Starting phenix.real_space_refine on Fri Mar 22 13:19:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wbb_32396/03_2024/7wbb_32396_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 33 5.49 5 S 131 5.16 5 C 21146 2.51 5 N 5771 2.21 5 O 6553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 251": "OD1" <-> "OD2" Residue "A GLU 262": "OE1" <-> "OE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B TYR 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B GLU 410": "OE1" <-> "OE2" Residue "B ASP 456": "OD1" <-> "OD2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B PHE 754": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "D GLU 62": "OE1" <-> "OE2" Residue "D PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 324": "OE1" <-> "OE2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 537": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 463": "OE1" <-> "OE2" Residue "E GLU 643": "OE1" <-> "OE2" Residue "E GLU 664": "OE1" <-> "OE2" Residue "E ARG 674": "NH1" <-> "NH2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "C PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 723": "OE1" <-> "OE2" Residue "C PHE 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 770": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33634 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "B" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "D" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "E" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "F" Number of atoms: 5348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 699, 5348 Classifications: {'peptide': 699} Link IDs: {'PTRANS': 39, 'TRANS': 659} Chain breaks: 4 Chain: "H" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'TRANS': 21} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'UNK:plan-1': 22} Unresolved non-hydrogen planarities: 22 Chain: "C" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5567 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 40, 'TRANS': 685} Chain breaks: 1 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.57, per 1000 atoms: 0.49 Number of scatterers: 33634 At special positions: 0 Unit cell: (153.265, 160.664, 125.783, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 33 15.00 O 6553 8.00 N 5771 7.00 C 21146 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: 13.15 Conformation dependent library (CDL) restraints added in 6.4 seconds 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8058 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 188 helices and 31 sheets defined 39.9% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.56 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 102 through 104 No H-bonds generated for 'chain 'A' and resid 102 through 104' Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.738A pdb=" N LEU A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 250 through 265 removed outlier: 3.593A pdb=" N LYS A 258 " --> pdb=" O GLU A 255 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE A 263 " --> pdb=" O ALA A 260 " (cutoff:3.500A) Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 322 through 337 removed outlier: 4.435A pdb=" N LEU A 327 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 350 No H-bonds generated for 'chain 'A' and resid 347 through 350' Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 397 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 419 through 430 Processing helix chain 'A' and resid 439 through 447 Processing helix chain 'A' and resid 454 through 476 Processing helix chain 'A' and resid 481 through 483 No H-bonds generated for 'chain 'A' and resid 481 through 483' Processing helix chain 'A' and resid 488 through 498 Processing helix chain 'A' and resid 522 through 537 removed outlier: 3.753A pdb=" N LEU A 534 " --> pdb=" O GLU A 530 " (cutoff:3.500A) Proline residue: A 535 - end of helix Processing helix chain 'A' and resid 540 through 545 Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 584 through 586 No H-bonds generated for 'chain 'A' and resid 584 through 586' Processing helix chain 'A' and resid 593 through 603 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 632 through 644 Processing helix chain 'A' and resid 662 through 664 No H-bonds generated for 'chain 'A' and resid 662 through 664' Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 702 through 705 No H-bonds generated for 'chain 'A' and resid 702 through 705' Processing helix chain 'A' and resid 711 through 715 Processing helix chain 'A' and resid 721 through 739 removed outlier: 3.667A pdb=" N ASP A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 removed outlier: 4.102A pdb=" N LYS A 755 " --> pdb=" O GLU A 751 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY A 756 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 776 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 100 through 106 removed outlier: 4.588A pdb=" N VAL B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLY B 106 " --> pdb=" O ILE B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 151 No H-bonds generated for 'chain 'B' and resid 148 through 151' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 251 through 266 removed outlier: 3.885A pdb=" N SER B 256 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 268 through 274 removed outlier: 4.638A pdb=" N PHE B 274 " --> pdb=" O LEU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 322 through 337 removed outlier: 4.392A pdb=" N LEU B 327 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 350 No H-bonds generated for 'chain 'B' and resid 347 through 350' Processing helix chain 'B' and resid 362 through 376 Processing helix chain 'B' and resid 392 through 394 No H-bonds generated for 'chain 'B' and resid 392 through 394' Processing helix chain 'B' and resid 402 through 405 No H-bonds generated for 'chain 'B' and resid 402 through 405' Processing helix chain 'B' and resid 416 through 429 Processing helix chain 'B' and resid 432 through 434 No H-bonds generated for 'chain 'B' and resid 432 through 434' Processing helix chain 'B' and resid 439 through 448 Processing helix chain 'B' and resid 454 through 475 Processing helix chain 'B' and resid 481 through 483 No H-bonds generated for 'chain 'B' and resid 481 through 483' Processing helix chain 'B' and resid 488 through 497 Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 522 through 537 removed outlier: 4.076A pdb=" N LEU B 534 " --> pdb=" O GLU B 530 " (cutoff:3.500A) Proline residue: B 535 - end of helix Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 563 through 572 Processing helix chain 'B' and resid 584 through 586 No H-bonds generated for 'chain 'B' and resid 584 through 586' Processing helix chain 'B' and resid 593 through 607 Processing helix chain 'B' and resid 618 through 620 No H-bonds generated for 'chain 