Starting phenix.real_space_refine on Thu Feb 22 11:43:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z11_14437/02_2024/7z11_14437_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.041 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 143 5.16 5 C 21430 2.51 5 N 5828 2.21 5 O 6645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 255": "OE1" <-> "OE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A GLU 717": "OE1" <-> "OE2" Residue "A GLU 738": "OE1" <-> "OE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B GLU 505": "OE1" <-> "OE2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 595": "OE1" <-> "OE2" Residue "B GLU 600": "OE1" <-> "OE2" Residue "B GLU 617": "OE1" <-> "OE2" Residue "B GLU 648": "OE1" <-> "OE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 770": "OE1" <-> "OE2" Residue "C GLU 47": "OE1" <-> "OE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "C GLU 408": "OE1" <-> "OE2" Residue "C GLU 505": "OE1" <-> "OE2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C GLU 593": "OE1" <-> "OE2" Residue "C GLU 649": "OE1" <-> "OE2" Residue "C GLU 704": "OE1" <-> "OE2" Residue "C GLU 730": "OE1" <-> "OE2" Residue "C GLU 764": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 229": "OE1" <-> "OE2" Residue "D GLU 240": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 410": "OE1" <-> "OE2" Residue "D GLU 505": "OE1" <-> "OE2" Residue "D GLU 540": "OE1" <-> "OE2" Residue "D GLU 600": "OE1" <-> "OE2" Residue "D GLU 617": "OE1" <-> "OE2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 649": "OE1" <-> "OE2" Residue "D GLU 717": "OE1" <-> "OE2" Residue "D GLU 746": "OE1" <-> "OE2" Residue "E GLU 440": "OE1" <-> "OE2" Residue "E ARG 544": "NH1" <-> "NH2" Residue "E GLU 617": "OE1" <-> "OE2" Residue "E GLU 730": "OE1" <-> "OE2" Residue "F PHE 271": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F GLU 346": "OE1" <-> "OE2" Residue "F GLU 408": "OE1" <-> "OE2" Residue "F ARG 429": "NH1" <-> "NH2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 505": "OE1" <-> "OE2" Residue "F GLU 540": "OE1" <-> "OE2" Residue "F TYR 556": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 703": "OE1" <-> "OE2" Residue "F GLU 746": "OE1" <-> "OE2" Residue "F GLU 751": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34079 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5575 Classifications: {'peptide': 727} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 1 Chain: "B" Number of atoms: 5602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5602 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 689} Chain breaks: 1 Chain: "C" Number of atoms: 5611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5611 Classifications: {'peptide': 731} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 690} Chain breaks: 1 Chain: "D" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5630 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 38, 'TRANS': 693} Chain breaks: 1 Chain: "E" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5630 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 693} Chain breaks: 1 Chain: "F" Number of atoms: 5590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5590 Classifications: {'peptide': 728} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 687} Chain breaks: 1 Chain: "G" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 100 Classifications: {'peptide': 20} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'TRANS': 19} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'UNK:plan-1': 20} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 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: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 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: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.31, per 1000 atoms: 0.57 Number of scatterers: 34079 At special positions: 0 Unit cell: (140.17, 154.08, 172.27, 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 143 16.00 P 33 15.00 O 6645 8.00 N 5828 7.00 C 21430 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.94 Conformation dependent library (CDL) restraints added in 6.2 seconds 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8162 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 209 helices and 31 sheets defined 40.0% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.09 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 removed outlier: 4.496A pdb=" N CYS A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 55 through 60 Processing helix chain 'A' and resid 100 through 106 removed outlier: 3.780A pdb=" N VAL A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLY A 106 " --> pdb=" O ILE A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 145 through 155 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 251 through 266 Proline residue: A 264 - end of helix Processing helix chain 'A' and resid 268 through 274 removed outlier: 3.625A pdb=" N SER A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 361 through 375 Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 416 through 433 removed outlier: 3.554A pdb=" N ARG A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 430 " --> pdb=" O GLN A 426 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N SER A 432 " --> pdb=" O SER A 428 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASP A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 448 Processing helix chain 'A' and resid 455 through 473 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 497 removed outlier: 3.697A pdb=" N VAL A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.603A pdb=" N MET A 531 " --> pdb=" O LYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 537 No H-bonds generated for 'chain 'A' and resid 534 through 537' Processing helix chain 'A' and resid 539 through 545 Processing helix chain 'A' and resid 564 through 573 Processing helix chain 'A' and resid 593 through 607 removed outlier: 3.573A pdb=" N ILE A 598 " --> pdb=" O SER A 594 " (cutoff:3.500A) 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 631 through 648 removed outlier: 3.703A pdb=" N HIS A 635 " --> pdb=" O SER A 631 " (cutoff:3.500A) 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 667 through 670 No H-bonds generated for 'chain 'A' and resid 667 through 670' Processing helix chain 'A' and resid 686 through 697 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 709 through 715 Processing helix chain 'A' and resid 721 through 738 removed outlier: 3.525A pdb=" N CYS A 728 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.779A pdb=" N GLY A 756 " --> pdb=" O LYS A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 774 removed outlier: 4.019A pdb=" N ALA A 773 " --> pdb=" O TYR A 769 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU A 774 " --> pdb=" O GLU A 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 55 through 61 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.719A pdb=" N SER B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 100 through 105' Processing helix chain 'B' and resid 139 through 142 No H-bonds generated for 'chain 'B' and resid 139 through 142' Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' 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 248 through 266 removed outlier: 5.198A pdb=" N LYS B 252 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 254 " --> pdb=" O ASP B 251 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU B 255 " --> pdb=" O LYS B 252 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU B 262 " --> pdb=" O SER B 259 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE B 263 " --> pdb=" O ALA B 260 " (cutoff:3.500A) Proline residue: B 264 - end of helix Processing helix chain 'B' and resid 268 through 274 removed outlier: 3.576A pdb=" N SER B 272 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 322 through 336 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 361 through 373 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 416 through 428 Processing helix chain 'B' and resid 441 through 448 Processing helix chain 'B' and resid 455 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 495 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 532 Processing helix chain 'B' and resid 534 through 537 No H-bonds generated for 'chain 'B' and resid 534 through 537' Processing helix chain 'B' and resid 539 through 545 Processing helix chain 'B' and resid 564 through 573 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 removed outlier: 3.827A pdb=" N ILE B 598 " --> pdb=" O SER B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 621 No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 631 through 644 removed outlier: 3.855A pdb=" N HIS B 635 " --> pdb=" O SER B 631 " (cutoff:3.500A) 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 686 through 696 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 709 through 715 Processing helix chain 'B' and resid 721 through 738 removed outlier: 3.529A pdb=" N CYS B 728 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.943A pdb=" N GLY B 756 " --> pdb=" O LYS B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.687A pdb=" N ARG B 775 " --> pdb=" O GLU B 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 49 removed outlier: 4.182A pdb=" N CYS C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 55 through 60 Processing helix chain 'C' and resid 100 through 106 removed outlier: 3.914A pdb=" N VAL C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 106 " --> pdb=" O ILE C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 142 No H-bonds generated for 'chain 'C' and resid 139 through 142' Processing helix chain 'C' and resid 145 through 153 removed outlier: 4.181A pdb=" N LYS C 150 " --> pdb=" O LYS C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 246 No H-bonds generated for 'chain 'C' and resid 244 through 246' Processing helix chain 'C' and resid 251 through 266 removed outlier: 3.772A pdb=" N ILE C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 268 through 274 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 361 through 374 Processing helix chain 'C' and resid 416 through 430 Processing helix chain 'C' and resid 440 through 448 Processing helix chain 'C' and resid 455 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 removed outlier: 3.791A pdb=" N VAL C 496 " --> pdb=" O GLU C 492 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP C 497 " --> pdb=" O SER C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 503 No H-bonds generated for 'chain 'C' and resid 501 through 503' Processing helix chain 'C' and resid 522 through 532 removed outlier: 3.518A pdb=" N MET C 531 " --> pdb=" O LYS C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 534 through 537 No H-bonds generated for 'chain 'C' and resid 534 through 537' Processing helix chain 'C' and resid 539 through 545 Processing helix chain 'C' and resid 563 through 573 Processing helix chain 'C' and resid 583 through 586 removed outlier: 3.854A pdb=" N ILE C 586 " --> pdb=" O GLY C 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 583 through 