (mt-10) REVERT: C 704 GLU cc_start: 0.9137 (tp30) cc_final: 0.8701 (tp30) REVERT: D 139 LEU cc_start: 0.9785 (mt) cc_final: 0.9571 (pp) REVERT: D 174 LYS cc_start: 0.9493 (tttp) cc_final: 0.8728 (ttpt) REVERT: D 178 ASN cc_start: 0.9424 (m110) cc_final: 0.8741 (p0) REVERT: D 214 GLU cc_start: 0.9514 (tm-30) cc_final: 0.9189 (tp30) REVERT: D 257 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8634 (mt-10) REVERT: D 261 PHE cc_start: 0.9173 (p90) cc_final: 0.8720 (p90) REVERT: D 290 THR cc_start: 0.9389 (p) cc_final: 0.9123 (t) REVERT: D 308 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8715 (tt0) REVERT: D 405 GLU cc_start: 0.9621 (tt0) cc_final: 0.8660 (tp30) REVERT: D 448 TYR cc_start: 0.7988 (t80) cc_final: 0.7296 (t80) REVERT: D 479 MET cc_start: 0.5542 (tpt) cc_final: 0.4944 (tmm) REVERT: D 488 MET cc_start: 0.8516 (mtp) cc_final: 0.8260 (ptp) REVERT: D 508 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5808 (tp) REVERT: D 532 LEU cc_start: 0.9336 (mt) cc_final: 0.8999 (tp) REVERT: D 562 MET cc_start: 0.9179 (tpt) cc_final: 0.8856 (tpp) REVERT: D 574 MET cc_start: 0.8787 (mmt) cc_final: 0.7640 (mmm) REVERT: D 677 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8889 (mmm) REVERT: D 704 GLU cc_start: 0.9163 (tp30) cc_final: 0.8827 (tp30) outliers start: 72 outliers final: 41 residues processed: 492 average time/residue: 0.2674 time to fit residues: 213.6046 Evaluate side-chains 464 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 417 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 585 HIS Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 201 ASP Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 677 MET Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 196 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 3 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.0670 chunk 211 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20424 Z= 0.180 Angle : 0.665 11.889 27620 Z= 0.323 Chirality : 0.040 0.282 3152 Planarity : 0.003 0.022 3420 Dihedral : 5.575 38.587 2708 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 4.17 % Allowed : 21.90 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.27 (0.17), residues: 2408 helix: 1.13 (0.13), residues: 1528 sheet: 2.67 (0.58), residues: 64 loop : -1.91 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 559 HIS 0.003 0.001 HIS D 426 PHE 0.014 0.001 PHE B 449 TYR 0.022 0.002 TYR A 575 ARG 0.002 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 434 time to evaluate : 2.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 ASN cc_start: 0.9434 (m110) cc_final: 0.8921 (p0) REVERT: A 244 HIS cc_start: 0.8895 (m90) cc_final: 0.7992 (m90) REVERT: A 261 PHE cc_start: 0.9290 (p90) cc_final: 0.8707 (p90) REVERT: A 263 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7522 (tt0) REVERT: A 284 ASN cc_start: 0.9070 (t0) cc_final: 0.8841 (t0) REVERT: A 290 THR cc_start: 0.9400 (OUTLIER) cc_final: 0.9188 (t) REVERT: A 293 ASP cc_start: 0.8387 (p0) cc_final: 0.7980 (p0) REVERT: A 308 GLU cc_start: 0.9335 (mm-30) cc_final: 0.8745 (tt0) REVERT: A 405 GLU cc_start: 0.9614 (tt0) cc_final: 0.9177 (pt0) REVERT: A 448 TYR cc_start: 0.7495 (t80) cc_final: 0.6527 (t80) REVERT: A 479 MET cc_start: 0.5359 (tpt) cc_final: 0.4836 (tmm) REVERT: A 508 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5740 (tp) REVERT: A 562 MET cc_start: 0.9245 (tpt) cc_final: 0.8598 (tpt) REVERT: A 601 PHE cc_start: 0.9149 (m-80) cc_final: 0.8746 (m-80) REVERT: A 676 LEU cc_start: 0.9634 (mm) cc_final: 0.9263 (mm) REVERT: A 704 GLU cc_start: 0.9226 (tp30) cc_final: 0.8743 (tp30) REVERT: B 139 LEU cc_start: 0.9777 (mt) cc_final: 0.9526 (pp) REVERT: B 174 LYS cc_start: 0.9482 (tttp) cc_final: 0.8650 (ttpt) REVERT: B 177 LEU cc_start: 0.9522 (mt) cc_final: 0.9287 (mt) REVERT: B 178 ASN cc_start: 0.9373 (m110) cc_final: 0.8845 (p0) REVERT: B 214 GLU cc_start: 0.9517 (tm-30) cc_final: 0.9228 (tp30) REVERT: B 257 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8626 (mt-10) REVERT: B 261 PHE cc_start: 0.9079 (p90) cc_final: 0.8651 (p90) REVERT: B 290 THR cc_start: 0.9425 (p) cc_final: 0.9200 (t) REVERT: B 308 GLU cc_start: 0.9276 (mm-30) cc_final: 0.8727 (tt0) REVERT: B 405 GLU cc_start: 0.9615 (tt0) cc_final: 0.8713 (tp30) REVERT: B 448 TYR cc_start: 0.7589 (t80) cc_final: 0.6463 (t80) REVERT: B 479 MET cc_start: 0.5581 (tpt) cc_final: 0.4877 (ttp) REVERT: B 488 MET cc_start: 0.8544 (mtp) cc_final: 0.8295 (ptp) REVERT: B 508 LEU cc_start: 0.6621 (OUTLIER) cc_final: 0.6017 (tp) REVERT: B 555 MET cc_start: 0.9354 (tpp) cc_final: 0.8923 (mmm) REVERT: B 562 MET cc_start: 0.9211 (tpt) cc_final: 0.8460 (tpt) REVERT: B 572 MET cc_start: 0.8848 (ppp) cc_final: 0.8409 (tmm) REVERT: B 574 MET cc_start: 0.8271 (mmt) cc_final: 0.7734 (mmt) REVERT: B 578 MET cc_start: 0.8714 (mmm) cc_final: 0.8466 (ppp) REVERT: B 672 MET cc_start: 0.9041 (tpp) cc_final: 0.8719 (tpt) REVERT: B 704 GLU cc_start: 0.9176 (tp30) cc_final: 0.8777 (tm-30) REVERT: B 721 CYS cc_start: 0.8088 (p) cc_final: 0.7773 (p) REVERT: C 174 LYS cc_start: 0.9532 (tttp) cc_final: 0.8755 (ttpt) REVERT: C 178 ASN cc_start: 0.9490 (m110) cc_final: 0.8770 (p0) REVERT: C 257 GLU cc_start: 0.9049 (mm-30) cc_final: 0.8662 (mt-10) REVERT: C 261 PHE cc_start: 0.9243 (p90) cc_final: 0.8794 (p90) REVERT: C 290 THR cc_start: 0.9416 (p) cc_final: 0.9178 (t) REVERT: C 308 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8678 (tt0) REVERT: C 405 GLU cc_start: 0.9624 (tt0) cc_final: 0.8705 (tp30) REVERT: C 447 PHE cc_start: 0.9160 (t80) cc_final: 0.8514 (t80) REVERT: C 448 TYR cc_start: 0.8103 (t80) cc_final: 0.7499 (t80) REVERT: C 479 MET cc_start: 0.5723 (tpt) cc_final: 0.5042 (tmm) REVERT: C 488 MET cc_start: 0.8467 (mtp) cc_final: 0.8219 (ptp) REVERT: C 508 LEU cc_start: 0.6544 (OUTLIER) cc_final: 0.5951 (tp) REVERT: C 555 MET cc_start: 0.8947 (mtp) cc_final: 0.8521 (mmm) REVERT: C 562 MET cc_start: 0.9212 (tpt) cc_final: 0.8963 (tpp) REVERT: C 574 MET cc_start: 0.8529 (mmt) cc_final: 0.8202 (mmm) REVERT: C 601 PHE cc_start: 0.9170 (m-80) cc_final: 0.8819 (m-80) REVERT: C 671 ASN cc_start: 0.9345 (t0) cc_final: 0.9142 (t0) REVERT: C 702 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8616 (mt-10) REVERT: C 704 GLU cc_start: 0.9158 (tp30) cc_final: 0.8743 (tp30) REVERT: D 139 LEU cc_start: 0.9799 (mt) cc_final: 0.9599 (pp) REVERT: D 174 LYS cc_start: 0.9519 (tttp) cc_final: 0.8719 (ttpt) REVERT: D 178 ASN cc_start: 0.9451 (m110) cc_final: 0.8761 (p0) REVERT: D 257 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8643 (mt-10) REVERT: D 261 PHE cc_start: 0.9210 (p90) cc_final: 0.8749 (p90) REVERT: D 290 THR cc_start: 0.9401 (p) cc_final: 0.9145 (t) REVERT: D 308 GLU cc_start: 0.9324 (mm-30) cc_final: 0.8686 (tt0) REVERT: D 405 GLU cc_start: 0.9609 (tt0) cc_final: 0.9173 (pt0) REVERT: D 448 TYR cc_start: 0.8132 (t80) cc_final: 0.7521 (t80) REVERT: D 479 MET cc_start: 0.5254 (tpt) cc_final: 0.4827 (ttp) REVERT: D 488 MET cc_start: 0.8548 (mtp) cc_final: 0.8267 (ptp) REVERT: D 508 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5712 (tp) REVERT: D 532 LEU cc_start: 0.9323 (mt) cc_final: 0.8989 (tp) REVERT: D 555 MET cc_start: 0.9312 (tpp) cc_final: 0.8841 (mmm) REVERT: D 562 MET cc_start: 0.9230 (tpt) cc_final: 0.9018 (tpp) REVERT: D 574 MET cc_start: 0.8478 (mmt) cc_final: 0.8049 (mmt) REVERT: D 704 GLU cc_start: 0.9246 (tp30) cc_final: 0.8909 (tp30) outliers start: 90 outliers final: 49 residues processed: 491 average time/residue: 0.2588 time to fit residues: 210.1283 Evaluate side-chains 466 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 411 time to evaluate : 2.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 171 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 585 HIS Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 79 optimal weight: 1.9990 chunk 212 optimal weight: 0.0050 chunk 46 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 236 optimal weight: 30.0000 chunk 195 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 123 optimal weight: 0.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 20424 Z= 0.156 Angle : 0.691 10.604 27620 Z= 0.324 Chirality : 0.040 0.253 3152 Planarity : 0.003 0.023 3420 Dihedral : 5.472 39.459 2708 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 3.43 % Allowed : 23.47 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2408 helix: 1.34 (0.13), residues: 1484 sheet: -0.16 (0.70), residues: 40 loop : -1.73 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 493 HIS 0.004 0.001 HIS D 426 PHE 0.014 0.001 PHE A 592 TYR 0.027 0.001 TYR A 575 ARG 0.002 0.000 ARG C 729 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 444 time to evaluate : 2.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9717 (mt) cc_final: 0.9414 (pp) REVERT: A 178 ASN cc_start: 0.9517 (m110) cc_final: 0.8844 (p0) REVERT: A 261 PHE cc_start: 0.9238 (p90) cc_final: 0.8617 (p90) REVERT: A 284 ASN cc_start: 0.9085 (t0) cc_final: 0.8849 (t0) REVERT: A 290 THR cc_start: 0.9409 (OUTLIER) cc_final: 0.9184 (t) REVERT: A 308 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8665 (tt0) REVERT: A 405 GLU cc_start: 0.9600 (tt0) cc_final: 0.9162 (pt0) REVERT: A 448 TYR cc_start: 0.7659 (t80) cc_final: 0.6578 (t80) REVERT: A 450 PHE cc_start: 0.9365 (m-10) cc_final: 0.9139 (t80) REVERT: A 479 MET cc_start: 0.5372 (tpt) cc_final: 0.4792 (tmm) REVERT: A 508 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.5797 (tp) REVERT: A 562 MET cc_start: 0.9270 (tpt) cc_final: 0.8569 (tpt) REVERT: A 601 PHE cc_start: 0.9193 (m-80) cc_final: 0.8775 (m-80) REVERT: A 704 GLU cc_start: 0.9196 (tp30) cc_final: 0.8842 (tp30) REVERT: A 715 PHE cc_start: 0.8946 (m-80) cc_final: 0.8720 (m-10) REVERT: B 174 LYS cc_start: 0.9482 (tttp) cc_final: 0.8644 (ttpt) REVERT: B 177 LEU cc_start: 0.9505 (mt) cc_final: 0.9270 (mt) REVERT: B 178 ASN cc_start: 0.9366 (m110) cc_final: 0.8779 (p0) REVERT: B 214 GLU cc_start: 0.9476 (tm-30) cc_final: 0.9230 (tp30) REVERT: B 257 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8650 (mt-10) REVERT: B 261 PHE cc_start: 0.9069 (p90) cc_final: 0.8692 (p90) REVERT: B 290 THR cc_start: 0.9405 (p) cc_final: 0.9184 (t) REVERT: B 308 GLU cc_start: 0.9265 (mm-30) cc_final: 0.8671 (tt0) REVERT: B 405 GLU cc_start: 0.9606 (tt0) cc_final: 0.9172 (pt0) REVERT: B 448 TYR cc_start: 0.7694 (t80) cc_final: 0.6481 (t80) REVERT: B 479 MET cc_start: 0.5401 (tpt) cc_final: 0.4867 (ttp) REVERT: B 488 MET cc_start: 0.8562 (mtp) cc_final: 0.8305 (ptp) REVERT: B 508 LEU cc_start: 0.6555 (OUTLIER) cc_final: 0.5880 (tt) REVERT: B 555 MET cc_start: 0.9352 (tpp) cc_final: 0.8955 (mmm) REVERT: B 562 MET cc_start: 0.9258 (tpt) cc_final: 0.8463 (tpt) REVERT: B 574 MET cc_start: 0.8370 (mmt) cc_final: 0.7817 (mmm) REVERT: B 575 TYR cc_start: 0.8481 (p90) cc_final: 0.8257 (p90) REVERT: B 672 MET cc_start: 0.9047 (tpp) cc_final: 0.8812 (tpt) REVERT: B 704 GLU cc_start: 0.9160 (tp30) cc_final: 0.8827 (tp30) REVERT: B 721 CYS cc_start: 0.7950 (p) cc_final: 0.7669 (p) REVERT: C 174 LYS cc_start: 0.9526 (tttp) cc_final: 0.8853 (ttpt) REVERT: C 178 ASN cc_start: 0.9498 (m110) cc_final: 0.8785 (p0) REVERT: C 257 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8670 (mt-10) REVERT: C 261 PHE cc_start: 0.9209 (p90) cc_final: 0.8798 (p90) REVERT: C 290 THR cc_start: 0.9405 (p) cc_final: 0.9170 (t) REVERT: C 308 GLU cc_start: 0.9310 (mm-30) cc_final: 0.8631 (tt0) REVERT: C 405 GLU cc_start: 0.9604 (tt0) cc_final: 0.8604 (tp30) REVERT: C 447 PHE cc_start: 0.9199 (t80) cc_final: 0.8549 (t80) REVERT: C 448 TYR cc_start: 0.8135 (t80) cc_final: 0.7485 (t80) REVERT: C 479 MET cc_start: 0.5816 (tpt) cc_final: 0.5120 (tmm) REVERT: C 488 MET cc_start: 0.8515 (mtp) cc_final: 0.8246 (ptp) REVERT: C 508 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.5936 (tp) REVERT: C 559 TRP cc_start: 0.9414 (m100) cc_final: 0.8842 (m100) REVERT: C 562 MET cc_start: 0.9279 (tpt) cc_final: 0.9063 (tpp) REVERT: C 574 MET cc_start: 0.8531 (mmt) cc_final: 0.8295 (mmm) REVERT: C 601 PHE cc_start: 0.9185 (m-80) cc_final: 0.8758 (m-80) REVERT: C 702 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8510 (mt-10) REVERT: C 704 GLU cc_start: 0.9146 (tp30) cc_final: 0.8725 (tp30) REVERT: D 139 LEU cc_start: 0.9790 (mt) cc_final: 0.9571 (pp) REVERT: D 174 LYS cc_start: 0.9516 (tttp) cc_final: 0.8744 (ttpt) REVERT: D 178 ASN cc_start: 0.9472 (m110) cc_final: 0.8785 (p0) REVERT: D 257 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8661 (mt-10) REVERT: D 261 PHE cc_start: 0.9176 (p90) cc_final: 0.8780 (p90) REVERT: D 290 THR cc_start: 0.9392 (p) cc_final: 0.9131 (t) REVERT: D 308 GLU cc_start: 0.9315 (mm-30) cc_final: 0.8662 (tt0) REVERT: D 405 GLU cc_start: 0.9600 (tt0) cc_final: 0.9151 (pt0) REVERT: D 448 TYR cc_start: 0.8189 (t80) cc_final: 0.7362 (t80) REVERT: D 479 MET cc_start: 0.5287 (tpt) cc_final: 0.4936 (ttp) REVERT: D 488 MET cc_start: 0.8537 (mtp) cc_final: 0.8237 (ptp) REVERT: D 508 LEU cc_start: 0.6374 (OUTLIER) cc_final: 0.5759 (tp) REVERT: D 532 LEU cc_start: 0.9324 (mt) cc_final: 0.8975 (tp) REVERT: D 555 MET cc_start: 0.9344 (tpp) cc_final: 0.8929 (mmm) REVERT: D 562 MET cc_start: 0.9260 (tpt) cc_final: 0.8999 (tpp) REVERT: D 574 MET cc_start: 0.8475 (mmt) cc_final: 0.8099 (mmt) REVERT: D 672 MET cc_start: 0.9034 (tpt) cc_final: 0.8685 (tmm) outliers start: 74 outliers final: 50 residues processed: 487 average time/residue: 0.2666 time to fit residues: 215.1564 Evaluate side-chains 468 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 413 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 585 HIS Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 227 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 172 optimal weight: 20.0000 chunk 133 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 235 optimal weight: 4.9990 chunk 147 optimal weight: 0.0270 chunk 143 optimal weight: 5.9990 chunk 108 optimal weight: 0.5980 overall best weight: 2.3244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20424 Z= 0.197 Angle : 0.711 14.143 27620 Z= 0.338 Chirality : 0.042 0.319 3152 Planarity : 0.003 0.024 3420 Dihedral : 5.496 38.897 2708 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.61 % Allowed : 23.89 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.26 (0.17), residues: 2408 helix: 1.27 (0.13), residues: 1504 sheet: -0.26 (0.72), residues: 40 loop : -1.81 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 559 HIS 0.003 0.001 HIS A 426 PHE 0.036 0.001 PHE D 715 TYR 0.029 0.002 TYR A 575 ARG 0.002 0.000 ARG D 729 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 427 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9749 (mt) cc_final: 0.9427 (pp) REVERT: A 178 ASN cc_start: 0.9534 (m110) cc_final: 0.8826 (p0) REVERT: A 261 PHE cc_start: 0.9300 (p90) cc_final: 0.8709 (p90) REVERT: A 284 ASN cc_start: 0.9136 (t0) cc_final: 0.8920 (t0) REVERT: A 290 THR cc_start: 0.9423 (OUTLIER) cc_final: 0.9205 (t) REVERT: A 308 GLU cc_start: 0.9373 (mm-30) cc_final: 0.8684 (tt0) REVERT: A 405 GLU cc_start: 0.9600 (tt0) cc_final: 0.9206 (pt0) REVERT: A 448 TYR cc_start: 0.7670 (t80) cc_final: 0.6858 (t80) REVERT: A 450 PHE cc_start: 0.9340 (m-10) cc_final: 0.9126 (t80) REVERT: A 479 MET cc_start: 0.5560 (tpt) cc_final: 0.4946 (tmm) REVERT: A 508 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.5896 (tp) REVERT: A 562 MET cc_start: 0.9349 (tpt) cc_final: 0.8948 (tpp) REVERT: A 565 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8838 (m-80) REVERT: A 601 PHE cc_start: 0.9099 (m-80) cc_final: 0.8617 (m-80) REVERT: A 715 PHE cc_start: 0.8978 (m-80) cc_final: 0.8717 (m-10) REVERT: B 174 LYS cc_start: 0.9557 (tttp) cc_final: 0.8808 (ttpt) REVERT: B 177 LEU cc_start: 0.9547 (mt) cc_final: 0.9306 (mt) REVERT: B 178 ASN cc_start: 0.9412 (m110) cc_final: 0.8777 (p0) REVERT: B 214 GLU cc_start: 0.9450 (tm-30) cc_final: 0.9237 (tp30) REVERT: B 257 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8708 (mt-10) REVERT: B 261 PHE cc_start: 0.9106 (p90) cc_final: 0.8724 (p90) REVERT: B 290 THR cc_start: 0.9434 (p) cc_final: 0.9217 (t) REVERT: B 308 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8703 (tt0) REVERT: B 405 GLU cc_start: 0.9612 (tt0) cc_final: 0.9181 (pt0) REVERT: B 448 TYR cc_start: 0.7729 (t80) cc_final: 0.7260 (t80) REVERT: B 479 MET cc_start: 0.5411 (tpt) cc_final: 0.4874 (ttp) REVERT: B 488 MET cc_start: 0.8562 (mtp) cc_final: 0.8302 (ptp) REVERT: B 508 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6069 (tp) REVERT: B 555 MET cc_start: 0.9401 (tpp) cc_final: 0.9023 (mmm) REVERT: B 574 MET cc_start: 0.8348 (mmt) cc_final: 0.7865 (mmm) REVERT: B 672 MET cc_start: 0.9062 (tpp) cc_final: 0.8709 (tpt) REVERT: B 704 GLU cc_start: 0.9266 (tp30) cc_final: 0.8957 (tp30) REVERT: B 721 CYS cc_start: 0.7937 (p) cc_final: 0.7706 (p) REVERT: C 174 LYS cc_start: 0.9575 (tttp) cc_final: 0.8861 (ttpt) REVERT: C 178 ASN cc_start: 0.9528 (m110) cc_final: 0.8756 (p0) REVERT: C 257 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8669 (mt-10) REVERT: C 261 PHE cc_start: 0.9238 (p90) cc_final: 0.8820 (p90) REVERT: C 290 THR cc_start: 0.9403 (p) cc_final: 0.9168 (t) REVERT: C 308 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8651 (tt0) REVERT: C 405 GLU cc_start: 0.9612 (tt0) cc_final: 0.9174 (pt0) REVERT: C 447 PHE cc_start: 0.9161 (t80) cc_final: 0.8469 (t80) REVERT: C 448 TYR cc_start: 0.8244 (t80) cc_final: 0.7586 (t80) REVERT: C 479 MET cc_start: 0.5813 (tpt) cc_final: 0.5113 (tmm) REVERT: C 488 MET cc_start: 0.8516 (mtp) cc_final: 0.8255 (ptp) REVERT: C 508 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5994 (tp) REVERT: C 562 MET cc_start: 0.9262 (tpt) cc_final: 0.9002 (tpp) REVERT: C 601 PHE cc_start: 0.9139 (m-80) cc_final: 0.8653 (m-80) REVERT: C 702 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8628 (mt-10) REVERT: C 704 GLU cc_start: 0.9205 (tp30) cc_final: 0.8782 (tp30) REVERT: D 139 LEU cc_start: 0.9809 (mt) cc_final: 0.9602 (pp) REVERT: D 174 LYS cc_start: 0.9573 (tttp) cc_final: 0.8762 (ttpt) REVERT: D 178 ASN cc_start: 0.9485 (m110) cc_final: 0.8754 (p0) REVERT: D 257 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8675 (mt-10) REVERT: D 261 PHE cc_start: 0.9232 (p90) cc_final: 0.8813 (p90) REVERT: D 290 THR cc_start: 0.9390 (p) cc_final: 0.9152 (t) REVERT: D 308 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8694 (tt0) REVERT: D 405 GLU cc_start: 0.9611 (tt0) cc_final: 0.9162 (pt0) REVERT: D 448 TYR cc_start: 0.8481 (t80) cc_final: 0.7784 (t80) REVERT: D 479 MET cc_start: 0.5161 (tpt) cc_final: 0.4860 (ttp) REVERT: D 488 MET cc_start: 0.8533 (mtp) cc_final: 0.8238 (ptp) REVERT: D 508 LEU cc_start: 0.6489 (OUTLIER) cc_final: 0.5897 (tp) REVERT: D 532 LEU cc_start: 0.9350 (mt) cc_final: 0.9006 (tp) REVERT: D 559 TRP cc_start: 0.9184 (m100) cc_final: 0.8133 (m100) REVERT: D 562 MET cc_start: 0.9318 (tpt) cc_final: 0.9052 (tpt) REVERT: D 574 MET cc_start: 0.8584 (mmt) cc_final: 0.7991 (mmt) REVERT: D 672 MET cc_start: 0.9052 (tpt) cc_final: 0.8693 (tmm) outliers start: 78 outliers final: 64 residues processed: 476 average time/residue: 0.2563 time to fit residues: 201.4813 Evaluate side-chains 483 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 413 time to evaluate : 2.