'B' and resid 618 through 620' Processing helix chain 'B' and resid 631 through 644 Processing helix chain 'B' and resid 662 through 664 No H-bonds generated for 'chain 'B' and resid 662 through 664' Processing helix chain 'B' and resid 667 through 670 No H-bonds generated for 'chain 'B' and resid 667 through 670' Processing helix chain 'B' and resid 686 through 697 Processing helix chain 'B' and resid 702 through 705 No H-bonds generated for 'chain 'B' and resid 702 through 705' Processing helix chain 'B' and resid 711 through 715 Processing helix chain 'B' and resid 721 through 739 removed outlier: 3.605A pdb=" N VAL B 725 " --> pdb=" O GLY B 721 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 756 Processing helix chain 'B' and resid 763 through 776 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'D' and resid 100 through 104 Processing helix chain 'D' and resid 146 through 154 removed outlier: 3.755A pdb=" N LEU D 151 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 266 Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 292 through 302 Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 320 through 336 removed outlier: 4.842A pdb=" N GLU D 324 " --> pdb=" O LEU D 320 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA D 325 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 327 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 350 No H-bonds generated for 'chain 'D' and resid 347 through 350' Processing helix chain 'D' and resid 361 through 374 Processing helix chain 'D' and resid 416 through 434 removed outlier: 3.691A pdb=" N MET D 430 " --> pdb=" O GLN D 426 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER D 432 " --> pdb=" O SER D 428 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP D 433 " --> pdb=" O ARG D 429 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG D 434 " --> pdb=" O MET D 430 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 448 Processing helix chain 'D' and resid 454 through 475 Processing helix chain 'D' and resid 481 through 483 No H-bonds generated for 'chain 'D' and resid 481 through 483' Processing helix chain 'D' and resid 489 through 497 Processing helix chain 'D' and resid 502 through 505 removed outlier: 3.840A pdb=" N GLU D 505 " --> pdb=" O ALA D 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 502 through 505' Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 522 through 537 removed outlier: 4.187A pdb=" N LEU D 534 " --> pdb=" O GLU D 530 " (cutoff:3.500A) Proline residue: D 535 - end of helix Processing helix chain 'D' and resid 539 through 545 Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 583 through 586 No H-bonds generated for 'chain 'D' and resid 583 through 586' Processing helix chain 'D' and resid 594 through 607 Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'D' and resid 633 through 645 Processing helix chain 'D' and resid 667 through 670 No H-bonds generated for 'chain 'D' and resid 667 through 670' Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 702 through 705 No H-bonds generated for 'chain 'D' and resid 702 through 705' Processing helix chain 'D' and resid 711 through 715 Processing helix chain 'D' and resid 721 through 739 Processing helix chain 'D' and resid 747 through 756 Processing helix chain 'D' and resid 763 through 774 Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 102 through 105 No H-bonds generated for 'chain 'E' and resid 102 through 105' Processing helix chain 'E' and resid 146 through 154 removed outlier: 3.767A pdb=" N LYS E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 251 through 266 removed outlier: 3.751A pdb=" N SER E 256 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 268 through 274 Processing helix chain 'E' and resid 292 through 301 Processing helix chain 'E' and resid 312 through 314 No H-bonds generated for 'chain 'E' and resid 312 through 314' Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 347 through 350 No H-bonds generated for 'chain 'E' and resid 347 through 350' Processing helix chain 'E' and resid 362 through 374 Processing helix chain 'E' and resid 416 through 429 Processing helix chain 'E' and resid 439 through 448 Processing helix chain 'E' and resid 454 through 473 removed outlier: 3.775A pdb=" N THR E 458 " --> pdb=" O GLY E 454 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU E 473 " --> pdb=" O ILE E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 494 Processing helix chain 'E' and resid 522 through 537 Proline residue: E 535 - end of helix Processing helix chain 'E' and resid 539 through 545 Processing helix chain 'E' and resid 565 through 574 removed outlier: 3.791A pdb=" N LEU E 570 " --> pdb=" O THR E 566 " (cutoff:3.500A) Processing helix chain 'E' and resid 583 through 586 No H-bonds generated for 'chain 'E' and resid 583 through 586' Processing helix chain 'E' and resid 593 through 607 Processing helix chain 'E' and resid 618 through 620 No H-bonds generated for 'chain 'E' and resid 618 through 620' Processing helix chain 'E' and resid 631 through 644 Processing helix chain 'E' and resid 662 through 664 No H-bonds generated for 'chain 'E' and resid 662 through 664' Processing helix chain 'E' and resid 667 through 670 No H-bonds generated for 'chain 'E' and resid 667 through 670' Processing helix chain 'E' and resid 686 through 699 removed outlier: 4.235A pdb=" N LYS E 699 " --> pdb=" O LYS E 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 702 through 705 No H-bonds generated for 'chain 'E' and resid 702 through 705' Processing helix chain 'E' and resid 710 through 717 Processing helix chain 'E' and resid 721 through 738 removed outlier: 3.712A pdb=" N VAL E 725 " --> pdb=" O GLY E 721 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 756 Processing helix chain 'E' and resid 763 through 774 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 100 through 105 removed outlier: 3.535A pdb=" N VAL F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 153 removed outlier: 3.549A pdb=" N LEU F 152 " --> pdb=" O ILE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 266 Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 268 through 274 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 323 through 336 Processing helix chain 'F' and resid 347 through 350 No H-bonds generated for 'chain 'F' and resid 347 through 350' Processing helix chain 'F' and resid 361 through 376 Processing helix chain 'F' and resid 416 through 429 Processing helix chain 'F' and resid 439 through 448 Processing helix chain 'F' and resid 457 through 476 removed outlier: 3.666A pdb=" N CYS F 461 " --> pdb=" O LEU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 481 through 483 No H-bonds generated for 'chain 'F' and resid 481 through 483' Processing helix chain 'F' and resid 489 through 498 Processing helix chain 