586' Processing helix chain 'C' and resid 593 through 607 removed outlier: 3.638A pdb=" N ILE C 598 " --> pdb=" O SER C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 620 No H-bonds generated for 'chain 'C' and resid 618 through 620' Processing helix chain 'C' and resid 631 through 644 Processing helix chain 'C' and resid 662 through 664 No H-bonds generated for 'chain 'C' and resid 662 through 664' Processing helix chain 'C' and resid 667 through 670 No H-bonds generated for 'chain 'C' and resid 667 through 670' Processing helix chain 'C' and resid 686 through 696 Processing helix chain 'C' and resid 709 through 715 Processing helix chain 'C' and resid 721 through 738 Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.578A pdb=" N GLY C 756 " --> pdb=" O LYS C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 775 removed outlier: 4.137A pdb=" N ARG C 775 " --> pdb=" O GLU C 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 100 through 106 removed outlier: 3.760A pdb=" N VAL D 105 " --> pdb=" O THR D 101 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY D 106 " --> pdb=" O ILE D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 142 No H-bonds generated for 'chain 'D' and resid 139 through 142' Processing helix chain 'D' and resid 145 through 155 Processing helix chain 'D' and resid 170 through 172 No H-bonds generated for 'chain 'D' and resid 170 through 172' 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 244 through 246 No H-bonds generated for 'chain 'D' and resid 244 through 246' Processing helix chain 'D' and resid 251 through 266 Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 268 through 274 Processing helix chain 'D' and resid 292 through 302 Processing helix chain 'D' and resid 312 through 315 removed outlier: 3.511A pdb=" N ILE D 315 " --> pdb=" O GLY D 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 312 through 315' Processing helix chain 'D' and resid 322 through 336 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 392 through 394 No H-bonds generated for 'chain 'D' and resid 392 through 394' Processing helix chain 'D' and resid 397 through 399 No H-bonds generated for 'chain 'D' and resid 397 through 399' Processing helix chain 'D' and resid 416 through 429 removed outlier: 3.702A pdb=" N ARG D 429 " --> pdb=" O LYS D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 448 Processing helix chain 'D' and resid 455 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 488 through 497 removed outlier: 3.965A pdb=" N ASP D 497 " --> pdb=" O SER D 493 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 503 No H-bonds generated for 'chain 'D' and resid 501 through 503' 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 532 Processing helix chain 'D' and resid 534 through 537 No H-bonds generated for 'chain 'D' and resid 534 through 537' Processing helix chain 'D' and resid 539 through 545 Processing helix chain 'D' and resid 563 through 573 Processing helix chain 'D' and resid 584 through 586 No H-bonds generated for 'chain 'D' and resid 584 through 586' Processing helix chain 'D' and resid 593 through 607 Processing helix chain 'D' and resid 636 through 644 Processing helix chain 'D' and resid 662 through 664 No H-bonds generated for 'chain 'D' and resid 662 through 664' Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 703 through 705 No H-bonds generated for 'chain 'D' and resid 703 through 705' Processing helix chain 'D' and resid 709 through 715 Processing helix chain 'D' and resid 721 through 738 removed outlier: 3.512A pdb=" N GLU D 738 " --> pdb=" O ALA D 734 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 755 removed outlier: 3.567A pdb=" N LYS D 755 " --> pdb=" O GLU D 751 " (cutoff:3.500A) Processing helix chain 'D' and resid 763 through 775 removed outlier: 3.721A pdb=" N LEU D 774 " --> pdb=" O GLU D 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 139 through 142 No H-bonds generated for 'chain 'E' and resid 139 through 142' Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 244 through 246 No H-bonds generated for 'chain 'E' and resid 244 through 246' Processing helix chain 'E' and resid 251 through 265 Proline residue: E 264 - end of helix Processing helix chain 'E' and resid 269 through 274 removed outlier: 4.908A pdb=" N PHE E 274 " --> pdb=" O LEU E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 302 Processing helix chain 'E' and resid 323 through 336 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 361 through 374 Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'E' and resid 397 through 399 No H-bonds generated for 'chain 'E' and resid 397 through 399' Processing helix chain 'E' and resid 418 through 428 removed outlier: 3.506A pdb=" N ASP E 421 " --> pdb=" O ALA E 418 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYS E 425 " --> pdb=" O ILE E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 434 No H-bonds generated for 'chain 'E' and resid 431 through 434' Processing helix chain 'E' and resid 440 through 448 removed outlier: 3.504A pdb=" N TYR E 444 " --> pdb=" O GLU E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 475 Processing helix chain 'E' and resid 481 through 483 No H-bonds generated for 'chain 'E' and resid 481 through 483' Processing helix chain 'E' and resid 488 through 497 removed outlier: 4.785A pdb=" N ASP E 497 " --> pdb=" O SER E 493 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 534 through 537 No H-bonds generated for 'chain 'E' and resid 534 through 537' Processing helix chain 'E' and resid 540 through 543 No H-bonds generated for 'chain 'E' and resid 540 through 543' Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 597 through 607 Processing helix chain 'E' and resid 618 through 621 No H-bonds generated for 'chain 'E' and resid 618 through 621' Processing helix chain 'E' and resid 636 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 696 Processing helix chain 'E' and resid 710 through 712 No H-bonds generated for 'chain 'E' and resid 710 through 712' Processing helix chain 'E' and resid 724 through 738 removed outlier: 3.598A pdb=" N MET E 737 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 738 " --> pdb=" O ALA E 734 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 756 Processing helix chain 'E' and resid 763 through 776 removed outlier: 3.908A pdb=" N ARG E 775 " --> pdb=" O GLU E 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 49 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 100 through 106 removed outlier: 3.605A pdb=" N VAL F 105 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY F 106 " --> pdb=" O ILE F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 251 through 265 Proline residue: F 264 - end of helix Processing helix chain 'F' and resid 269 through 272 No H-bonds generated for 'chain 'F' and resid 269 through 272' Processing helix chain 'F' and resid 292 through 302 Processing helix chain 'F' and resid 322 through 333 removed outlier: 3.852A pdb=" N ALA F 326 " --> pdb=" O GLU F 322 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE F 330 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE F 331 " --> pdb=" O LEU F 327 " (cutoff:3.500A) 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 362 through 373 removed outlier: 4.016A pdb=" N THR F 372 " --> pdb=" O ALA F 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 392 through 394 No H-bonds generated for 'chain 'F' and resid 392 through 394' Processing helix chain 'F' and resid 397 through 400 Processing helix chain 'F' and resid 416 through 429 removed outlier: 3.719A pdb=" N PHE F 420 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG F 429 " --> pdb=" O LYS F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 442 through 448 Processing helix chain 'F' and resid 455 through 475 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 488 through 497 removed outlier: 4.201A pdb=" N VAL F 496 " --> pdb=" O GLU F 492 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ASP F 497 " --> pdb=" O SER F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 501 through 504 Processing helix chain 'F' and resid 515 through 517 No H-bonds generated for 'chain 'F' and resid 515 through 517' Processing helix chain 'F' and resid 522 through 537 removed outlier: 4.300A pdb=" N LEU F 534 " --> pdb=" O GLU F 530 " (cutoff:3.500A) Proline residue: F 535 - end of helix Processing helix chain 'F' and resid 539 through 545 Processing helix chain 'F' and resid 563 through 572 Processing helix chain 'F' and resid 583 through 586 No H-bonds generated for 'chain 'F' and resid 583 through 586' Processing helix chain 'F' and resid 593 through 607 removed outlier: 4.316A pdb=" N SER F 607 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 620 No H-bonds generated for 'chain 'F' and resid 618 through 620' Processing helix chain 'F' and resid 635 through 646 removed outlier: 4.215A pdb=" N ASP F 645 " --> pdb=" O LEU F 641 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY F 646 " --> pdb=" O ASN F 642 " (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 No H-bonds generated for 'chain 'F' and resid 667 through 670' Processing helix chain 'F' and resid 686 through 696 Processing helix chain 'F' and resid 702 through 705 No H-bonds generated for 'chain 'F' and resid 702 through 705' Processing helix chain 'F' and resid 709 through 715 removed outlier: 4.269A pdb=" N ASP F 714 " --> pdb=" O HIS F 710 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 738 removed outlier: 3.803A pdb=" N GLU F 730 " --> pdb=" O LEU F 727 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 731 " --> pdb=" O CYS F 728 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET F 737 " --> pdb=" O ALA F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 756 removed outlier: 3.784A pdb=" N GLY F 756 " --> pdb=" O LYS F 752 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 38 Processing sheet with id= B, first strand: chain 'A' and resid 50 through 53 removed outlier: 8.192A pdb=" N ALA A 51 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A 82 " --> pdb=" O ALA A 51 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ILE A 53 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ARG A 84 " --> pdb=" O ILE A 53 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 223 through 226 removed outlier: 3.601A pdb=" N ASP A 182 " --> pdb=" O THR A 130 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY A 132 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 180 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 407 through 411 removed outlier: 8.598A pdb=" N ILE A 282 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL A 385 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU A 284 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA A 387 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY A 286 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR A 389 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N SER A 340 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE A 386 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE A 342 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ALA