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain B residue 720 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 730 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 145 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 160 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 184 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20424 Z= 0.170 Angle : 0.729 13.268 27620 Z= 0.338 Chirality : 0.041 0.321 3152 Planarity : 0.003 0.024 3420 Dihedral : 5.413 38.993 2708 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.75 % Allowed : 24.40 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.33 (0.17), residues: 2408 helix: 1.36 (0.13), residues: 1496 sheet: -0.20 (0.73), residues: 40 loop : -1.84 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 559 HIS 0.003 0.001 HIS B 426 PHE 0.024 0.001 PHE D 715 TYR 0.031 0.001 TYR C 575 ARG 0.002 0.000 ARG C 226 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 435 time to evaluate : 2.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9738 (mt) cc_final: 0.9439 (pp) REVERT: A 177 LEU cc_start: 0.9780 (OUTLIER) cc_final: 0.9488 (mt) REVERT: A 178 ASN cc_start: 0.9538 (m110) cc_final: 0.8943 (p0) REVERT: A 261 PHE cc_start: 0.9275 (p90) cc_final: 0.8731 (p90) REVERT: A 263 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7321 (pt0) REVERT: A 284 ASN cc_start: 0.9092 (t0) cc_final: 0.8863 (t0) REVERT: A 290 THR cc_start: 0.9374 (OUTLIER) cc_final: 0.9149 (t) REVERT: A 306 VAL cc_start: 0.9683 (t) cc_final: 0.9437 (p) REVERT: A 308 GLU cc_start: 0.9384 (mm-30) cc_final: 0.8671 (tt0) REVERT: A 448 TYR cc_start: 0.7676 (t80) cc_final: 0.6847 (t80) REVERT: A 450 PHE cc_start: 0.9354 (m-10) cc_final: 0.9143 (t80) REVERT: A 479 MET cc_start: 0.5301 (tpt) cc_final: 0.4636 (tmm) REVERT: A 508 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6018 (tp) REVERT: A 562 MET cc_start: 0.9384 (tpt) cc_final: 0.8974 (tpp) REVERT: A 569 PHE cc_start: 0.7399 (t80) cc_final: 0.6849 (t80) REVERT: A 715 PHE cc_start: 0.8936 (m-80) cc_final: 0.8690 (m-10) REVERT: B 174 LYS cc_start: 0.9535 (tttp) cc_final: 0.8842 (ttpt) REVERT: B 178 ASN cc_start: 0.9406 (m110) cc_final: 0.8789 (p0) REVERT: B 214 GLU cc_start: 0.9457 (tm-30) cc_final: 0.9244 (tp30) REVERT: B 257 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8701 (mt-10) REVERT: B 261 PHE cc_start: 0.9056 (p90) cc_final: 0.8677 (p90) REVERT: B 290 THR cc_start: 0.9416 (p) cc_final: 0.9193 (t) REVERT: B 308 GLU cc_start: 0.9338 (mm-30) cc_final: 0.8650 (tt0) REVERT: B 405 GLU cc_start: 0.9600 (tt0) cc_final: 0.9181 (pt0) REVERT: B 448 TYR cc_start: 0.7891 (t80) cc_final: 0.7284 (t80) REVERT: B 479 MET cc_start: 0.5371 (tpt) cc_final: 0.4861 (ttp) REVERT: B 488 MET cc_start: 0.8552 (mtp) cc_final: 0.8296 (ptp) REVERT: B 508 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6070 (tp) REVERT: B 555 MET cc_start: 0.9409 (tpp) cc_final: 0.9032 (mmm) REVERT: B 574 MET cc_start: 0.8273 (mmt) cc_final: 0.7723 (mmm) REVERT: B 672 MET cc_start: 0.9104 (tpp) cc_final: 0.8774 (tpt) REVERT: B 704 GLU cc_start: 0.9250 (tp30) cc_final: 0.8936 (tp30) REVERT: B 721 CYS cc_start: 0.7989 (p) cc_final: 0.7738 (p) REVERT: C 174 LYS cc_start: 0.9565 (tttp) cc_final: 0.8969 (ttpt) REVERT: C 257 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8720 (mt-10) REVERT: C 261 PHE cc_start: 0.9186 (p90) cc_final: 0.8788 (p90) REVERT: C 290 THR cc_start: 0.9397 (p) cc_final: 0.9167 (t) REVERT: C 308 GLU cc_start: 0.9367 (mm-30) cc_final: 0.8675 (tt0) REVERT: C 447 PHE cc_start: 0.9187 (t80) cc_final: 0.8491 (t80) REVERT: C 448 TYR cc_start: 0.8270 (t80) cc_final: 0.7570 (t80) REVERT: C 479 MET cc_start: 0.5669 (tpt) cc_final: 0.5097 (tmm) REVERT: C 488 MET cc_start: 0.8542 (mtp) cc_final: 0.8275 (ptp) REVERT: C 508 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6026 (tp) REVERT: C 532 LEU cc_start: 0.9333 (mt) cc_final: 0.8956 (tp) REVERT: C 555 MET cc_start: 0.9014 (mmm) cc_final: 0.8354 (mmm) REVERT: C 562 MET cc_start: 0.9309 (tpt) cc_final: 0.8984 (tpp) REVERT: C 578 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8949 (ppp) REVERT: C 672 MET cc_start: 0.9216 (tpp) cc_final: 0.9013 (tmm) REVERT: C 674 ILE cc_start: 0.9750 (mm) cc_final: 0.9484 (mm) REVERT: C 702 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8588 (mt-10) REVERT: C 704 GLU cc_start: 0.9184 (tp30) cc_final: 0.8794 (tp30) REVERT: D 139 LEU cc_start: 0.9818 (mt) cc_final: 0.9593 (pp) REVERT: D 174 LYS cc_start: 0.9566 (tttp) cc_final: 0.8791 (ttpt) REVERT: D 178 ASN cc_start: 0.9482 (m110) cc_final: 0.8753 (p0) REVERT: D 257 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8724 (mt-10) REVERT: D 261 PHE cc_start: 0.9188 (p90) cc_final: 0.8793 (p90) REVERT: D 290 THR cc_start: 0.9372 (p) cc_final: 0.9139 (t) REVERT: D 308 GLU cc_start: 0.9351 (mm-30) cc_final: 0.8658 (tt0) REVERT: D 447 PHE cc_start: 0.9057 (t80) cc_final: 0.8489 (t80) REVERT: D 448 TYR cc_start: 0.8533 (t80) cc_final: 0.7959 (t80) REVERT: D 479 MET cc_start: 0.5100 (tpt) cc_final: 0.4800 (ttp) REVERT: D 488 MET cc_start: 0.8547 (mtp) cc_final: 0.8298 (ptp) REVERT: D 508 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.5904 (tp) REVERT: D 532 LEU cc_start: 0.9347 (mt) cc_final: 0.9002 (tp) REVERT: D 555 MET cc_start: 0.9112 (mmm) cc_final: 0.8673 (mmm) REVERT: D 559 TRP cc_start: 0.9239 (m100) cc_final: 0.8370 (m100) REVERT: D 562 MET cc_start: 0.9328 (tpt) cc_final: 0.9084 (tpt) REVERT: D 574 MET cc_start: 0.8629 (mmt) cc_final: 0.7887 (mmt) REVERT: D 597 PHE cc_start: 0.8146 (t80) cc_final: 0.7896 (t80) REVERT: D 672 MET cc_start: 0.9000 (tpt) cc_final: 0.8659 (tmm) REVERT: D 677 MET cc_start: 0.8715 (mmm) cc_final: 0.8461 (mmm) outliers start: 81 outliers final: 66 residues processed: 486 average time/residue: 0.2560 time to fit residues: 206.6043 Evaluate side-chains 484 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 410 time to evaluate : 2.