'F' and resid 522 through 537 removed outlier: 4.001A pdb=" N THR F 526 " --> pdb=" O GLU F 522 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS F 527 " --> pdb=" O GLU F 523 " (cutoff:3.500A) Proline residue: F 535 - end of helix Processing helix chain 'F' and resid 540 through 545 Processing helix chain 'F' and resid 563 through 574 Processing helix chain 'F' and resid 600 through 608 removed outlier: 3.707A pdb=" N ALA F 605 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG F 606 " --> pdb=" O PHE F 602 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 622 No H-bonds generated for 'chain 'F' and resid 619 through 622' Processing helix chain 'F' and resid 631 through 650 removed outlier: 4.447A pdb=" N ASN F 642 " --> pdb=" O THR F 638 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLU F 643 " --> pdb=" O SER F 639 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU F 650 " --> pdb=" O GLY F 646 " (cutoff:3.500A) Processing helix chain 'F' and resid 662 through 664 No H-bonds generated for 'chain 'F' and resid 662 through 664' Processing helix chain 'F' and resid 667 through 670 Processing helix chain 'F' and resid 686 through 699 removed outlier: 4.251A pdb=" N LYS F 699 " --> pdb=" O LYS F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 711 through 715 Processing helix chain 'F' and resid 723 through 738 Processing helix chain 'F' and resid 747 through 756 Processing helix chain 'F' and resid 763 through 776 Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 100 through 105 Processing helix chain 'C' and resid 146 through 150 Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 251 through 265 Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 313 through 315 No H-bonds generated for 'chain 'C' and resid 313 through 315' Processing helix chain 'C' and resid 322 through 336 removed outlier: 4.199A pdb=" N LEU C 327 " --> pdb=" O THR C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 350 No H-bonds generated for 'chain 'C' and resid 347 through 350' Processing helix chain 'C' and resid 362 through 374 Processing helix chain 'C' and resid 392 through 394 No H-bonds generated for 'chain 'C' and resid 392 through 394' Processing helix chain 'C' and resid 402 through 405 No H-bonds generated for 'chain 'C' and resid 402 through 405' Processing helix chain 'C' and resid 416 through 429 Processing helix chain 'C' and resid 439 through 448 Processing helix chain 'C' and resid 454 through 475 Processing helix chain 'C' and resid 481 through 483 No H-bonds generated for 'chain 'C' and resid 481 through 483' Processing helix chain 'C' and resid 488 through 497 Processing helix chain 'C' and resid 515 through 517 No H-bonds generated for 'chain 'C' and resid 515 through 517' Processing helix chain 'C' and resid 522 through 537 removed outlier: 4.037A pdb=" N LEU C 534 " --> pdb=" O GLU C 530 " (cutoff:3.500A) Proline residue: C 535 - end of helix Processing helix chain 'C' and resid 539 through 545 Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 593 through 608 Processing helix chain 'C' and resid 618 through 621 No H-bonds generated for 'chain 'C' and resid 618 through 621' Processing helix chain 'C' and resid 631 through 645 Processing helix chain 'C' and resid 686 through 697 Processing helix chain 'C' and resid 702 through 705 No H-bonds generated for 'chain 'C' and resid 702 through 705' Processing helix chain 'C' and resid 711 through 715 Processing helix chain 'C' and resid 721 through 739 removed outlier: 3.693A pdb=" N VAL C 725 " --> pdb=" O GLY C 721 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 756 Processing helix chain 'C' and resid 763 through 776 Processing sheet with id= A, first strand: chain 'A' and resid 78 through 82 removed outlier: 3.536A pdb=" N VAL A 71 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR A 70 " --> pdb=" O LYS A 117 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS A 117 " --> pdb=" O THR A 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY A 72 " --> pdb=" O GLU A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 129 through 131 Processing sheet with id= C, first strand: chain 'A' and resid 341 through 345 removed outlier: 7.059A pdb=" N VAL A 384 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE A 344 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE A 386 " --> pdb=" O ILE A 344 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 552 through 556 removed outlier: 7.062A pdb=" N ILE A 655 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N LEU A 555 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ALA A 657 " --> pdb=" O LEU A 555 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 579 through 581 removed outlier: 3.840A pdb=" N PHE A 614 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL A 581 " --> pdb=" O PHE A 614 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 70 through 72 removed outlier: 4.166A pdb=" N THR B 70 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS B 117 " --> pdb=" O THR B 70 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY B 72 " --> pdb=" O GLU B 115 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 129 through 132 removed outlier: 3.619A pdb=" N VAL B 131 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 407 through 411 removed outlier: 3.981A pdb=" N GLN B 407 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS B 285 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ILE B 282 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL B 385 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 284 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ALA B 387 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLY B 286 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR B 389 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 677 through 679 removed outlier: 3.587A pdb=" N TYR B 556 " --> pdb=" O ILE B 679 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE B 655 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU B 555 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 657 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'D' and resid 79 through 82 removed outlier: 3.512A pdb=" N GLY D 72 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 223 through 226 removed outlier: 3.926A pdb=" N ASP D 182 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N GLY D 132 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE D 180 " --> pdb=" O GLY D 132 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 407 through 411 removed outlier: 3.749A pdb=" N GLY D 286 " --> pdb=" O THR D 389 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 677 through 679 removed outlier: 3.743A pdb=" N ARG D 677 " --> pdb=" O GLY D 552 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ILE D 655 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 