A 388 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ILE A 344 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N HIS A 306 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 343 " --> pdb=" O HIS A 306 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LEU A 308 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP A 345 " --> pdb=" O LEU A 308 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 677 through 680 removed outlier: 8.465A pdb=" N VAL A 553 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE A 655 " --> pdb=" O VAL A 553 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU A 555 " --> pdb=" O ILE A 655 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA A 657 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N SER A 611 " --> pdb=" O VAL A 654 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N VAL A 656 " --> pdb=" O SER A 611 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE A 613 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ALA A 658 " --> pdb=" O ILE A 613 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N PHE A 615 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 579 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N ASP A 616 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL A 581 " --> pdb=" O ASP A 616 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= G, first strand: chain 'B' and resid 79 through 82 Processing sheet with id= H, first strand: chain 'B' and resid 223 through 226 removed outlier: 5.972A pdb=" N GLY B 132 " --> pdb=" O ILE B 180 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE B 180 " --> pdb=" O GLY B 132 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 157 through 159 Processing sheet with id= J, first strand: chain 'B' and resid 407 through 410 removed outlier: 8.683A pdb=" N ILE B 282 " --> pdb=" O VAL B 383 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 385 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU B 284 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA B 387 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER B 340 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N ILE B 386 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ILE B 342 " --> pdb=" O ILE B 386 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ALA B 388 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 344 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N HIS B 306 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N PHE B 343 " --> pdb=" O HIS B 306 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 308 " --> pdb=" O PHE B 343 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASP B 345 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B 310 " --> pdb=" O ASP B 345 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 677 through 680 removed outlier: 8.880A pdb=" N VAL B 553 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE B 655 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LEU B 555 " --> pdb=" O ILE B 655 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA B 657 " --> pdb=" O LEU B 555 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER B 611 " --> pdb=" O VAL B 654 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL B 656 " --> pdb=" O SER B 611 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE B 613 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N ALA B 658 " --> pdb=" O ILE B 613 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE B 615 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN B 577 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N PHE B 614 " --> pdb=" O ASN B 577 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 579 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ASP B 616 " --> pdb=" O LEU B 579 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL B 581 " --> pdb=" O ASP B 616 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 35 through 38 Processing sheet with id= M, first strand: chain 'C' and resid 50 through 54 removed outlier: 8.111A pdb=" N ALA C 51 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 82 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N ILE C 53 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ARG C 84 " --> pdb=" O ILE C 53 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 407 through 410 removed outlier: 8.413A pdb=" N ILE C 282 " --> pdb=" O VAL C 383 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 385 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU C 284 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA C 387 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N SER C 340 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ILE C 386 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE C 342 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA C 388 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 344 " --> pdb=" O ALA C 388 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N HIS C 306 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N PHE C 343 " --> pdb=" O HIS C 306 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LEU C 308 " --> pdb=" O PHE C 343 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ASP C 345 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE C 310 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 677 through 680 removed outlier: 8.782A pdb=" N VAL C 553 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 655 " --> pdb=" O VAL C 553 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU C 555 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALA C 657 " --> pdb=" O LEU C 555 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER C 611 " --> pdb=" O VAL C 654 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N VAL C 656 " --> pdb=" O SER C 611 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ILE C 613 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA C 658 " --> pdb=" O ILE C 613 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N PHE C 615 " --> pdb=" O ALA C 658 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 577 " --> pdb=" O ILE C 612 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N PHE C 614 " --> pdb=" O ASN C 577 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU C 579 " --> pdb=" O PHE C 614 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ASP C 616 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL C 581 " --> pdb=" O ASP C 616 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 133 removed outlier: 3.797A pdb=" N ASP C 182 " --> pdb=" O THR C 130 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLY C 132 " --> pdb=" O ILE C 180 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N ILE C 180 " --> pdb=" O GLY C 132 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 35 through 38 Processing sheet with id= R, first strand: chain 'D' and resid 50 through 53 removed outlier: 7.812A pdb=" N ALA D 51 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE D 82 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N ILE D 53 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ARG D 84 " --> pdb=" O ILE D 53 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY D 72 " --> pdb=" O GLU D 115 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 182 through 184 removed outlier: 3.717A pdb=" N ASP D 182 " --> pdb=" O THR D 130 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N HIS D 223 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL D 131 " --> pdb=" O HIS D 223 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 225 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 407 through 410 removed outlier: 3.590A pdb=" N HIS D 285 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER D 340 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ILE D 386 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ILE D 342 " --> pdb=" O ILE D 386 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA D 388 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE D 344 " --> pdb=" O ALA D 388 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N HIS D 306 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE D 343 " --> pdb=" O HIS D 306 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N LEU D 308 " --> pdb=" O PHE D 343 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N ASP D 345 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE D 310 " --> pdb=" O ASP D 345 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 677 through 680 removed outlier: 8.919A pdb=" N VAL D 553 " --> pdb=" O VAL D 653 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE D 655 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N LEU D 555 " --> pdb=" O ILE D 655 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA D 657 " --> pdb=" O LEU D 555 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N SER D 611 " --> pdb=" O VAL D 654 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL D 656 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE D 613 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N ALA D 658 " --> pdb=" O ILE D 613 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N PHE D 615 " --> pdb=" O ALA D 658 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN D 577 " --> pdb=" O ILE D 612 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N PHE D 614 " --> pdb=" O ASN D 577 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU D 579 " --> pdb=" O PHE D 614 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ASP D 616 " --> pdb=" O LEU D 579 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL D 581 " --> pdb=" O ASP D 616 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= W, first strand: chain 'E' and resid 52 through 54 removed outlier: 5.623A pdb=" N ARG E 84 " --> pdb=" O ILE E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 67 through 71 removed outlier: 3.502A pdb=" N SER E 67 " --> pdb=" O ALA E 83 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 223 through 226 removed outlier: 5.696A pdb=" N GLY E 132 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE E 180 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 407 through 411 removed outlier: 3.510A pdb=" N HIS E 285 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ILE E 282 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL E 385 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N LEU E 284 " --> pdb=" O VAL E 385 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA E 387 " --> pdb=" O LEU E 284 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N GLY E 286 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR E 389 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER E 340 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ILE E 386 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE E 342 " --> pdb=" O ILE E 386 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA E 388 " --> pdb=" O ILE E 342 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 344 " --> pdb=" O ALA E 388 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N HIS E 306 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE E 343 " --> pdb=" O