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 413 ILE Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 201 ASP Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 450 PHE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 636 THR Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 575 TYR Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 720 LEU Chi-restraints excluded: chain D residue 730 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 213 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 205 optimal weight: 9.9990 chunk 219 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 172 optimal weight: 4.9990 chunk 67 optimal weight: 0.4980 chunk 198 optimal weight: 2.9990 chunk 207 optimal weight: 0.4980 chunk 218 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20424 Z= 0.158 Angle : 0.730 12.792 27620 Z= 0.339 Chirality : 0.043 0.370 3152 Planarity : 0.003 0.024 3420 Dihedral : 5.309 39.023 2708 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.66 % Allowed : 24.77 % Favored : 71.57 % 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: 0.34 (0.17), residues: 2408 helix: 1.37 (0.13), residues: 1496 sheet: -0.32 (0.73), residues: 40 loop : -1.84 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 559 HIS 0.004 0.001 HIS D 426 PHE 0.020 0.001 PHE D 715 TYR 0.029 0.001 TYR C 575 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 435 time to evaluate : 2.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9736 (mt) cc_final: 0.9430 (pp) REVERT: A 177 LEU cc_start: 0.9777 (OUTLIER) cc_final: 0.9485 (mt) REVERT: A 178 ASN cc_start: 0.9556 (m110) cc_final: 0.8933 (p0) REVERT: A 261 PHE cc_start: 0.9258 (p90) cc_final: 0.8717 (p90) REVERT: A 263 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7300 (pt0) REVERT: A 284 ASN cc_start: 0.9103 (t0) cc_final: 0.8859 (t0) REVERT: A 290 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9151 (t) REVERT: A 306 VAL cc_start: 0.9682 (t) cc_final: 0.9451 (p) REVERT: A 308 GLU cc_start: 0.9357 (mm-30) cc_final: 0.8633 (tt0) REVERT: A 405 GLU cc_start: 0.9600 (tt0) cc_final: 0.8842 (tp30) REVERT: A 448 TYR cc_start: 0.7720 (t80) cc_final: 0.7135 (t80) REVERT: A 479 MET cc_start: 0.5202 (tpt) cc_final: 0.4513 (tmm) REVERT: A 508 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6092 (tp) REVERT: B 174 LYS cc_start: 0.9525 (tttp) cc_final: 0.8838 (ttpt) REVERT: B 178 ASN cc_start: 0.9411 (m110) cc_final: 0.8810 (p0) REVERT: B 257 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8724 (mt-10) REVERT: B 261 PHE cc_start: 0.9000 (p90) cc_final: 0.8609 (p90) REVERT: B 290 THR cc_start: 0.9406 (p) cc_final: 0.9186 (t) REVERT: B 306 VAL cc_start: 0.9721 (t) cc_final: 0.9514 (p) REVERT: B 308 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8602 (tt0) REVERT: B 322 ASP cc_start: 0.9508 (t70) cc_final: 0.9299 (t70) REVERT: B 405 GLU cc_start: 0.9598 (tt0) cc_final: 0.9178 (pt0) REVERT: B 448 TYR cc_start: 0.7915 (t80) cc_final: 0.7294 (t80) REVERT: B 479 MET cc_start: 0.5388 (tpt) cc_final: 0.4886 (ttp) REVERT: B 488 MET cc_start: 0.8545 (mtp) cc_final: 0.8283 (ptp) REVERT: B 508 LEU cc_start: 0.6585 (OUTLIER) cc_final: 0.5969 (tp) REVERT: B 672 MET cc_start: 0.9082 (tpp) cc_final: 0.8843 (tmm) REVERT: B 704 GLU cc_start: 0.9204 (tp30) cc_final: 0.8867 (tp30) REVERT: C 174 LYS cc_start: 0.9578 (tttp) cc_final: 0.8964 (ttpt) REVERT: C 257 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8723 (mt-10) REVERT: C 261 PHE cc_start: 0.9126 (p90) cc_final: 0.8740 (p90) REVERT: C 290 THR cc_start: 0.9390 (p) cc_final: 0.9176 (t) REVERT: C 308 GLU cc_start: 0.9369 (mm-30) cc_final: 0.8553 (tt0) REVERT: C 405 GLU cc_start: 0.9586 (tt0) cc_final: 0.9177 (pt0) REVERT: C 447 PHE cc_start: 0.9193 (t80) cc_final: 0.8514 (t80) REVERT: C 448 TYR cc_start: 0.8350 (t80) cc_final: 0.7598 (t80) REVERT: C 479 MET cc_start: 0.5658 (tpt) cc_final: 0.5069 (tmm) REVERT: C 488 MET cc_start: 0.8530 (mtp) cc_final: 0.8266 (ptp) REVERT: C 508 LEU cc_start: 0.6584 (OUTLIER) cc_final: 0.5975 (tp) REVERT: C 532 LEU cc_start: 0.9302 (mt) cc_final: 0.8987 (tp) REVERT: C 555 MET cc_start: 0.9028 (mmm) cc_final: 0.8695 (mmm) REVERT: C 562 MET cc_start: 0.9350 (tpt) cc_final: 0.8993 (tpp) REVERT: C 578 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8894 (ppp) REVERT: C 601 PHE cc_start: 0.9091 (m-80) cc_final: 0.8558 (m-80) REVERT: C 672 MET cc_start: 0.9210 (tpp) cc_final: 0.8979 (tmm) REVERT: C 676 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9308 (mm) REVERT: C 702 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8608 (mt-10) REVERT: C 704 GLU cc_start: 0.9186 (tp30) cc_final: 0.8805 (tp30) REVERT: D 139 LEU cc_start: 0.9809 (mt) cc_final: 0.9591 (pp) REVERT: D 174 LYS cc_start: 0.9567 (tttp) cc_final: 0.8808 (ttpt) REVERT: D 178 ASN cc_start: 0.9490 (m110) cc_final: 0.8775 (p0) REVERT: D 257 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8739 (mt-10) REVERT: D 261 PHE cc_start: 0.9099 (p90) cc_final: 0.8706 (p90) REVERT: D 290 THR cc_start: 0.9370 (p) cc_final: 0.9137 (t) REVERT: D 308 GLU cc_start: 0.9355 (mm-30) cc_final: 0.8624 (tt0) REVERT: D 405 GLU cc_start: 0.9583 (tt0) cc_final: 0.9167 (pt0) REVERT: D 447 PHE cc_start: 0.9040 (t80) cc_final: 0.8492 (t80) REVERT: D 448 TYR cc_start: 0.8585 (t80) cc_final: 0.7972 (t80) REVERT: D 479 MET cc_start: 0.5061 (tpt) cc_final: 0.4762 (ttp) REVERT: D 488 MET cc_start: 0.8538 (mtp) cc_final: 0.8296 (ptp) REVERT: D 508 LEU cc_start: 0.6389 (OUTLIER) cc_final: 0.5769 (tp) REVERT: D 532 LEU cc_start: 0.9346 (mt) cc_final: 0.9008 (tp) REVERT: D 555 MET cc_start: 0.9167 (mmm) cc_final: 0.8706 (mmm) REVERT: D 559 TRP cc_start: 0.9219 (m100) cc_final: 0.8294 (m100) REVERT: D 562 MET cc_start: 0.9369 (tpt) cc_final: 0.9115 (tpt) REVERT: D 574 MET cc_start: 0.8476 (mmt) cc_final: 0.7631 (mmt) REVERT: D 597 PHE cc_start: 0.8459 (t80) cc_final: 0.8238 (t80) REVERT: D 601 PHE cc_start: 0.9351 (m-80) cc_final: 0.8908 (m-80) REVERT: D 672 MET cc_start: 0.9006 (tpt) cc_final: 0.8705 (tmm) outliers start: 79 outliers final: 62 residues processed: 483 average time/residue: 0.2552 time to fit residues: 204.7299 Evaluate side-chains 475 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 404 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 263 GLU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 488 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 585 HIS Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 413 ILE Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 575 TYR Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 665 THR Chi-restraints excluded: chain C residue 676 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 325 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 676 LEU Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 143 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 109 optimal weight: 20.0000 chunk 161 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 193 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 chunk 118 optimal weight: 7.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 401 ASN D 339 ASN D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20424 Z= 0.308 Angle : 0.791 12.951 27620 Z= 0.387 Chirality : 0.044 0.298 3152 Planarity : 0.004 0.027 3420 Dihedral : 5.722 37.870 2708 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.66 % Allowed : 25.46 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 0.00 (0.17), residues: 2408 helix: 1.03 (0.13), residues: 1524 sheet: -0.72 (0.78), residues: 40 loop : -1.91 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 559 HIS 0.004 0.001 HIS C 244 PHE 0.037 0.002 PHE A 715 TYR 0.030 0.002 TYR C 575 ARG 0.006 0.001 ARG A 716 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4816 Ramachandran restraints generated. 2408 Oldfield, 0 Emsley, 2408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 393 time to evaluate : 2.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 LEU cc_start: 0.9777 (mt) cc_final: 0.9459 (pp) REVERT: A 177 LEU cc_start: 0.9745 (OUTLIER) cc_final: 0.9391 (mt) REVERT: A 261 PHE cc_start: 0.9422 (p90) cc_final: 0.8873 (p90) REVERT: A 290 THR cc_start: 0.9436 (OUTLIER) cc_final: 0.9229 (t) REVERT: A 405 GLU cc_start: 0.9622 (tt0) cc_final: 0.8897 (tp30) REVERT: A 448 TYR cc_start: 0.7812 (t80) cc_final: 0.7183 (t80) REVERT: A 479 MET cc_start: 0.5281 (tpt) cc_final: 0.4561 (tmm) REVERT: A 578 MET cc_start: 0.9277 (OUTLIER) cc_final: 0.8813 (ppp) REVERT: B 178 ASN cc_start: 0.9487 (m110) cc_final: 0.8944 (p0) REVERT: B 261 PHE cc_start: 0.9235 (p90) cc_final: 0.8847 (p90) REVERT: B 290 THR cc_start: 0.9478 (p) cc_final: 0.9258 (t) REVERT: B 405 GLU cc_start: 0.9615 (tt0) cc_final: 0.9374 (tt0) REVERT: B 448 TYR cc_start: 0.7999 (t80) cc_final: 0.7332 (t80) REVERT: B 479 MET cc_start: 0.5447 (tpt) cc_final: 0.4921 (ttp) REVERT: B 488 MET cc_start: 0.8543 (mtp) cc_final: 0.8305 (ptp) REVERT: B 555 MET cc_start: 0.9240 (mmm) cc_final: 0.8544 (mmm) REVERT: B 672 MET cc_start: 0.9138 (tpp) cc_final: 0.8920 (tmm) REVERT: C 257 GLU cc_start: 0.9075 (mm-30) cc_final: 0.8717 (mt-10) REVERT: C 261 PHE cc_start: 0.9304 (p90) cc_final: 0.8888 (p90) REVERT: C 290 THR cc_start: 0.9471 (p) cc_final: 0.9249 (t) REVERT: C 405 GLU cc_start: 0.9627 (tt0) cc_final: 0.9368 (tt0) REVERT: C 447 PHE cc_start: 0.9174 (t80) cc_final: 0.8500 (t80) REVERT: C 448 TYR cc_start: 0.8349 (t80) cc_final: 0.7737 (t80) REVERT: C 479 MET cc_start: 0.5658 (tpt) cc_final: 0.5024 (tmm) REVERT: C 488 MET cc_start: 0.8508 (mtp) cc_final: 0.8253 (ptp) REVERT: C 508 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6250 (tp) REVERT: C 532 LEU cc_start: 0.9307 (mt) cc_final: 0.8979 (tp) REVERT: C 562 MET cc_start: 0.9286 (tpt) cc_final: 0.9007 (tpt) REVERT: C 578 MET cc_start: 0.9300 (OUTLIER) cc_final: 0.8934 (ppp) REVERT: C 601 PHE cc_start: 0.9252 (m-80) cc_final: 0.8616 (m-80) REVERT: C 702 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8702 (mt-10) REVERT: C 704 GLU cc_start: 0.9230 (tp30) cc_final: 0.8883 (tm-30) REVERT: D 178 ASN cc_start: 0.9535 (m110) cc_final: 0.8817 (p0) REVERT: D 257 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8748 (mt-10) REVERT: D 261 PHE cc_start: 0.9294 (p90) cc_final: 0.8822 (p90) REVERT: D 290 THR cc_start: 0.9448 (p) cc_final: 0.9223 (t) REVERT: D 405 GLU cc_start: 0.9618 (tt0) cc_final: 0.8904 (tp30) REVERT: D 448 TYR cc_start: 0.8547 (t80) cc_final: 0.7807 (t80) REVERT: D 479 MET cc_start: 0.5323 (tpt) cc_final: 0.4869 (ttp) REVERT: D 488 MET cc_start: 0.8578 (mtp) cc_final: 0.8299 (ptm) REVERT: D 532 LEU cc_start: 0.9374 (mt) cc_final: 0.9029 (tp) REVERT: D 555 MET cc_start: 0.9278 (mmm) cc_final: 0.8879 (mmm) REVERT: D 559 TRP cc_start: 0.9270 (m100) cc_final: 0.8340 (m100) REVERT: D 562 MET cc_start: 0.9322 (tpt) cc_final: 0.9010 (tpt) REVERT: D 597 PHE cc_start: 0.8522 (t80) cc_final: 0.8008 (t80) REVERT: D 601 PHE cc_start: 0.9372 (m-80) cc_final: 0.8752 (m-80) REVERT: D 672 MET cc_start: 0.9044 (tpt) cc_final: 0.8749 (tmm) outliers start: 79 outliers final: 54 residues processed: 442 average time/residue: 0.2485 time to fit residues: 184.2580 Evaluate side-chains 432 residues out of total 2164 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 373 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 578 MET Chi-restraints excluded: chain A residue 597 PHE Chi-restraints excluded: chain A residue 636 THR Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 720 LEU Chi-restraints excluded: chain B residue 173 MET Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain B residue 508 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 575 TYR Chi-restraints excluded: chain B residue 636 THR Chi-restraints excluded: chain B residue 681 VAL Chi-restraints excluded: chain B residue 694 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 173 MET Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 271 CYS Chi-restraints excluded: chain C residue 303 LEU Chi-restraints excluded: chain C residue 370 LEU Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 578 MET Chi-restraints excluded: chain C residue 580 GLN Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain D residue 173 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 303 LEU Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 423 GLU Chi-restraints excluded: chain D residue 508 LEU Chi-restraints excluded: chain D residue 579 ILE Chi-restraints excluded: chain D residue 580 GLN Chi-restraints excluded: chain D residue 636 THR Chi-restraints excluded: chain D residue 665 THR Chi-restraints excluded: chain D residue 681 VAL Chi-restraints excluded: chain D residue 694 LEU Chi-restraints excluded: chain D residue 720 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 153 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 193 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 199 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.085803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061709 restraints weight = 76818.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063921 restraints weight = 38136.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.065355 restraints weight = 23871.207| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20424 Z= 0.166 Angle : 0.779 12.875 27620 Z= 0.358 Chirality : 0.045 0.344 3152 Planarity : 0.003 0.024 3420 Dihedral : 5.483 39.996 2708 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 2.55 % Allowed : 26.94 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.15 (0.17), residues: 2408 helix: 1.17 (0.13), residues: 1500 sheet: -0.36 (0.77), residues: 40 loop : -1.84 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 559 HIS 0.004 0.001 HIS C 426 PHE 0.032 0.001 PHE A 715 TYR 0.035 0.002 TYR C 575 ARG 0.002 0.000 ARG A 714 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4472.09 seconds wall clock time: 82 minutes 30.27 seconds (4950.27 seconds total)