8.434A pdb=" N LEU D 555 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA D 657 " --> pdb=" O LEU D 555 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 35 through 38 Processing sheet with id= Q, first strand: chain 'E' and resid 51 through 53 Processing sheet with id= R, first strand: chain 'E' and resid 79 through 82 Processing sheet with id= S, first strand: chain 'E' and resid 407 through 411 removed outlier: 3.792A pdb=" N GLN E 407 " --> pdb=" O GLY E 281 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL E 385 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N LEU E 284 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ALA E 387 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N GLY E 286 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N THR E 389 " --> pdb=" O GLY E 286 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 552 through 556 removed outlier: 6.769A pdb=" N ILE E 655 " --> pdb=" O VAL E 553 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N LEU E 555 " --> pdb=" O ILE E 655 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ALA E 657 " --> pdb=" O LEU E 555 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA E 658 " --> pdb=" O PHE E 615 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU E 579 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 129 through 131 removed outlier: 3.853A pdb=" N ASP E 182 " --> pdb=" O THR E 130 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 35 through 37 removed outlier: 3.668A pdb=" N ARG F 37 " --> pdb=" O ILE F 96 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 50 through 52 removed outlier: 7.095A pdb=" N ILE F 82 " --> pdb=" O ALA F 51 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 70 through 72 removed outlier: 4.128A pdb=" N THR F 70 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS F 117 " --> pdb=" O THR F 70 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY F 72 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'F' and resid 130 through 133 removed outlier: 6.006A pdb=" N THR F 225 " --> pdb=" O VAL F 131 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER F 133 " --> pdb=" O THR F 225 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER F 227 " --> pdb=" O SER F 133 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'F' and resid 408 through 411 removed outlier: 7.492A pdb=" N VAL F 409 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU F 283 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N ILE F 411 " --> pdb=" O LEU F 283 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N HIS F 285 " --> pdb=" O ILE F 411 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N ILE F 282 " --> pdb=" O VAL F 383 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL F 385 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU F 284 " --> pdb=" O VAL F 385 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA F 387 " --> pdb=" O LEU F 284 " (cutoff:3.500A) removed outlier: 9.188A pdb=" N GLY F 286 " --> pdb=" O ALA F 387 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N SER F 340 " --> pdb=" O VAL F 384 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE F 386 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N HIS F 306 " --> pdb=" O ILE F 341 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE F 343 " --> pdb=" O HIS F 306 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU F 308 " --> pdb=" O PHE F 343 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'F' and resid 677 through 680 removed outlier: 3.751A pdb=" N LEU F 554 " --> pdb=" O ARG F 677 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR F 556 " --> pdb=" O ILE F 679 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ILE F 655 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N LEU F 555 " --> pdb=" O ILE F 655 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ALA F 657 " --> pdb=" O LEU F 555 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= AC, first strand: chain 'C' and resid 115 through 118 removed outlier: 3.518A pdb=" N LYS C 117 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 70 " --> pdb=" O LYS C 117 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'C' and resid 407 through 410 removed outlier: 3.951A pdb=" N GLN C 407 " --> pdb=" O GLY C 281 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ILE C 282 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N VAL C 385 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU C 284 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ALA C 387 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER C 340 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE C 386 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE C 342 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ALA C 388 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 344 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N HIS C 306 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE C 343 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 308 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASP C 345 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ILE C 310 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'C' and resid 677 through 679 removed outlier: 3.706A pdb=" N TYR C 556 " --> pdb=" O ILE C 679 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL C 553 " --> pdb=" O ILE C 655 " (cutoff:3.500A) 1045 hydrogen bonds defined for protein. 3078 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: 11.16 Time building geometry restraints manager: 14.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5748 1.31 - 1.43: 8077 1.43 - 1.56: 20129 1.56 - 1.69: 55 1.69 - 1.82: 220 Bond restraints: 34229 Sorted by residual: bond pdb=" C PRO A 264 " pdb=" O PRO A 264 " ideal model delta sigma weight residual 1.235 1.179 0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" N LYS B 563 " pdb=" CA LYS B 563 " ideal model delta sigma weight residual 1.459 1.498 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ILE A 261 " pdb=" CA ILE A 261 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N GLY A 248 " pdb=" CA GLY A 248 " ideal model delta sigma weight residual 1.444 1.475 -0.032 1.02e-02 9.61e+03 9.55e+00 bond pdb=" N SER B 562 " pdb=" CA SER B 562 " ideal model delta sigma weight residual 1.457 1.497 -0.039 1.29e-02 6.01e+03 9.32e+00 ... (remaining 34224 not shown) Histogram of bond angle deviations from ideal: 99.96 - 107.95: 1474 107.95 - 115.95: 21648 115.95 - 123.94: 22480 123.94 - 131.93: 773 131.93 - 139.92: 40 Bond angle restraints: 46415 Sorted by residual: angle pdb=" C LYS B 563 " pdb=" N THR B 564 " pdb=" CA THR B 564 " ideal model delta sigma weight residual 120.29 129.36 -9.07 1.42e+00 4.96e-01 4.08e+01 angle pdb=" C SER E 432 " pdb=" N ASP E 433 " pdb=" CA ASP E 433 " ideal