HIS E 306 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LEU E 308 " --> pdb=" O PHE E 343 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP E 345 " --> pdb=" O LEU E 308 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'F' and resid 35 through 38 removed outlier: 3.762A pdb=" N LEU F 98 " --> pdb=" O ARG F 37 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ALA F 51 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE F 82 " --> pdb=" O ALA F 51 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 53 " --> pdb=" O ILE F 82 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG F 84 " --> pdb=" O ILE F 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER F 67 " --> pdb=" O ALA F 83 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY F 72 " --> pdb=" O GLU F 115 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 223 through 227 removed outlier: 4.072A pdb=" N SER F 133 " --> pdb=" O SER F 227 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLY F 132 " --> pdb=" O ILE F 180 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N ILE F 180 " --> pdb=" O GLY F 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'F' and resid 157 through 159 Processing sheet with id= AD, first strand: chain 'F' and resid 282 through 285 removed outlier: 6.840A pdb=" N ILE F 342 " --> pdb=" O ILE F 386 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ALA F 388 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ILE F 344 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 677 through 680 removed outlier: 5.825A pdb=" N SER F 611 " --> pdb=" O VAL F 654 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N VAL F 656 " --> pdb=" O SER F 611 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE F 613 " --> pdb=" O VAL F 656 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N ALA F 658 " --> pdb=" O ILE F 613 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE F 615 " --> pdb=" O ALA F 658 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN F 577 " --> pdb=" O ILE F 612 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE F 614 " --> pdb=" O ASN F 577 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU F 579 " --> pdb=" O PHE F 614 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 2904 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: 12.97 Time building geometry restraints manager: 13.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.31: 5877 1.31 - 1.47: 12809 1.47 - 1.63: 15768 1.63 - 1.79: 60 1.79 - 1.95: 173 Bond restraints: 34687 Sorted by residual: bond pdb=" C THR F 323 " pdb=" O THR F 323 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.29e-02 6.01e+03 4.22e+01 bond pdb=" CA LYS D 589 " pdb=" C LYS D 589 " ideal model delta sigma weight residual 1.526 1.471 0.055 1.23e-02 6.61e+03 1.97e+01 bond pdb=" C ILE F 342 " pdb=" O ILE F 342 " ideal model delta sigma weight residual 1.234 1.182 0.052 1.17e-02 7.31e+03 1.95e+01 bond pdb=" N TYR D 590 " pdb=" CA TYR D 590 " ideal model delta sigma weight residual 1.455 1.396 0.059 1.36e-02 5.41e+03 1.85e+01 bond pdb=" N ILE F 342 " pdb=" CA ILE F 342 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.15e-02 7.56e+03 1.73e+01 ... (remaining 34682 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.48: 541 103.48 - 111.12: 13970 111.12 - 118.76: 14431 118.76 - 126.41: 17679 126.41 - 134.05: 415 Bond angle restraints: 47036 Sorted by residual: angle pdb=" CA SER A 611 " pdb=" C SER A 611 " pdb=" O SER A 611 " ideal model delta sigma weight residual 121.36 111.87 9.49 1.06e+00 8.90e-01 8.02e+01 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 114.14 -3.41 4.52e-01 4.89e+00 5.69e+01 angle pdb=" CA ASP D 406 " pdb=" CB ASP D 406 " pdb=" CG ASP D 406 " ideal model delta sigma weight residual 112.60 119.38 -6.78 1.00e+00 1.00e+00 4.59e+01 angle pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " pdb=" N1 AGS F 901 " ideal model delta sigma weight residual 117.53 122.67 -5.14 7.63e-01 1.72e+00 4.53e+01 angle pdb=" CA PRO C 239 " pdb=" N PRO C 239 " pdb=" CD PRO C 239 " ideal model delta sigma weight residual 112.00 102.97 9.03 1.40e+00 5.10e-01 4.16e+01 ... (remaining 47031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 20963 35.65 - 71.31: 338 71.31 - 106.96: 31 106.96 - 142.61: 1 142.61 - 178.27: 2 Dihedral angle restraints: 21335 sinusoidal: 8680 harmonic: 12655 Sorted by residual: dihedral pdb=" CA LEU F 437 " pdb=" C LEU F 437 " pdb=" N ASP F 438 " pdb=" CA ASP F 438 " ideal model delta harmonic sigma weight residual -180.00 -130.09 -49.91 0 5.00e+00 4.00e-02 9.96e+01 dihedral pdb=" CA ASP F 438 " pdb=" C ASP F 438 " pdb=" N SER F 439 " pdb=" CA SER F 439 " ideal model delta harmonic sigma weight residual 180.00 147.53 32.47 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA GLU B 648 " pdb=" C GLU B 648 " pdb=" N GLU B 649 " pdb=" CA GLU B 649 " ideal model delta harmonic sigma weight residual -180.00 -152.13 -27.87 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 21332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.391: 5454 0.391 - 0.782: 0 0.782 - 1.173: 0 1.173 - 1.563: 0 1.563 - 1.954: 1 Chirality restraints: 5455 Sorted by residual: chirality pdb=" CG LEU E 621 " pdb=" CB LEU E 621 " pdb=" CD1 LEU E 621 " pdb=" CD2 LEU E 621 " both_signs ideal model delta sigma weight residual False -2.59 -0.64 -1.95 2.00e-01 2.50e+01 9.55e+01 chirality pdb=" PA AGS F 901 " pdb=" O2A AGS F 901 " pdb=" O3A AGS F 901 " pdb=" O5' AGS F 901 " both_signs ideal model delta sigma weight residual True 3.18 -2.89 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA LYS D 318 " pdb=" N LYS D 318 " pdb=" C LYS D 318 " pdb=" CB LYS D 318 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 5452 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' AGS F 901 " -0.257 2.00e-02 2.50e+03 1.06e-01 3.07e+02 pdb=" C2 AGS F 901 " 0.048 2.00e-02 2.50e+03 pdb=" C4 AGS F 901 " 0.069 2.00e-02 2.50e+03 pdb=" C5 AGS F 901 " 0.031 2.00e-02 2.50e+03 pdb=" C6 AGS F 901 " -0.049 2.00e-02 2.50e+03 pdb=" C8 AGS F 901 " 0.101 2.00e-02 2.50e+03 pdb=" N1 AGS F 901 " -0.044 2.00e-02 2.50e+03 pdb=" N3 AGS F 901 " 0.099 2.00e-02 2.50e+03 pdb=" N6 AGS F 901 " -0.127 2.00e-02 2.50e+03 pdb=" N7 AGS F 901 " 0.061 2.00e-02 2.50e+03 pdb=" N9 AGS F 901 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 263 " -0.099 5.00e-02 4.00e+02 1.49e-01 3.54e+01 pdb=" N PRO E 264 " 0.257 5.00e-02 4.00e+02 pdb=" CA PRO E 264 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO E 264 " -0.078 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 510 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO F 511 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO F 511 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO F 511 " -0.065 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 150 2.47 - 3.08: 25374 3.08 - 3.69: 50805 3.69 - 4.29: 75806 4.29 - 4.90: 124480 Nonbonded interactions: 276615 Sorted by model distance: nonbonded pdb=" OG SER B 720 " pdb=" OE1 GLU B 723 " model vdw 1.867 2.440 nonbonded pdb=" O LEU E 570 " pdb=" OG SER E 574 " model vdw 1.955 2.440 nonbonded pdb=" OD2 ASP E 619 " pdb=" OG1 THR E 659 " model vdw 1.966 2.440 nonbonded pdb=" OG1 THR C 468 " pdb=" OD2 ASP C 490 " model vdw 2.008 2.440 nonbonded pdb=" O ASN B 64 " pdb=" OG SER B 67 " model vdw 2.011 2.440 ... (remaining 276610 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 774 or resid 902)) selection = (chain 'B' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'C' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'D' and (resid 29 through 184 or resid 207 through 774 or resid 902)) selection = (chain 'E' and (resid 29 through 184 or resid 207 through 774 or resid 901)) selection = (chain 'F' and (resid 29 through 184 or resid 207 through 774 or resid 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.540 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: 0.040 Extract box with map and model: 5.440 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 91.990 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.170 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.118 34687 Z= 0.297 Angle : 0.800 16.321 47036 Z= 0.481 Chirality : 0.055 1.954 5455 Planarity : 0.007 0.149 6062 Dihedral : 13.990 178.268 13173 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.26 % Favored : 93.65 % Rotamer: Outliers : 0.35 % Allowed : 0.46 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.13), residues: 4360 helix: -0.28 (0.12), residues: 1679 sheet: -0.84 (0.21), residues: 580 loop : -1.00 (0.14), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 515 HIS 0.009 0.001 HIS A 91 PHE 0.043 0.002 PHE E 271 TYR 0.049 0.002 TYR C 319 ARG 0.024 0.001 ARG C 689 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 802 time to evaluate : 3.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7585 (mt) cc_final: 0.7196 (mt) REVERT: A 109 ILE cc_start: 0.8236 (pt) cc_final: 0.7986 (pt) REVERT: A 324 GLU cc_start: 0.6377 (tt0) cc_final: 0.5979 (tt0) REVERT: A 329 ASP cc_start: 0.7655 (t70) cc_final: 0.7288 (t0) REVERT: A 346 GLU cc_start: 0.6686 (mp0) cc_final: 0.6279 (mp0) REVERT: A 371 LEU cc_start: 0.7778 (mt) cc_final: 0.7227 (mt) REVERT: A 389 THR cc_start: 0.7886 (t) cc_final: 0.7685 (t) REVERT: A 448 LYS cc_start: 0.8066 (mmpt) cc_final: 0.7861 (mmpt) REVERT: A 503 MET cc_start: 0.7937 (mmp) cc_final: 0.7676 (mmp) REVERT: A 514 TYR cc_start: 0.8529 (m-80) cc_final: 0.8280 (m-80) REVERT: A 593 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7291 (tp30) REVERT: A 600 GLU cc_start: 0.7233 (tp30) cc_final: 0.6929 (tp30) REVERT: A 601 ILE cc_start: 0.8617 (tt) cc_final: 0.8383 (tt) REVERT: A 695 LYS cc_start: 0.7658 (tmtt) cc_final: 0.7420 (tttt) REVERT: A 715 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: A 717 GLU cc_start: 0.8024 (tp30) cc_final: 0.7528 (tp30) REVERT: B 263 ILE cc_start: 0.8743 (tp) cc_final: 0.8489 (tp) REVERT: B 322 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6588 (mm-30) REVERT: B 377 MET cc_start: -0.0092 (ppp) cc_final: -0.0480 (ppp) REVERT: B 417 ASP cc_start: 0.7481 (m-30) cc_final: 0.7254 (m-30) REVERT: B 484 LEU cc_start: 0.8870 (mt) cc_final: 0.8634 (mp) REVERT: C 95 VAL cc_start: 0.8735 (t) cc_final: 0.8474 (p) REVERT: C 377 MET cc_start: 0.7885 (mtp) cc_final: 0.7535 (mtp) REVERT: C 463 GLU cc_start: 0.7028 (mm-30) cc_final: 0.6817 (mm-30) REVERT: C 754 PHE cc_start: 0.7218 (t80) cc_final: 0.6985 (t80) REVERT: D 128 LYS cc_start: 0.7512 (tttt) cc_final: 0.7271 (tttt) REVERT: D 347 ILE cc_start: 0.8090 (tp) cc_final: 0.7877 (tt) REVERT: D 530 GLU cc_start: 0.7321 (mm-30) cc_final: 0.6761 (mm-30) REVERT: D 548 SER cc_start: 0.8025 (m) cc_final: 0.7682 (p) REVERT: D 589 LYS cc_start: 0.8219 (tttt) cc_final: 0.7996 (tttt) REVERT: D 664 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6314 (mm-30) REVERT: D 699 LYS cc_start: 0.8694 (mtpp) cc_final: 0.8255 (mtpt) REVERT: D 704 GLU cc_start: 0.6423 (mp0) cc_final: 0.6116 (mp0) REVERT: D 769 TYR cc_start: 0.8198 (m-80) cc_final: 0.7852 (m-80) REVERT: E 37 ARG cc_start: 0.6922 (mtp85) cc_final: 0.5455 (tpt90) REVERT: E 103 ARG cc_start: 0.7672 (mtm-85) cc_final: 0.6926 (mtp180) REVERT: E 177 ASP cc_start: 0.5691 (m-30) cc_final: 0.5470 (m-30) REVERT: E 319 TYR cc_start: 0.3521 (OUTLIER) cc_final: 0.3163 (m-80) REVERT: E 320 LEU cc_start: 0.6036 (OUTLIER) cc_final: 0.5708 (mp) REVERT: E 322 GLU cc_start: 0.5455 (OUTLIER) cc_final: 0.5201 (pm20) REVERT: E 399 LEU cc_start: 0.7494 (mt) cc_final: 0.7278 (mt) REVERT: E 453 VAL cc_start: 0.8081 (m) cc_final: 0.7588 (p) REVERT: E 656 VAL cc_start: 0.7704 (m) cc_final: 0.7459 (p) REVERT: E 664 GLU cc_start: 0.6761 (mm-30) cc_final: 0.6413 (mm-30) REVERT: F 244 TYR cc_start: 0.8609 (m-80) cc_final: 0.8350 (m-80) REVERT: F 255 GLU cc_start: 0.5953 (tp30) cc_final: 0.5716 (tp30) REVERT: F 417 ASP cc_start: 0.8033 (t70) cc_final: 0.7144 (t0) REVERT: F 421 ASP cc_start: 0.6926 (m-30) cc_final: 0.6232 (m-30) REVERT: F 430 MET cc_start: 0.5981 (mpp) cc_final: 0.5748 (mtm) REVERT: F 443 LYS cc_start: 0.7744 (mppt) cc_final: 0.7441 (mptt) REVERT: F 456 ASP cc_start: 0.7540 (m-30) cc_final: 0.7291 (m-30) REVERT: F 468 THR cc_start: 0.7543 (m) cc_final: 0.7336 (m) REVERT: F 643 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6422 (mm-30) REVERT: F 663 ASP cc_start: 0.7479 (p0) cc_final: 0.7261 (p0) REVERT: F 770 GLU cc_start: 0.6258 (tp30) cc_final: 0.6006 (tp30) outliers start: 13 outliers final: 1 residues processed: 813 average time/residue: 0.5413 time to fit residues: 665.0152 Evaluate side-chains 729 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 725 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 319 TYR Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 319 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 369 optimal weight: 50.0000 chunk 331 optimal weight: 7.9990 chunk 184 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 177 optimal weight: 0.8980 chunk 343 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 208 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 397 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 338 GLN B 356 ASN B 426 GLN C 311 ASN C 338 GLN C 353 ASN C 407 GLN C 660 ASN D 634 ASN E 56 ASN E 107 ASN E 301 ASN E 332 ASN F 301 ASN F 304 ASN F 426 GLN F 642 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 34687 Z= 0.264 Angle : 0.633 8.741 47036 Z= 0.325 Chirality : 0.046 0.198 5455 Planarity : 0.005 0.089 6062 Dihedral : 9.738 179.269 4951 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 1.43 % Allowed : 7.66 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.63 (0.13), residues: 4360 helix: 0.16 (0.12), residues: 1697 sheet: -0.64 (0.21), residues: 600 loop : -0.74 (0.14), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 515 HIS 0.011 0.001 HIS A 91 PHE 0.019 0.001 PHE F 578 TYR 0.021 0.001 TYR D 768 ARG 0.010 0.001 ARG E 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 741 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 LEU cc_start: 0.7465 (mt) cc_final: 0.7231 (mt) REVERT: A 294 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7360 (ttt) REVERT: A 329 ASP cc_start: 0.7687 (t70) cc_final: 0.7347 (t0) REVERT: A 345 ASP cc_start: 0.7112 (t70) cc_final: 0.6120 (t0) REVERT: A 346 GLU cc_start: 0.6587 (mp0) cc_final: 0.6356 (mp0) REVERT: A 371 LEU cc_start: 0.7496 (mt) cc_final: 0.7279 (mt) REVERT: A 593 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7142 (tp30) REVERT: A 600 GLU cc_start: 0.7225 (tp30) cc_final: 0.6962 (tp30) REVERT: A 660 ASN cc_start: 0.7330 (t0) cc_final: 0.7116 (t0) REVERT: A 695 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7415 (tttt) REVERT: A 715 ARG cc_start: 0.7785 (mtm-85) cc_final: 0.7509 (mtm-85) REVERT: B 112 ASP cc_start: 0.7245 (m-30) cc_final: 0.7025 (m-30) REVERT: B 263 ILE cc_start: 0.8833 (tp) cc_final: 0.8567 (tp) REVERT: B 322 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 377 MET cc_start: -0.0084 (ppp) cc_final: -0.0373 (ppp) REVERT: B 390 ASN cc_start: 0.7357 (t0) cc_final: 0.7156 (t0) REVERT: B 417 ASP cc_start: 0.7540 (m-30) cc_final: 0.7296 (m-30) REVERT: B 510 MET cc_start: 0.8166 (mtp) cc_final: 0.7928 (mtp) REVERT: C 329 ASP cc_start: 0.7344 (t0) cc_final: 0.7141 (t0) REVERT: C 754 PHE cc_start: 0.7209 (t80) cc_final: 0.6955 (t80) REVERT: D 319 TYR cc_start: 0.7960 (m-80) cc_final: 0.7623 (m-80) REVERT: D 448 LYS cc_start: 0.7290 (tttm) cc_final: 0.6934 (tttm) REVERT: D 574 SER cc_start: 0.8451 (m) cc_final: 0.8236 (p) REVERT: D 589 LYS cc_start: 0.8100 (tttt) cc_final: 0.7885 (tttt) REVERT: D 660 ASN cc_start: 0.7691 (p0) cc_final: 0.7353 (p0) REVERT: D 664 GLU cc_start: 0.6545 (mm-30) cc_final: 0.6237 (mm-30) REVERT: D 699 LYS cc_start: 0.8726 (mtpp) cc_final: 0.8243 (mtpt) REVERT: D 704 GLU cc_start: 0.6465 (mp0) cc_final: 0.6154 (mp0) REVERT: E 37 ARG cc_start: 0.6791 (mtp85) cc_final: 0.5480 (tpt90) REVERT: E 107 ASN cc_start: 0.7381 (t0) cc_final: 0.6996 (t0) REVERT: E 269 THR cc_start: 0.7626 (p) cc_final: 0.6688 (m) REVERT: E 448 LYS cc_start: 0.8006 (pptt) cc_final: 0.7781 (pptt) REVERT: E 463 GLU cc_start: 0.6446 (mm-30) cc_final: 0.6192 (mm-30) REVERT: E 492 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5556 (mt-10) REVERT: E 603 ARG cc_start: 0.7263 (ttp80) cc_final: 0.7009 (ttp80) REVERT: E 656 VAL cc_start: 0.7853 (m) cc_final: 0.7605 (p) REVERT: E 664 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6324 (mm-30) REVERT: F 162 MET cc_start: 0.6798 (mmm) cc_final: 0.6492 (mmm) REVERT: F 244 TYR cc_start: 0.8501 (m-80) cc_final: 0.8288 (m-80) REVERT: F 252 LYS cc_start: 0.8290 (mppt) cc_final: 0.7771 (mtmm) REVERT: F 274 PHE cc_start: 0.6487 (m-10) cc_final: 0.6257 (m-10) REVERT: F 417 ASP cc_start: 0.8050 (t70) cc_final: 0.7138 (t0) REVERT: F 419 ARG cc_start: 0.7891 (mtm-85) cc_final: 0.7526 (mtm180) REVERT: F 421 ASP cc_start: 0.6823 (m-30) cc_final: 0.6181 (m-30) REVERT: F 434 ARG cc_start: 0.5820 (ttp80) cc_final: 0.5617 (ttp80) REVERT: F 468 THR cc_start: 0.7519 (m) cc_final: 0.7302 (m) REVERT: F 503 MET cc_start: 0.8314 (mmm) cc_final: 0.8093 (mmm) REVERT: F 596 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6401 (mtp85) REVERT: F 599 ARG cc_start: 0.6036 (ptt90) cc_final: 0.5092 (ptt90) REVERT: F 717 GLU cc_start: 0.8254 (tp30) cc_final: 0.6447 (mm-30) REVERT: F 770 GLU cc_start: 0.6292 (tp30) cc_final: 0.6052 (tp30) outliers start: 53 outliers final: 32 residues processed: 759 average time/residue: 0.5377 time to fit residues: 616.9058 Evaluate side-chains 722 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 689 time to evaluate : 3.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 744 LYS Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 345 ASP Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 712 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 428 SER Chi-restraints excluded: chain F residue 488 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 221 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 331 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 398 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 354 optimal weight: 10.0000 chunk 395 optimal weight: 5.9990 chunk 135 optimal weight: 0.9990 chunk 319 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 338 GLN B 353 ASN C 338 GLN C 353 ASN C 660 ASN ** E 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN F 426 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 34687 Z= 0.335 Angle : 0.623 8.226 47036 Z= 0.320 Chirality : 0.047 0.219 5455 Planarity : 0.005 0.068 6062 Dihedral : 9.563 175.979 4944 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.51 % Favored : 93.46 % Rotamer: Outliers : 2.00 % Allowed : 10.64 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 4360 helix: 0.28 (0.13), residues: 1691 sheet: -0.59 (0.21), residues: 605 loop : -0.73 (0.14), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 515 HIS 0.007 0.001 HIS A 39 PHE 0.028 0.002 PHE E 578 TYR 0.019 0.002 TYR D 768 ARG 0.005 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 801 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 727 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ASP cc_start: 0.7727 (t70) cc_final: 0.7357 (t0) REVERT: A 345 ASP cc_start: 0.7189 (t70) cc_final: 0.6340 (t0) REVERT: A 600 GLU cc_start: 0.7206 (tp30) cc_final: 0.6970 (tp30) REVERT: A 660 ASN cc_start: 0.7365 (t0) cc_final: 0.7113 (t0) REVERT: A 695 LYS cc_start: 0.7648 (tmtt) cc_final: 0.7423 (tttt) REVERT: A 715 ARG cc_start: 0.7778 (mtm-85) cc_final: 0.7278 (mtm-85) REVERT: A 751 GLU cc_start: 0.7117 (tp30) cc_final: 0.6828 (tp30) REVERT: B 112 ASP cc_start: 0.7282 (m-30) cc_final: 0.7078 (m-30) REVERT: B 251 ASP cc_start: 0.7516 (t70) cc_final: 0.7254 (t0) REVERT: B 263 ILE cc_start: 0.8847 (tp) cc_final: 0.8571 (tp) REVERT: B 322 GLU cc_start: 0.6958 (mm-30) cc_final: 0.6557 (mm-30) REVERT: B 377 MET cc_start: -0.0161 (ppp) cc_final: -0.0376 (ppp) REVERT: B 390 ASN cc_start: 0.7413 (t0) cc_final: 0.7210 (t0) REVERT: B 417 ASP cc_start: 0.7592 (m-30) cc_final: 0.7325 (m-30) REVERT: C 329 ASP cc_start: 0.7361 (t0) cc_final: 0.7134 (t0) REVERT: C 463 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6629 (mm-30) REVERT: C 714 ASP cc_start: 0.6944 (m-30) cc_final: 0.6714 (m-30) REVERT: D 319 TYR cc_start: 0.7994 (m-80) cc_final: 0.7679 (m-80) REVERT: D 503 MET cc_start: 0.7334 (mmt) cc_final: 0.7046 (tpp) REVERT: D 527 LYS cc_start: 0.8546 (mttm) cc_final: 0.8330 (mttt) REVERT: D 548 SER cc_start: 0.7905 (m) cc_final: 0.7582 (p) REVERT: D 660 ASN cc_start: 0.7657 (p0) cc_final: 0.7421 (p0) REVERT: D 699 LYS cc_start: 0.8740 (mtpp) cc_final: 0.8439 (mtpt) REVERT: D 704 GLU cc_start: 0.6507 (mp0) cc_final: 0.6202 (mp0) REVERT: E 37 ARG cc_start: 0.6717 (mtp85) cc_final: 0.5418 (tpt90) REVERT: E 103 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.6953 (mtp180) REVERT: E 107 ASN cc_start: 0.7290 (t0) cc_final: 0.6743 (t0) REVERT: E 269 THR cc_start: 0.7612 (p) cc_final: 0.6673 (m) REVERT: E 346 GLU cc_start: 0.6620 (tp30) cc_final: 0.6281 (tp30) REVERT: E 419 ARG cc_start: 0.7192 (mtt90) cc_final: 0.6732 (mtt-85) REVERT: E 448 LYS cc_start: 0.8026 (pptt) cc_final: 0.7783 (pptt) REVERT: E 453 VAL cc_start: 0.8192 (m) cc_final: 0.7694 (p) REVERT: E 495 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5687 (pmm) REVERT: E 530 GLU cc_start: 0.6753 (tp30) cc_final: 0.6417 (tp30) REVERT: E 603 ARG cc_start: 0.7187 (ttp80) cc_final: 0.6957 (ttp80) REVERT: E 656 VAL cc_start: 0.7786 (m) cc_final: 0.7484 (p) REVERT: E 664 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6286 (mm-30) REVERT: E 723 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6743 (tp30) REVERT: E 730 GLU cc_start: 0.7151 (tm-30) cc_final: 0.6836 (tm-30) REVERT: F 162 MET cc_start: 0.6773 (mmm) cc_final: 0.6291 (mmm) REVERT: F 252 LYS cc_start: 0.8290 (mppt) cc_final: 0.7785 (mtmm) REVERT: F 258 LYS cc_start: 0.7962 (mmmt) cc_final: 0.7701 (mmmm) REVERT: F 399 LEU cc_start: 0.8381 (mt) cc_final: 0.8140 (mm) REVERT: F 417 ASP cc_start: 0.8072 (t70) cc_final: 0.7616 (t0) REVERT: F 419 ARG cc_start: 0.7933 (mtm-85) cc_final: 0.7399 (mtm180) REVERT: F 468 THR cc_start: 0.7551 (m) cc_final: 0.7348 (m) REVERT: F 497 ASP cc_start: 0.7298 (m-30) cc_final: 0.7053 (t0) REVERT: F 503 MET cc_start: 0.8303 (mmm) cc_final: 0.8061 (mmm) REVERT: F 510 MET cc_start: 0.5166 (mpp) cc_final: 0.4954 (mpp) REVERT: F 564 THR cc_start: 0.7768 (OUTLIER) cc_final: 0.7368 (t) REVERT: F 596 ARG cc_start: 0.6827 (mtp85) cc_final: 0.6147 (mtp85) REVERT: F 599 ARG cc_start: 0.6020 (ptt90) cc_final: 0.5051 (ptt90) REVERT: F 717 GLU cc_start: 0.8282 (tp30) cc_final: 0.6839 (tp30) REVERT: F 770 GLU cc_start: 0.6324 (tp30) cc_final: 0.6068 (tp30) outliers start: 74 outliers final: 48 residues processed: 758 average time/residue: 0.5418 time to fit residues: 621.2513 Evaluate side-chains 743 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 692 time to evaluate : 3.