model delta sigma weight residual 123.91 134.12 -10.21 1.66e+00 3.63e-01 3.78e+01 angle pdb=" C ILE A 261 " pdb=" N GLU A 262 " pdb=" CA GLU A 262 " ideal model delta sigma weight residual 120.29 128.54 -8.25 1.42e+00 4.96e-01 3.37e+01 angle pdb=" O ILE A 261 " pdb=" C ILE A 261 " pdb=" N GLU A 262 " ideal model delta sigma weight residual 121.83 127.22 -5.39 1.03e+00 9.43e-01 2.74e+01 angle pdb=" N LYS B 563 " pdb=" CA LYS B 563 " pdb=" C LYS B 563 " ideal model delta sigma weight residual 111.07 116.32 -5.25 1.07e+00 8.73e-01 2.41e+01 ... (remaining 46410 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 18833 17.86 - 35.71: 1875 35.71 - 53.57: 430 53.57 - 71.42: 51 71.42 - 89.28: 18 Dihedral angle restraints: 21207 sinusoidal: 8714 harmonic: 12493 Sorted by residual: dihedral pdb=" C LYS E 563 " pdb=" N LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual -122.60 -133.85 11.25 0 2.50e+00 1.60e-01 2.02e+01 dihedral pdb=" CA SER E 99 " pdb=" C SER E 99 " pdb=" N THR E 100 " pdb=" CA THR E 100 " ideal model delta harmonic sigma weight residual 180.00 158.69 21.31 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CA LYS E 563 " pdb=" CB LYS E 563 " ideal model delta harmonic sigma weight residual 122.80 132.13 -9.33 0 2.50e+00 1.60e-01 1.39e+01 ... (remaining 21204 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 4755 0.068 - 0.136: 588 0.136 - 0.205: 21 0.205 - 0.273: 4 0.273 - 0.341: 2 Chirality restraints: 5370 Sorted by residual: chirality pdb=" CA LYS E 563 " pdb=" N LYS E 563 " pdb=" C LYS E 563 " pdb=" CB LYS E 563 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA THR E 564 " pdb=" N THR E 564 " pdb=" C THR E 564 " pdb=" CB THR E 564 " both_signs ideal model delta sigma weight residual False 2.53 2.22 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CB ILE C 310 " pdb=" CA ILE C 310 " pdb=" CG1 ILE C 310 " pdb=" CG2 ILE C 310 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5367 not shown) Planarity restraints: 5976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 609 " 0.058 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 610 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 610 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 610 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " -0.013 2.00e-02 2.50e+03 2.84e-02 8.09e+00 pdb=" C ILE A 261 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE A 261 " -0.019 2.00e-02 2.50e+03 pdb=" N GLU A 262 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 432 " 0.013 2.00e-02 2.50e+03 2.69e-02 7.24e+00 pdb=" C SER E 432 " -0.047 2.00e-02 2.50e+03 pdb=" O SER E 432 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 433 " 0.015 2.00e-02 2.50e+03 ... (remaining 5973 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3200 2.75 - 3.28: 34400 3.28 - 3.82: 55624 3.82 - 4.36: 61298 4.36 - 4.90: 105397 Nonbonded interactions: 259919 Sorted by model distance: nonbonded pdb=" OD1 ASP C 456 " pdb=" OG SER C 501 " model vdw 2.206 2.440 nonbonded pdb=" O ASN E 660 " pdb=" OH TYR E 769 " model vdw 2.214 2.440 nonbonded pdb=" OG SER A 720 " pdb=" OE1 GLU A 723 " model vdw 2.229 2.440 nonbonded pdb=" O ASN E 577 " pdb=" OG SER E 611 " model vdw 2.233 2.440 nonbonded pdb=" O ALA E 334 " pdb=" OG SER E 340 " model vdw 2.239 2.440 ... (remaining 259914 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' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'B' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'C' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'D' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = (chain 'E' and (resid 29 through 504 or resid 513 through 585 or resid 599 throu \ gh 623 or resid 630 through 777 or resid 801)) selection = chain 'F' } 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.760 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 82.470 Find NCS groups from input model: 2.620 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 : 0.002 0.056 34229 Z= 0.153 Angle : 0.551 10.207 46415 Z= 0.302 Chirality : 0.043 0.341 5370 Planarity : 0.004 0.088 5976 Dihedral : 14.717 89.278 13149 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.05 % Favored : 94.60 % Rotamer: Outliers : 0.11 % Allowed : 0.49 % Favored : 99.40 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.13), residues: 4299 helix: 1.99 (0.13), residues: 1732 sheet: 0.58 (0.27), residues: 426 loop : -0.55 (0.14), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 515 HIS 0.007 0.000 HIS F 450 PHE 0.017 0.001 PHE B 274 TYR 0.012 0.000 TYR A 337 ARG 0.005 0.000 ARG F 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 327 time to evaluate : 3.936 Fit side-chains REVERT: B 374 MET cc_start: 0.8744 (tpp) cc_final: 0.8539 (tpp) REVERT: E 109 ILE cc_start: 0.8793 (mt) cc_final: 0.8303 (tt) REVERT: E 507 PHE cc_start: 0.3057 (t80) cc_final: 0.2852 (t80) REVERT: E 755 LYS cc_start: 0.6469 (ptmt) cc_final: 0.5691 (mmtm) outliers start: 4 outliers final: 1 residues processed: 330 average time/residue: 0.3760 time to fit residues: 215.8451 Evaluate side-chains 239 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 238 time to evaluate : 4.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 518 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 363 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 220 optimal weight: 4.9990 chunk 174 optimal weight: 0.0060 chunk 337 optimal weight: 50.0000 chunk 130 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 391 optimal weight: 10.0000 overall best weight: 3.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 ASN B 44 HIS D 407 GLN ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN F 149 GLN F 285 HIS F 306 HIS C 231 GLN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 34229 Z= 0.336 Angle : 0.636 9.050 46415 Z= 0.321 Chirality : 0.046 0.230 5370 Planarity : 0.005 0.055 5976 Dihedral : 8.969 86.365 5037 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 5.51 % Favored : 94.11 % Rotamer: Outliers : 1.37 % Allowed : 8.48 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.13), residues: 4299 helix: 1.52 (0.13), residues: 1720 sheet: 0.27 (0.25), residues: 467 loop : -0.67 (0.14), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 515 HIS 0.022 0.002 HIS A 266 PHE 0.024 0.002 PHE E 614 TYR 0.024 0.002 TYR B 337 ARG 0.018 0.001 ARG A 434 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 233 time to evaluate : 3.954 Fit side-chains revert: symmetry clash REVERT: A 765 MET cc_start: 0.7410 (ptt) cc_final: 0.7147 (ptp) REVERT: B 151 LEU cc_start: 0.7008 (pt) cc_final: 0.6785 (pt) REVERT: B 270 LEU cc_start: 0.8240 (mm) cc_final: 0.7992 (mp) REVERT: E 143 MET cc_start: 0.4247 (OUTLIER) cc_final: 0.1969 (tmm) REVERT: E 503 MET cc_start: 0.6017 (tpt) cc_final: 0.5651 (tpt) REVERT: F 159 MET cc_start: 0.4313 (mmm) cc_final: 0.4100 (mmm) REVERT: F 261 