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 547 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 503 MET Chi-restraints excluded: chain E residue 723 GLU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 319 TYR Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 664 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 393 optimal weight: 0.9990 chunk 299 optimal weight: 6.9990 chunk 206 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 399 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 208 optimal weight: 0.4980 chunk 379 optimal weight: 6.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN C 311 ASN C 338 GLN C 353 ASN C 407 GLN C 660 ASN D 533 GLN D 634 ASN E 233 ASN E 332 ASN F 301 ASN F 426 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 34687 Z= 0.241 Angle : 0.572 8.589 47036 Z= 0.293 Chirality : 0.045 0.210 5455 Planarity : 0.005 0.069 6062 Dihedral : 9.343 179.434 4944 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.24 % Favored : 93.74 % Rotamer: Outliers : 2.57 % Allowed : 11.96 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.13), residues: 4360 helix: 0.52 (0.13), residues: 1691 sheet: -0.54 (0.21), residues: 610 loop : -0.67 (0.14), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 515 HIS 0.009 0.001 HIS E 285 PHE 0.018 0.001 PHE F 578 TYR 0.018 0.001 TYR D 768 ARG 0.007 0.000 ARG B 434 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 816 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 721 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ASP cc_start: 0.7720 (t70) cc_final: 0.7341 (t0) REVERT: A 600 GLU cc_start: 0.7157 (tp30) cc_final: 0.6938 (tp30) REVERT: A 660 ASN cc_start: 0.7294 (t0) cc_final: 0.7093 (t0) REVERT: A 695 LYS cc_start: 0.7660 (tmtt) cc_final: 0.7376 (tttt) REVERT: A 715 ARG cc_start: 0.7799 (mtm-85) cc_final: 0.7226 (mtm-85) REVERT: A 751 GLU cc_start: 0.7066 (tp30) cc_final: 0.6743 (tp30) REVERT: B 112 ASP cc_start: 0.7299 (m-30) cc_final: 0.7077 (m-30) REVERT: B 263 ILE cc_start: 0.8833 (tp) cc_final: 0.8549 (tp) REVERT: B 322 GLU cc_start: 0.6901 (mm-30) cc_final: 0.6523 (mm-30) REVERT: B 390 ASN cc_start: 0.7437 (t0) cc_final: 0.7200 (t0) REVERT: B 417 ASP cc_start: 0.7601 (m-30) cc_final: 0.7339 (m-30) REVERT: B 770 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 329 ASP cc_start: 0.7328 (t0) cc_final: 0.7126 (t0) REVERT: C 714 ASP cc_start: 0.7006 (m-30) cc_final: 0.6731 (m-30) REVERT: C 737 MET cc_start: 0.7584 (mmm) cc_final: 0.7323 (mmt) REVERT: D 109 ILE cc_start: 0.7695 (mt) cc_final: 0.7408 (mt) REVERT: D 319 TYR cc_start: 0.7953 (m-80) cc_final: 0.7739 (m-80) REVERT: D 363 GLU cc_start: 0.5971 (mp0) cc_final: 0.5753 (mp0) REVERT: D 486 VAL cc_start: 0.8360 (p) cc_final: 0.8127 (m) REVERT: D 503 MET cc_start: 0.7171 (mmt) cc_final: 0.6801 (tpp) REVERT: D 548 SER cc_start: 0.7917 (m) cc_final: 0.7611 (p) REVERT: D 568 LYS cc_start: 0.7963 (mttm) cc_final: 0.7732 (mtpp) REVERT: D 660 ASN cc_start: 0.7664 (p0) cc_final: 0.7409 (p0) REVERT: D 704 GLU cc_start: 0.6505 (mp0) cc_final: 0.6201 (mp0) REVERT: E 37 ARG cc_start: 0.6638 (mtp85) cc_final: 0.5259 (tpt90) REVERT: E 103 ARG cc_start: 0.7855 (mtm-85) cc_final: 0.6915 (mtp180) REVERT: E 107 ASN cc_start: 0.7286 (t0) cc_final: 0.6744 (t0) REVERT: E 269 THR cc_start: 0.7604 (p) cc_final: 0.6681 (m) REVERT: E 338 GLN cc_start: 0.8031 (mt0) cc_final: 0.7774 (mt0) REVERT: E 419 ARG cc_start: 0.7028 (mtt90) cc_final: 0.6693 (mtt-85) REVERT: E 453 VAL cc_start: 0.8096 (m) cc_final: 0.7611 (p) REVERT: E 495 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5676 (pmm) REVERT: E 530 GLU cc_start: 0.6689 (tp30) cc_final: 0.6363 (tp30) REVERT: E 656 VAL cc_start: 0.7678 (m) cc_final: 0.7458 (p) REVERT: E 664 GLU cc_start: 0.6616 (mm-30) cc_final: 0.6228 (mm-30) REVERT: E 723 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6739 (tp30) REVERT: E 730 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6779 (tm-30) REVERT: E 737 MET cc_start: 0.5909 (mmm) cc_final: 0.5522 (mmm) REVERT: F 162 MET cc_start: 0.6758 (mmm) cc_final: 0.6414 (mmm) REVERT: F 252 LYS cc_start: 0.8262 (mppt) cc_final: 0.7782 (mtmm) REVERT: F 417 ASP cc_start: 0.8056 (t70) cc_final: 0.7765 (t0) REVERT: F 425 LYS cc_start: 0.8253 (mtmm) cc_final: 0.8052 (mtpt) REVERT: F 468 THR cc_start: 0.7597 (m) cc_final: 0.7392 (m) REVERT: F 497 ASP cc_start: 0.7326 (m-30) cc_final: 0.7057 (t0) REVERT: F 503 MET cc_start: 0.8283 (mmm) cc_final: 0.7988 (mmm) REVERT: F 530 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: F 564 THR cc_start: 0.7679 (OUTLIER) cc_final: 0.7312 (t) REVERT: F 573 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7101 (tm-30) REVERT: F 717 GLU cc_start: 0.8223 (tp30) cc_final: 0.6801 (tp30) REVERT: F 770 GLU cc_start: 0.6284 (tp30) cc_final: 0.6051 (tp30) outliers start: 95 outliers final: 56 residues processed: 757 average time/residue: 0.5415 time to fit residues: 622.0846 Evaluate side-chains 758 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 698 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 660 ASN Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 723 GLU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain F residue 385 VAL Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 530 GLU Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 664 GLU Chi-restraints excluded: chain F residue 691 GLU Chi-restraints excluded: chain F residue 762 THR Chi-restraints excluded: chain F residue 765 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 352 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 315 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 361 optimal weight: 5.9990 chunk 292 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 380 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS A 135 GLN A 138 ASN B 338 GLN B 426 GLN C 311 ASN C 338 GLN C 353 ASN C 407 GLN C 660 ASN D 634 ASN E 233 ASN F 301 ASN F 426 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 34687 Z= 0.367 Angle : 0.614 8.886 47036 Z= 0.313 Chirality : 0.047 0.292 5455 Planarity : 0.005 0.063 6062 Dihedral : 9.394 174.613 4942 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.83 % Favored : 93.14 % Rotamer: Outliers : 2.95 % Allowed : 13.10 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.43 (0.13), residues: 4360 helix: 0.45 (0.13), residues: 1689 sheet: -0.63 (0.21), residues: 621 loop : -0.72 (0.14), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 515 HIS 0.014 0.001 HIS E 285 PHE 0.033 0.002 PHE E 578 TYR 0.024 0.002 TYR F 244 ARG 0.007 0.000 ARG F 596 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 718 time to evaluate : 4.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7135 (tm-30) cc_final: 0.6797 (tm-30) REVERT: A 329 ASP cc_start: 0.7728 (t70) cc_final: 0.7361 (t0) REVERT: A 600 GLU cc_start: 0.7163 (tp30) cc_final: 0.6939 (tp30) REVERT: A 660 ASN cc_start: 0.7420 (t0) cc_final: 0.7145 (t0) REVERT: A 695 LYS cc_start: 0.7686 (tmtt) cc_final: 0.7407 (tttt) REVERT: A 715 ARG cc_start: 0.7831 (mtm-85) cc_final: 0.7531 (mtm-85) REVERT: A 746 GLU cc_start: 0.7349 (pt0) cc_final: 0.7115 (pm20) REVERT: B 71 VAL cc_start: 0.7306 (OUTLIER) cc_final: 0.7081 (m) REVERT: B 263 ILE cc_start: 0.8848 (tp) cc_final: 0.8551 (tp) REVERT: B 322 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6553 (mm-30) REVERT: B 390 ASN cc_start: 0.7511 (t0) cc_final: 0.7297 (t0) REVERT: B 417 ASP cc_start: 0.7629 (m-30) cc_final: 0.7358 (m-30) REVERT: B 487 THR cc_start: 0.8207 (m) cc_final: 0.7831 (p) REVERT: B 770 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7229 (mm-30) REVERT: C 162 MET cc_start: 0.6264 (mtt) cc_final: 0.6047 (mtt) REVERT: C 329 ASP cc_start: 0.7331 (t0) cc_final: 0.7130 (t0) REVERT: C 553 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8383 (t) REVERT: C 737 MET cc_start: 0.7626 (mmm) cc_final: 0.7356 (mmt) REVERT: D 109 ILE cc_start: 0.7703 (mt) cc_final: 0.7428 (mt) REVERT: D 231 GLN cc_start: 0.7581 (mp-120) cc_final: 0.6941 (mp-120) REVERT: D 319 TYR cc_start: 0.7964 (m-80) cc_final: 0.7756 (m-80) REVERT: D 363 GLU cc_start: 0.6034 (mp0) cc_final: 0.5764 (mp0) REVERT: D 548 SER cc_start: 0.7942 (m) cc_final: 0.7614 (p) REVERT: D 704 GLU cc_start: 0.6517 (mp0) cc_final: 0.6198 (mp0) REVERT: E 37 ARG cc_start: 0.6671 (mtp85) cc_final: 0.5255 (tpt90) REVERT: E 103 ARG cc_start: 0.7919 (mtm-85) cc_final: 0.6976 (mtp180) REVERT: E 107 ASN cc_start: 0.7359 (t0) cc_final: 0.6685 (t0) REVERT: E 269 THR cc_start: 0.7656 (p) cc_final: 0.6798 (m) REVERT: E 338 GLN cc_start: 0.8099 (mt0) cc_final: 0.7841 (mt0) REVERT: E 419 ARG cc_start: 0.7171 (mtt90) cc_final: 0.6666 (mtm180) REVERT: E 453 VAL cc_start: 0.8078 (m) cc_final: 0.7582 (p) REVERT: E 495 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.5457 (pmm) REVERT: E 530 GLU cc_start: 0.6750 (tp30) cc_final: 0.6422 (tp30) REVERT: E 656 VAL cc_start: 0.7674 (m) cc_final: 0.7454 (p) REVERT: E 664 GLU cc_start: 0.6611 (mm-30) cc_final: 0.6220 (mm-30) REVERT: E 723 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6763 (tp30) REVERT: E 730 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6702 (tm-30) REVERT: E 737 MET cc_start: 0.5936 (mmm) cc_final: 0.5547 (mmm) REVERT: F 162 MET cc_start: 0.6789 (mmm) cc_final: 0.6257 (mmm) REVERT: F 252 LYS cc_start: 0.8280 (mppt) cc_final: 0.7706 (mtmm) REVERT: F 258 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7716 (mmmm) REVERT: F 399 LEU cc_start: 0.8322 (mp) cc_final: 0.8084 (mm) REVERT: F 417 ASP cc_start: 0.8102 (t70) cc_final: 0.7823 (t0) REVERT: F 419 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7224 (mtm180) REVERT: F 430 MET cc_start: 0.6255 (pmm) cc_final: 0.5999 (pmm) REVERT: F 468 THR cc_start: 0.7589 (m) cc_final: 0.7380 (m) REVERT: F 497 ASP cc_start: 0.7356 (m-30) cc_final: 0.7100 (t0) REVERT: F 503 MET cc_start: 0.8261 (mmm) cc_final: 0.7949 (mmm) REVERT: F 564 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7328 (t) REVERT: F 573 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7129 (tm-30) REVERT: F 596 ARG cc_start: 0.6601 (mtp85) cc_final: 0.6301 (mtp85) REVERT: F 641 LEU cc_start: 0.6070 (mm) cc_final: 0.5478 (mm) REVERT: F 717 GLU cc_start: 0.8201 (tp30) cc_final: 0.6768 (tp30) REVERT: F 770 GLU cc_start: 0.6334 (tp30) cc_final: 0.6081 (tp30) outliers start: 109 outliers final: 80 residues processed: 763 average time/residue: 0.5545 time to fit residues: 647.0127 Evaluate side-chains 787 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 702 time to evaluate : 3.