ILE cc_start: 0.8534 (pt) cc_final: 0.8259 (mt) REVERT: C 679 ILE cc_start: 0.8908 (mm) cc_final: 0.8613 (mm) outliers start: 50 outliers final: 36 residues processed: 271 average time/residue: 0.3824 time to fit residues: 182.3139 Evaluate side-chains 241 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 204 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 68 PHE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 105 VAL Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 153 ASP Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 553 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 217 optimal weight: 2.9990 chunk 121 optimal weight: 20.0000 chunk 325 optimal weight: 8.9990 chunk 266 optimal weight: 5.9990 chunk 107 optimal weight: 0.8980 chunk 392 optimal weight: 0.9980 chunk 423 optimal weight: 7.9990 chunk 349 optimal weight: 50.0000 chunk 388 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 314 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 266 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34229 Z= 0.204 Angle : 0.523 9.502 46415 Z= 0.262 Chirality : 0.042 0.244 5370 Planarity : 0.004 0.055 5976 Dihedral : 8.931 86.007 5037 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.14 % Favored : 94.46 % Rotamer: Outliers : 1.84 % Allowed : 11.01 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.13), residues: 4299 helix: 1.68 (0.13), residues: 1732 sheet: 0.18 (0.24), residues: 481 loop : -0.72 (0.14), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 515 HIS 0.007 0.001 HIS F 450 PHE 0.014 0.001 PHE C 209 TYR 0.031 0.001 TYR C 210 ARG 0.004 0.000 ARG E 462 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 206 time to evaluate : 3.035 Fit side-chains REVERT: A 224 ILE cc_start: 0.1709 (OUTLIER) cc_final: 0.1429 (pt) REVERT: A 430 MET cc_start: 0.7978 (ppp) cc_final: 0.7452 (ppp) REVERT: A 765 MET cc_start: 0.7642 (ptt) cc_final: 0.7332 (ptp) REVERT: B 159 MET cc_start: 0.6805 (mmm) cc_final: 0.6482 (mmm) REVERT: B 740 LEU cc_start: 0.7907 (tp) cc_final: 0.7562 (tt) REVERT: D 650 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8808 (pp) REVERT: E 507 PHE cc_start: 0.3253 (t80) cc_final: 0.2930 (t80) REVERT: E 748 ARG cc_start: 0.7076 (tpm170) cc_final: 0.6820 (tpm170) REVERT: F 261 ILE cc_start: 0.8425 (pt) cc_final: 0.8188 (mt) REVERT: C 82 ILE cc_start: 0.6025 (OUTLIER) cc_final: 0.5806 (pt) REVERT: C 294 MET cc_start: 0.8485 (ttm) cc_final: 0.8113 (ttm) REVERT: C 679 ILE cc_start: 0.8960 (mm) cc_final: 0.8694 (mm) outliers start: 67 outliers final: 48 residues processed: 257 average time/residue: 0.3791 time to fit residues: 171.3417 Evaluate side-chains 246 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 195 time to evaluate : 3.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 650 LEU Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 387 optimal weight: 5.9990 chunk 294 optimal weight: 0.2980 chunk 203 optimal weight: 4.9990 chunk 43 optimal weight: 9.9990 chunk 187 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 393 optimal weight: 5.9990 chunk 416 optimal weight: 0.8980 chunk 205 optimal weight: 0.8980 chunk 372 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 149 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 34229 Z= 0.252 Angle : 0.546 9.375 46415 Z= 0.275 Chirality : 0.043 0.175 5370 Planarity : 0.004 0.058 5976 Dihedral : 8.647 86.334 5037 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.79 % Favored : 93.81 % Rotamer: Outliers : 2.66 % Allowed : 12.33 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 4299 helix: 1.60 (0.13), residues: 1736 sheet: 0.10 (0.24), residues: 488 loop : -0.76 (0.14), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 515 HIS 0.006 0.001 HIS F 450 PHE 0.021 0.001 PHE B 34 TYR 0.029 0.001 TYR C 210 ARG 0.011 0.000 ARG E 471 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 201 time to evaluate : 3.741 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7908 (ppp) cc_final: 0.7234 (ppp) REVERT: D 215 PHE cc_start: 0.7776 (m-80) cc_final: 0.7566 (m-80) REVERT: C 294 MET cc_start: 0.8625 (ttm) cc_final: 0.8220 (ttm) REVERT: C 460 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9140 (tt) REVERT: C 679 ILE cc_start: 0.8995 (mm) cc_final: 0.8695 (mm) outliers start: 97 outliers final: 62 residues processed: 283 average time/residue: 0.3695 time to fit residues: 184.5277 Evaluate side-chains 245 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 182 time to evaluate : 3.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 270 LEU Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 612 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 346 optimal weight: 20.0000 chunk 236 optimal weight: 0.9980 chunk 6 optimal weight: 40.0000 chunk 310 optimal weight: 5.9990 chunk 171 optimal weight: 2.9990 chunk 355 optimal weight: 40.0000 chunk 287 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 212 optimal weight: 0.5980 chunk 373 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN F 450 HIS ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34229 Z= 0.230 Angle : 0.538 9.409 46415 Z= 0.270 Chirality : 0.042 0.181 5370 Planarity : 0.004 0.058 5976 Dihedral : 8.658 89.068 5037 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.40 % Favored : 94.18 % Rotamer: Outliers : 2.44 % Allowed : 14.09 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.13), residues: 4299 helix: 1.57 (0.13), residues: 1748 sheet: 0.08 (0.24), residues: 496 loop : -0.83 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 515 HIS 0.017 0.001 HIS A 266 PHE 0.016 0.001 PHE C 215 TYR 0.014 0.001 TYR D 768 ARG 0.004 0.000 ARG F 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 193 time to evaluate : 3.767 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7935 (ppp) cc_final: 0.7220 (ppp) REVERT: B 74 ILE cc_start: 0.8531 (mm) cc_final: 0.8014 (mm) REVERT: B 595 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7683 (mp0) REVERT: D 215 PHE cc_start: 0.7815 (m-80) cc_final: 0.7561 (m-80) REVERT: E 138 ASN cc_start: 0.4141 (OUTLIER) cc_final: 0.3259 (t0) REVERT: C 294 MET cc_start: 0.8630 (ttm) cc_final: 0.8420 (ttm) REVERT: C 679 ILE cc_start: 0.9037 (mm) cc_final: 0.8802 (mm) outliers start: 89 outliers final: 69 residues processed: 270 average time/residue: 0.3746 time to fit residues: 178.0607 Evaluate side-chains 254 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 184 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 138 ASN Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 518 ILE Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 140 optimal weight: 4.9990 chunk 375 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 417 optimal weight: 1.9990 chunk 346 optimal weight: 8.9990 chunk 193 optimal weight: 0.7980 chunk 34 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 ASN E 138 ASN E 301 ASN ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 729 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 34229 Z= 0.344 Angle : 0.602 9.913 46415 Z= 0.303 Chirality : 0.044 0.190 5370 Planarity : 0.005 0.062 5976 Dihedral : 8.588 86.842 5037 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.23 % Favored : 93.32 % Rotamer: Outliers : 3.02 % Allowed : 15.02 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.13), residues: 4299 helix: 1.42 (0.13), residues: 1735 sheet: -0.04 (0.24), residues: 504 loop : -0.92 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 515 HIS 0.007 0.001 HIS C 450 PHE 0.031 0.001 PHE E 507 TYR 0.020 0.001 TYR D 768 ARG 0.006 0.000 ARG F 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 198 time to evaluate : 4.120 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3097 (pt) cc_final: 0.2559 (tp) REVERT: A 430 MET cc_start: 0.7925 (ppp) cc_final: 0.7132 (ppp) REVERT: B 42 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7680 (mtmt) REVERT: B 74 ILE cc_start: 0.8632 (mm) cc_final: 0.8166 (mm) REVERT: D 215 PHE cc_start: 0.7887 (m-80) cc_final: 0.7684 (m-80) REVERT: E 311 ASN cc_start: 0.7587 (OUTLIER) cc_final: 0.7349 (p0) REVERT: E 430 MET cc_start: 0.6552 (tmm) cc_final: 0.5847 (mtm) REVERT: F 137 TYR cc_start: 0.4927 (m-10) cc_final: 0.4578 (m-10) REVERT: C 460 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9206 (tt) outliers start: 110 outliers final: 81 residues processed: 293 average time/residue: 0.3888 time to fit residues: 199.4657 Evaluate side-chains 262 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 179 time to evaluate : 3.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 70 THR Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 402 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 237 optimal weight: 0.8980 chunk 304 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 351 optimal weight: 20.0000 chunk 232 optimal weight: 0.7980 chunk 415 optimal weight: 0.9990 chunk 259 optimal weight: 7.9990 chunk 253 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34229 Z= 0.239 Angle : 0.555 9.400 46415 Z= 0.279 Chirality : 0.043 0.170 5370 Planarity : 0.004 0.075 5976 Dihedral : 8.469 89.697 5037 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.77 % Favored : 93.79 % Rotamer: Outliers : 2.61 % Allowed : 15.76 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.13), residues: 4299 helix: 1.48 (0.13), residues: 1740 sheet: -0.06 (0.24), residues: 497 loop : -0.93 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 PHE 0.018 0.001 PHE E 754 TYR 0.018 0.001 TYR D 680 ARG 0.008 0.000 ARG A 759 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 187 time to evaluate : 3.790 Fit side-chains revert: symmetry clash REVERT: A 140 LEU cc_start: 0.3267 (pt) cc_final: 0.2624 (tp) REVERT: A 430 MET cc_start: 0.7822 (ppp) cc_final: 0.7028 (ppp) REVERT: B 74 ILE cc_start: 0.8612 (mm) cc_final: 0.8147 (mm) REVERT: D 215 PHE cc_start: 0.7838 (m-80) cc_final: 0.7635 (m-80) REVERT: E 311 ASN cc_start: 0.7673 (OUTLIER) cc_final: 0.7414 (p0) REVERT: E 430 MET cc_start: 0.6592 (tmm) cc_final: 0.5942 (mtm) REVERT: F 137 TYR cc_start: 0.4877 (m-10) cc_final: 0.4538 (m-10) REVERT: C 294 MET cc_start: 0.8534 (ttm) cc_final: 0.8216 (ttm) outliers start: 95 outliers final: 79 residues processed: 270 average time/residue: 0.4032 time to fit residues: 191.0911 Evaluate side-chains 259 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 179 time to evaluate : 3.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 256 optimal weight: 9.9990 chunk 165 optimal weight: 0.0270 chunk 248 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 81 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 8.9990 chunk 283 optimal weight: 10.0000 chunk 205 optimal weight: 5.9990 chunk 38 optimal weight: 20.0000 chunk 326 optimal weight: 9.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34229 Z= 0.316 Angle : 0.600 15.475 46415 Z= 0.301 Chirality : 0.044 0.175 5370 Planarity : 0.005 0.061 5976 Dihedral : 8.494 88.643 5037 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 6.30 % Favored : 93.25 % Rotamer: Outliers : 2.86 % Allowed : 16.01 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.13), residues: 4299 helix: 1.36 (0.13), residues: 1738 sheet: -0.20 (0.24), residues: 500 loop : -0.98 (0.14), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 515 HIS 0.006 0.001 HIS C 450 PHE 0.018 0.001 PHE E 754 TYR 0.024 0.001 TYR D 680 ARG 0.005 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 186 time to evaluate : 3.735 Fit side-chains REVERT: A 140 LEU cc_start: 0.3185 (pt) cc_final: 0.2482 (tp) REVERT: B 74 ILE cc_start: 0.8668 (mm) cc_final: 0.8205 (mm) REVERT: D 143 MET cc_start: 0.6767 (mpp) cc_final: 0.5453 (tpt) REVERT: E 311 ASN cc_start: 0.7734 (OUTLIER) cc_final: 0.7479 (p0) REVERT: E 430 MET cc_start: 0.6763 (tmm) cc_final: 0.6201 (mtm) REVERT: E 621 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7254 (pp) REVERT: F 137 TYR cc_start: 0.4859 (m-10) cc_final: 0.4578 (m-10) REVERT: C 294 MET cc_start: 0.8711 (ttm) cc_final: 0.8442 (ttm) REVERT: C 460 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9206 (tt) outliers start: 104 outliers final: 87 residues processed: 273 average time/residue: 0.3793 time to fit residues: 181.3534 Evaluate side-chains 269 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 179 time to evaluate : 3.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 390 ASN Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 180 ILE Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 727 LEU Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 513 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 377 optimal weight: 9.9990 chunk 397 optimal weight: 2.9990 chunk 363 optimal weight: 4.9990 chunk 387 optimal weight: 0.4980 chunk 232 optimal weight: 0.0040 chunk 168 optimal weight: 2.9990 chunk 303 optimal weight: 40.0000 chunk 118 optimal weight: 5.9990 chunk 349 optimal weight: 30.0000 chunk 366 optimal weight: 4.9990 chunk 385 optimal weight: 4.9990 overall best weight: 2.