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 691 GLU Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 269 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 272 SER Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 487 THR Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 536 LEU Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 698 LYS Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain C residue 757 ILE Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 159 MET Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 235 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 634 ASN Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 602 PHE Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 675 LEU Chi-restraints excluded: chain E residue 723 GLU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 664 GLU Chi-restraints excluded: chain F residue 691 GLU Chi-restraints excluded: chain F residue 765 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 142 optimal weight: 2.9990 chunk 381 optimal weight: 0.1980 chunk 83 optimal weight: 0.0570 chunk 248 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 423 optimal weight: 8.9990 chunk 351 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 222 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS A 135 GLN C 311 ASN C 332 ASN C 338 GLN C 353 ASN C 407 GLN C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 ASN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 34687 Z= 0.156 Angle : 0.541 8.837 47036 Z= 0.276 Chirality : 0.043 0.275 5455 Planarity : 0.004 0.056 6062 Dihedral : 9.078 176.745 4942 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.62 % Favored : 94.36 % Rotamer: Outliers : 2.25 % Allowed : 14.07 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.12 (0.13), residues: 4360 helix: 0.74 (0.13), residues: 1704 sheet: -0.45 (0.21), residues: 615 loop : -0.56 (0.14), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 515 HIS 0.009 0.001 HIS A 435 PHE 0.018 0.001 PHE C 750 TYR 0.023 0.001 TYR F 244 ARG 0.014 0.000 ARG E 603 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 731 time to evaluate : 3.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6819 (tm-30) REVERT: A 329 ASP cc_start: 0.7672 (t70) cc_final: 0.7319 (t0) REVERT: A 337 TYR cc_start: 0.7929 (m-10) cc_final: 0.7623 (m-10) REVERT: A 514 TYR cc_start: 0.8728 (m-80) cc_final: 0.8396 (m-80) REVERT: A 600 GLU cc_start: 0.7034 (tp30) cc_final: 0.6786 (tp30) REVERT: A 660 ASN cc_start: 0.7276 (t0) cc_final: 0.7035 (t0) REVERT: A 695 LYS cc_start: 0.7646 (tmtt) cc_final: 0.7340 (tttt) REVERT: A 715 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7306 (mtm180) REVERT: A 746 GLU cc_start: 0.7307 (pt0) cc_final: 0.7104 (pm20) REVERT: B 247 VAL cc_start: 0.7393 (OUTLIER) cc_final: 0.7148 (t) REVERT: B 263 ILE cc_start: 0.8831 (tp) cc_final: 0.8566 (tp) REVERT: B 282 ILE cc_start: 0.8506 (mt) cc_final: 0.8289 (mt) REVERT: B 322 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6545 (mm-30) REVERT: B 390 ASN cc_start: 0.7462 (t0) cc_final: 0.7187 (t0) REVERT: B 417 ASP cc_start: 0.7609 (m-30) cc_final: 0.7326 (m-30) REVERT: B 510 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7406 (mtp) REVERT: C 162 MET cc_start: 0.6162 (mtt) cc_final: 0.5947 (mtt) REVERT: C 329 ASP cc_start: 0.7330 (t0) cc_final: 0.7089 (t0) REVERT: C 553 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8390 (t) REVERT: C 664 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6550 (mt-10) REVERT: C 714 ASP cc_start: 0.7053 (m-30) cc_final: 0.6773 (m-30) REVERT: C 768 TYR cc_start: 0.7774 (t80) cc_final: 0.7489 (t80) REVERT: D 109 ILE cc_start: 0.7667 (mt) cc_final: 0.7423 (mt) REVERT: D 170 LYS cc_start: 0.6511 (mmtt) cc_final: 0.6191 (mmtp) REVERT: D 218 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6155 (mtp85) REVERT: D 231 GLN cc_start: 0.7568 (mp-120) cc_final: 0.6914 (mp-120) REVERT: D 363 GLU cc_start: 0.5926 (mp0) cc_final: 0.5633 (mp0) REVERT: D 548 SER cc_start: 0.7901 (m) cc_final: 0.7579 (p) REVERT: D 568 LYS cc_start: 0.7949 (mttm) cc_final: 0.7695 (mtpp) REVERT: D 704 GLU cc_start: 0.6525 (mp0) cc_final: 0.6224 (mp0) REVERT: E 37 ARG cc_start: 0.6463 (mtp85) cc_final: 0.5238 (tpt90) REVERT: E 103 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.6807 (mtp180) REVERT: E 107 ASN cc_start: 0.7324 (t0) cc_final: 0.6722 (t0) REVERT: E 269 THR cc_start: 0.7645 (p) cc_final: 0.6744 (m) REVERT: E 396 ASP cc_start: 0.7958 (t0) cc_final: 0.7735 (t0) REVERT: E 419 ARG cc_start: 0.6840 (mtt90) cc_final: 0.6315 (mtm-85) REVERT: E 453 VAL cc_start: 0.8027 (m) cc_final: 0.7528 (p) REVERT: E 495 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.4827 (pmm) REVERT: E 530 GLU cc_start: 0.6644 (tp30) cc_final: 0.6285 (tp30) REVERT: E 656 VAL cc_start: 0.7638 (m) cc_final: 0.7414 (p) REVERT: E 664 GLU cc_start: 0.6528 (mm-30) cc_final: 0.6118 (mm-30) REVERT: E 723 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6648 (tp30) REVERT: E 737 MET cc_start: 0.5609 (mmm) cc_final: 0.5268 (mmm) REVERT: F 162 MET cc_start: 0.6721 (mmm) cc_final: 0.6356 (mmm) REVERT: F 258 LYS cc_start: 0.7846 (mmmt) cc_final: 0.7630 (mmmm) REVERT: F 262 GLU cc_start: 0.6610 (mt-10) cc_final: 0.6366 (mt-10) REVERT: F 417 ASP cc_start: 0.8098 (t70) cc_final: 0.7781 (t0) REVERT: F 419 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7155 (mtm-85) REVERT: F 497 ASP cc_start: 0.7331 (m-30) cc_final: 0.7070 (t0) REVERT: F 503 MET cc_start: 0.8255 (mmm) cc_final: 0.7949 (mmm) REVERT: F 564 THR cc_start: 0.7611 (OUTLIER) cc_final: 0.7248 (t) REVERT: F 573 GLU cc_start: 0.7321 (tm-30) cc_final: 0.6981 (tm-30) REVERT: F 641 LEU cc_start: 0.6010 (mm) cc_final: 0.5438 (mm) REVERT: F 661 ARG cc_start: 0.6866 (mtm-85) cc_final: 0.6306 (mtm-85) outliers start: 83 outliers final: 55 residues processed: 767 average time/residue: 0.5428 time to fit residues: 634.3908 Evaluate side-chains 761 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 699 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 516 SER Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 150 LYS Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 723 GLU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 691 GLU Chi-restraints excluded: chain F residue 755 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 408 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 309 optimal weight: 7.9990 chunk 239 optimal weight: 0.1980 chunk 356 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 422 optimal weight: 20.0000 chunk 264 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 chunk 194 optimal weight: 0.5980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS A 135 GLN B 338 GLN B 426 GLN C 311 ASN C 338 GLN C 407 GLN C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 338 GLN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 34687 Z= 0.224 Angle : 0.555 9.461 47036 Z= 0.281 Chirality : 0.044 0.464 5455 Planarity : 0.005 0.067 6062 Dihedral : 9.066 179.112 4942 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.06 % Favored : 93.92 % Rotamer: Outliers : 2.22 % Allowed : 14.51 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 4360 helix: 0.70 (0.13), residues: 1725 sheet: -0.42 (0.21), residues: 631 loop : -0.54 (0.15), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 515 HIS 0.009 0.001 HIS E 285 PHE 0.019 0.001 PHE C 750 TYR 0.018 0.001 TYR E 236 ARG 0.011 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 709 time to evaluate : 3.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7176 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 329 ASP cc_start: 0.7690 (t70) cc_final: 0.7334 (t0) REVERT: A 337 TYR cc_start: 0.8013 (m-10) cc_final: 0.7753 (m-10) REVERT: A 600 GLU cc_start: 0.7034 (tp30) cc_final: 0.6805 (tp30) REVERT: A 660 ASN cc_start: 0.7299 (t0) cc_final: 0.7072 (t0) REVERT: A 695 LYS cc_start: 0.7654 (tmtt) cc_final: 0.7377 (tttt) REVERT: A 715 ARG cc_start: 0.7740 (mtm-85) cc_final: 0.7308 (mtm180) REVERT: A 746 GLU cc_start: 0.7333 (pt0) cc_final: 0.7115 (pm20) REVERT: B 263 ILE cc_start: 0.8849 (tp) cc_final: 0.8568 (tp) REVERT: B 282 ILE cc_start: 0.8513 (mt) cc_final: 0.8299 (mt) REVERT: B 322 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6558 (mm-30) REVERT: B 390 ASN cc_start: 0.7502 (t0) cc_final: 0.7248 (t0) REVERT: B 417 ASP cc_start: 0.7618 (m-30) cc_final: 0.7334 (m-30) REVERT: C 329 ASP cc_start: 0.7337 (t0) cc_final: 0.7113 (t0) REVERT: C 553 VAL cc_start: 0.8703 (OUTLIER) cc_final: 0.8415 (t) REVERT: C 664 GLU cc_start: 0.6842 (mt-10) cc_final: 0.6578 (mt-10) REVERT: C 714 ASP cc_start: 0.7061 (m-30) cc_final: 0.6758 (m-30) REVERT: D 109 ILE cc_start: 0.7729 (mt) cc_final: 0.7471 (mt) REVERT: D 170 LYS cc_start: 0.6560 (mmtt) cc_final: 0.6274 (mmtp) REVERT: D 218 ARG cc_start: 0.6898 (OUTLIER) cc_final: 0.6201 (mtp85) REVERT: D 231 GLN cc_start: 0.7551 (mp-120) cc_final: 0.6918 (mp-120) REVERT: D 363 GLU cc_start: 0.5978 (mp0) cc_final: 0.5694 (mp0) REVERT: D 548 SER cc_start: 0.7910 (m) cc_final: 0.7605 (p) REVERT: D 568 LYS cc_start: 0.7972 (mttm) cc_final: 0.7727 (mtpp) REVERT: D 704 GLU cc_start: 0.6449 (mp0) cc_final: 0.6166 (mp0) REVERT: E 37 ARG cc_start: 0.6482 (mtp85) cc_final: 0.5262 (tpt90) REVERT: E 103 ARG cc_start: 0.7852 (mtm-85) cc_final: 0.6814 (mtp180) REVERT: E 107 ASN cc_start: 0.7332 (t0) cc_final: 0.6626 (t0) REVERT: E 269 THR cc_start: 0.7714 (p) cc_final: 0.6858 (m) REVERT: E 419 ARG cc_start: 0.6925 (mtt90) cc_final: 0.6478 (mtm180) REVERT: E 453 VAL cc_start: 0.8032 (m) cc_final: 0.7599 (p) REVERT: E 495 MET cc_start: 0.6114 (OUTLIER) cc_final: 0.4923 (pmm) REVERT: E 528 MET cc_start: 0.7953 (mmm) cc_final: 0.7199 (tpp) REVERT: E 530 GLU cc_start: 0.6661 (tp30) cc_final: 0.6305 (tp30) REVERT: E 532 ILE cc_start: 0.7998 (mm) cc_final: 0.7562 (pt) REVERT: E 656 VAL cc_start: 0.7655 (m) cc_final: 0.7418 (p) REVERT: E 664 GLU cc_start: 0.6516 (mm-30) cc_final: 0.6120 (mm-30) REVERT: E 737 MET cc_start: 0.5641 (mmm) cc_final: 0.5321 (mmm) REVERT: F 162 MET cc_start: 0.6678 (mmm) cc_final: 0.6339 (mmm) REVERT: F 258 LYS cc_start: 0.7847 (mmmt) cc_final: 0.7622 (mmmm) REVERT: F 262 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6363 (mt-10) REVERT: F 399 LEU cc_start: 0.8331 (mt) cc_final: 0.8116 (mm) REVERT: F 417 ASP cc_start: 0.8101 (t70) cc_final: 0.7797 (t0) REVERT: F 503 MET cc_start: 0.8254 (mmm) cc_final: 0.7942 (mmm) REVERT: F 564 THR cc_start: 0.7606 (OUTLIER) cc_final: 0.7237 (t) REVERT: F 573 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7020 (tm-30) REVERT: F 661 ARG cc_start: 0.6893 (mtm-85) cc_final: 0.6349 (mtm-85) REVERT: F 717 GLU cc_start: 0.8132 (tp30) cc_final: 0.6914 (tp30) outliers start: 82 outliers final: 65 residues processed: 747 average time/residue: 0.5436 time to fit residues: 616.8931 Evaluate side-chains 775 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 706 time to evaluate : 3.