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34229 Z= 0.224 Angle : 0.568 11.357 46415 Z= 0.283 Chirality : 0.043 0.333 5370 Planarity : 0.004 0.058 5976 Dihedral : 8.318 89.475 5037 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.89 % Favored : 93.70 % Rotamer: Outliers : 2.55 % Allowed : 16.69 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 4299 helix: 1.48 (0.13), residues: 1725 sheet: -0.13 (0.24), residues: 489 loop : -0.95 (0.14), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 PHE 0.017 0.001 PHE E 754 TYR 0.024 0.001 TYR D 680 ARG 0.005 0.000 ARG D 677 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 191 time to evaluate : 3.921 Fit side-chains REVERT: A 140 LEU cc_start: 0.3371 (pt) cc_final: 0.2569 (tp) REVERT: B 74 ILE cc_start: 0.8654 (mm) cc_final: 0.8203 (mm) REVERT: D 122 GLN cc_start: 0.8054 (tp40) cc_final: 0.7355 (tp-100) REVERT: D 143 MET cc_start: 0.6976 (mpp) cc_final: 0.5608 (tpt) REVERT: D 528 MET cc_start: 0.8593 (mmm) cc_final: 0.8220 (mmm) REVERT: D 621 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8370 (pp) REVERT: D 770 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: E 311 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.7496 (p0) REVERT: E 430 MET cc_start: 0.6730 (tmm) cc_final: 0.6234 (mtm) REVERT: C 294 MET cc_start: 0.8622 (ttm) cc_final: 0.8340 (ttm) outliers start: 93 outliers final: 86 residues processed: 269 average time/residue: 0.3936 time to fit residues: 186.1739 Evaluate side-chains 269 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 180 time to evaluate : 3.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 350 ILE Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 390 ASN Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 612 ILE Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 254 optimal weight: 10.0000 chunk 409 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 284 optimal weight: 7.9990 chunk 429 optimal weight: 1.9990 chunk 395 optimal weight: 0.6980 chunk 341 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 264 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34229 Z= 0.193 Angle : 0.558 12.097 46415 Z= 0.277 Chirality : 0.042 0.323 5370 Planarity : 0.004 0.058 5976 Dihedral : 8.164 88.432 5037 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.98 % Favored : 93.60 % Rotamer: Outliers : 2.58 % Allowed : 16.69 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 4299 helix: 1.52 (0.13), residues: 1734 sheet: -0.15 (0.24), residues: 469 loop : -0.91 (0.14), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 PHE 0.017 0.001 PHE E 754 TYR 0.024 0.001 TYR D 680 ARG 0.005 0.000 ARG D 677 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8598 Ramachandran restraints generated. 4299 Oldfield, 0 Emsley, 4299 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 184 time to evaluate : 4.298 Fit side-chains REVERT: A 140 LEU cc_start: 0.3448 (pt) cc_final: 0.2605 (tp) REVERT: B 74 ILE cc_start: 0.8633 (mm) cc_final: 0.8179 (mm) REVERT: D 122 GLN cc_start: 0.7989 (tp40) cc_final: 0.7351 (tp-100) REVERT: D 528 MET cc_start: 0.8568 (mmm) cc_final: 0.8187 (mmm) REVERT: D 621 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8352 (pp) REVERT: D 733 LEU cc_start: 0.8743 (tp) cc_final: 0.8539 (tt) REVERT: D 770 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6672 (mp0) REVERT: E 311 ASN cc_start: 0.7711 (OUTLIER) cc_final: 0.7456 (p0) REVERT: C 294 MET cc_start: 0.8612 (ttm) cc_final: 0.8255 (ttm) outliers start: 94 outliers final: 85 residues processed: 265 average time/residue: 0.3843 time to fit residues: 179.2827 Evaluate side-chains 268 residues out of total 3642 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 180 time to evaluate : 3.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 224 ILE Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 561 CYS Chi-restraints excluded: chain A residue 647 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 687 ASN Chi-restraints excluded: chain A residue 697 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 109 ILE Chi-restraints excluded: chain B residue 254 ILE Chi-restraints excluded: chain B residue 290 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 553 VAL Chi-restraints excluded: chain B residue 697 THR Chi-restraints excluded: chain B residue 723 GLU Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 774 LEU Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 147 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 261 ILE Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 357 ASP Chi-restraints excluded: chain D residue 362 VAL Chi-restraints excluded: chain D residue 390 ASN Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 653 VAL Chi-restraints excluded: chain D residue 655 ILE Chi-restraints excluded: chain D residue 656 VAL Chi-restraints excluded: chain D residue 749 HIS Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain E residue 36 THR Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 69 CYS Chi-restraints excluded: chain E residue 102 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 143 MET Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 261 ILE Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 311 ASN Chi-restraints excluded: chain E residue 324 GLU Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 406 ASP Chi-restraints excluded: chain E residue 561 CYS Chi-restraints excluded: chain E residue 619 ASP Chi-restraints excluded: chain E residue 621 LEU Chi-restraints excluded: chain E residue 653 VAL Chi-restraints excluded: chain E residue 762 THR Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 290 THR Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 701 ASN Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 64 ASN Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 254 ILE Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 594 SER Chi-restraints excluded: chain C residue 598 ILE Chi-restraints excluded: chain C residue 612 ILE Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 676 ASP Chi-restraints excluded: chain C residue 737 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 431 random chunks: chunk 271 optimal weight: 3.9990 chunk 364 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 342 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 351 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** D 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN ** C 642 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.131902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091949 restraints weight = 73725.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090656 restraints weight = 53302.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.091189 restraints weight = 45803.166| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34229 Z= 0.184 Angle : 0.554 11.799 46415 Z= 0.274 Chirality : 0.042 0.319 5370 Planarity : 0.004 0.059 5976 Dihedral : 8.046 87.670 5037 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.42 % Allowed : 5.95 % Favored : 93.63 % Rotamer: Outliers : 2.50 % Allowed : 17.13 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.13), residues: 4299 helix: 1.55 (0.13), residues: 1739 sheet: -0.17 (0.24), residues: 468 loop : -0.91 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 515 HIS 0.004 0.001 HIS E 306 PHE 0.017 0.001 PHE E 754 TYR 0.021 0.001 TYR D 680 ARG 0.005 0.000 ARG D 677 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5064.43 seconds wall clock time: 94 minutes 14.19 seconds (5654.19 seconds total)