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 158 ILE Chi-restraints excluded: chain C residue 257 LEU Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 531 MET Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 553 VAL Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 254 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 660 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 640 LEU Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 745 VAL Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 261 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 252 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 82 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 268 optimal weight: 0.0030 chunk 287 optimal weight: 0.0070 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 331 optimal weight: 10.0000 overall best weight: 0.5008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS A 135 GLN B 338 GLN B 426 GLN C 332 ASN C 338 GLN C 407 GLN C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 34687 Z= 0.157 Angle : 0.533 9.425 47036 Z= 0.268 Chirality : 0.043 0.424 5455 Planarity : 0.004 0.069 6062 Dihedral : 8.886 177.038 4942 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 2.14 % Allowed : 14.86 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.07 (0.13), residues: 4360 helix: 0.88 (0.13), residues: 1725 sheet: -0.31 (0.21), residues: 620 loop : -0.49 (0.15), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 515 HIS 0.007 0.001 HIS E 285 PHE 0.015 0.001 PHE F 578 TYR 0.015 0.001 TYR D 768 ARG 0.013 0.000 ARG B 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 708 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 329 ASP cc_start: 0.7658 (t70) cc_final: 0.7318 (t0) REVERT: A 337 TYR cc_start: 0.7866 (m-10) cc_final: 0.7539 (m-10) REVERT: A 514 TYR cc_start: 0.8730 (m-80) cc_final: 0.8426 (m-80) REVERT: A 600 GLU cc_start: 0.6979 (tp30) cc_final: 0.6748 (tp30) REVERT: A 606 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7535 (mtm-85) REVERT: A 660 ASN cc_start: 0.7250 (t0) cc_final: 0.7022 (t0) REVERT: A 695 LYS cc_start: 0.7627 (tmtt) cc_final: 0.7335 (tttt) REVERT: A 715 ARG cc_start: 0.7721 (mtm-85) cc_final: 0.7289 (mtm180) REVERT: B 263 ILE cc_start: 0.8819 (tp) cc_final: 0.8547 (tp) REVERT: B 322 GLU cc_start: 0.6859 (mm-30) cc_final: 0.6601 (mm-30) REVERT: B 390 ASN cc_start: 0.7494 (t0) cc_final: 0.7223 (t0) REVERT: B 417 ASP cc_start: 0.7618 (m-30) cc_final: 0.7346 (m-30) REVERT: B 510 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7381 (mtp) REVERT: C 162 MET cc_start: 0.6266 (mtt) cc_final: 0.5908 (mtt) REVERT: C 329 ASP cc_start: 0.7337 (t0) cc_final: 0.7052 (t0) REVERT: C 332 ASN cc_start: 0.7524 (m-40) cc_final: 0.6971 (m110) REVERT: C 664 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6578 (mt-10) REVERT: D 84 ARG cc_start: 0.7410 (mmt180) cc_final: 0.7203 (mpt180) REVERT: D 109 ILE cc_start: 0.7697 (mt) cc_final: 0.7456 (mt) REVERT: D 231 GLN cc_start: 0.7536 (mp-120) cc_final: 0.6910 (mp-120) REVERT: D 363 GLU cc_start: 0.5911 (mp0) cc_final: 0.5654 (mp0) REVERT: D 548 SER cc_start: 0.7914 (m) cc_final: 0.7620 (p) REVERT: D 704 GLU cc_start: 0.6456 (mp0) cc_final: 0.6170 (mp0) REVERT: E 37 ARG cc_start: 0.6383 (mtp85) cc_final: 0.5547 (tpt90) REVERT: E 103 ARG cc_start: 0.7880 (mtm-85) cc_final: 0.6816 (mtp180) REVERT: E 107 ASN cc_start: 0.7328 (t0) cc_final: 0.6616 (t0) REVERT: E 269 THR cc_start: 0.7731 (p) cc_final: 0.6849 (m) REVERT: E 336 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7702 (ttpp) REVERT: E 495 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.4873 (pmm) REVERT: E 528 MET cc_start: 0.7928 (mmm) cc_final: 0.7591 (mmm) REVERT: E 664 GLU cc_start: 0.6447 (mm-30) cc_final: 0.6066 (mm-30) REVERT: E 737 MET cc_start: 0.5580 (mmm) cc_final: 0.5293 (mmm) REVERT: F 258 LYS cc_start: 0.7809 (mmmt) cc_final: 0.7592 (mmmm) REVERT: F 399 LEU cc_start: 0.8304 (mt) cc_final: 0.8098 (mm) REVERT: F 417 ASP cc_start: 0.8080 (t70) cc_final: 0.7777 (t0) REVERT: F 419 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7332 (mtp180) REVERT: F 497 ASP cc_start: 0.7235 (m-30) cc_final: 0.7000 (t0) REVERT: F 503 MET cc_start: 0.8249 (mmm) cc_final: 0.7929 (mmm) REVERT: F 564 THR cc_start: 0.7544 (OUTLIER) cc_final: 0.7193 (t) REVERT: F 573 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7003 (tm-30) REVERT: F 661 ARG cc_start: 0.6860 (mtm-85) cc_final: 0.6408 (mtm-85) REVERT: F 717 GLU cc_start: 0.8111 (tp30) cc_final: 0.6891 (tp30) outliers start: 79 outliers final: 57 residues processed: 745 average time/residue: 0.5372 time to fit residues: 608.1711 Evaluate side-chains 764 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 704 time to evaluate : 3.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 33 GLU Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 374 MET Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 660 ASN Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain D residue 660 ASN Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 460 LEU Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Chi-restraints excluded: chain F residue 664 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 384 optimal weight: 3.9990 chunk 404 optimal weight: 5.9990 chunk 368 optimal weight: 30.0000 chunk 393 optimal weight: 0.2980 chunk 236 optimal weight: 0.7980 chunk 171 optimal weight: 0.0010 chunk 308 optimal weight: 2.9990 chunk 120 optimal weight: 0.9980 chunk 355 optimal weight: 7.9990 chunk 372 optimal weight: 1.9990 chunk 392 optimal weight: 0.9980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS B 338 GLN B 426 GLN C 311 ASN C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 34687 Z= 0.166 Angle : 0.538 10.302 47036 Z= 0.269 Chirality : 0.042 0.244 5455 Planarity : 0.005 0.082 6062 Dihedral : 8.798 178.301 4942 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.37 % Favored : 94.61 % Rotamer: Outliers : 2.11 % Allowed : 14.88 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.16 (0.13), residues: 4360 helix: 0.97 (0.13), residues: 1712 sheet: -0.28 (0.21), residues: 639 loop : -0.42 (0.15), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 515 HIS 0.010 0.001 HIS E 285 PHE 0.018 0.001 PHE F 578 TYR 0.015 0.001 TYR D 768 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 700 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6791 (tm-30) REVERT: A 329 ASP cc_start: 0.7654 (t70) cc_final: 0.7316 (t0) REVERT: A 337 TYR cc_start: 0.7851 (m-10) cc_final: 0.7533 (m-10) REVERT: A 514 TYR cc_start: 0.8731 (m-80) cc_final: 0.8409 (m-80) REVERT: A 600 GLU cc_start: 0.6972 (tp30) cc_final: 0.6746 (tp30) REVERT: A 606 ARG cc_start: 0.7803 (ttm-80) cc_final: 0.7556 (mtm-85) REVERT: A 660 ASN cc_start: 0.7258 (t0) cc_final: 0.7029 (t0) REVERT: A 695 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7335 (tttt) REVERT: A 715 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7294 (mtm180) REVERT: B 263 ILE cc_start: 0.8827 (tp) cc_final: 0.8554 (tp) REVERT: B 322 GLU cc_start: 0.6898 (mm-30) cc_final: 0.6650 (mm-30) REVERT: B 390 ASN cc_start: 0.7514 (t0) cc_final: 0.7249 (t0) REVERT: B 406 ASP cc_start: 0.7081 (m-30) cc_final: 0.6872 (m-30) REVERT: B 417 ASP cc_start: 0.7628 (m-30) cc_final: 0.7338 (m-30) REVERT: B 510 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7465 (mtp) REVERT: C 329 ASP cc_start: 0.7345 (t0) cc_final: 0.7104 (t0) REVERT: C 664 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6553 (mt-10) REVERT: C 768 TYR cc_start: 0.7792 (t80) cc_final: 0.7425 (t80) REVERT: D 84 ARG cc_start: 0.7415 (mmt180) cc_final: 0.7200 (mpt180) REVERT: D 109 ILE cc_start: 0.7713 (mt) cc_final: 0.7459 (mt) REVERT: D 218 ARG cc_start: 0.6790 (OUTLIER) cc_final: 0.6214 (mtp85) REVERT: D 231 GLN cc_start: 0.7528 (mp-120) cc_final: 0.6897 (mp-120) REVERT: D 363 GLU cc_start: 0.5973 (mp0) cc_final: 0.5654 (mp0) REVERT: D 377 MET cc_start: 0.6914 (mtm) cc_final: 0.6360 (mtm) REVERT: D 497 ASP cc_start: 0.7251 (t0) cc_final: 0.7001 (t0) REVERT: D 548 SER cc_start: 0.7912 (m) cc_final: 0.7630 (p) REVERT: D 704 GLU cc_start: 0.6491 (mp0) cc_final: 0.6163 (mp0) REVERT: E 37 ARG cc_start: 0.6357 (mtp85) cc_final: 0.5571 (tpt90) REVERT: E 107 ASN cc_start: 0.7333 (t0) cc_final: 0.6629 (t0) REVERT: E 269 THR cc_start: 0.7736 (p) cc_final: 0.6867 (m) REVERT: E 336 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7706 (ttpp) REVERT: E 495 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.4802 (pmm) REVERT: E 528 MET cc_start: 0.7869 (mmm) cc_final: 0.7176 (tpp) REVERT: E 532 ILE cc_start: 0.7900 (mm) cc_final: 0.7448 (pt) REVERT: E 664 GLU cc_start: 0.6407 (mm-30) cc_final: 0.6004 (mm-30) REVERT: E 737 MET cc_start: 0.5558 (mmm) cc_final: 0.5268 (mmm) REVERT: F 399 LEU cc_start: 0.8311 (mt) cc_final: 0.8104 (mm) REVERT: F 417 ASP cc_start: 0.8067 (t70) cc_final: 0.7743 (t0) REVERT: F 419 ARG cc_start: 0.7773 (mtm-85) cc_final: 0.7241 (mtp180) REVERT: F 434 ARG cc_start: 0.6147 (ttp80) cc_final: 0.5815 (ttp80) REVERT: F 503 MET cc_start: 0.8250 (mmm) cc_final: 0.7930 (mmm) REVERT: F 564 THR cc_start: 0.7491 (OUTLIER) cc_final: 0.7148 (t) REVERT: F 573 GLU cc_start: 0.7327 (tm-30) cc_final: 0.6969 (tm-30) REVERT: F 661 ARG cc_start: 0.6877 (mtm-85) cc_final: 0.6428 (mtm-85) REVERT: F 699 LYS cc_start: 0.8753 (mmtp) cc_final: 0.8387 (mttm) REVERT: F 717 GLU cc_start: 0.8122 (tp30) cc_final: 0.6812 (tp30) outliers start: 78 outliers final: 60 residues processed: 738 average time/residue: 0.5500 time to fit residues: 620.0921 Evaluate side-chains 756 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 692 time to evaluate : 3.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LYS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 252 LYS Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 410 GLU Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 258 optimal weight: 0.6980 chunk 415 optimal weight: 0.9980 chunk 253 optimal weight: 0.9980 chunk 197 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 436 optimal weight: 10.0000 chunk 401 optimal weight: 0.9990 chunk 347 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 268 optimal weight: 0.0670 chunk 213 optimal weight: 2.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 34687 Z= 0.177 Angle : 0.540 9.722 47036 Z= 0.270 Chirality : 0.043 0.197 5455 Planarity : 0.005 0.076 6062 Dihedral : 8.728 178.760 4942 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 1.92 % Allowed : 15.21 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.20 (0.13), residues: 4360 helix: 1.02 (0.13), residues: 1705 sheet: -0.23 (0.22), residues: 626 loop : -0.43 (0.15), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 515 HIS 0.009 0.001 HIS E 285 PHE 0.018 0.001 PHE F 578 TYR 0.019 0.001 TYR C 444 ARG 0.006 0.000 ARG A 365 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8720 Ramachandran restraints generated. 4360 Oldfield, 0 Emsley, 4360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 707 time to evaluate : 3.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 240 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6792 (tm-30) REVERT: A 276 VAL cc_start: 0.8430 (t) cc_final: 0.7957 (p) REVERT: A 304 ASN cc_start: 0.7126 (OUTLIER) cc_final: 0.6900 (m110) REVERT: A 329 ASP cc_start: 0.7679 (t70) cc_final: 0.7322 (t0) REVERT: A 337 TYR cc_start: 0.7873 (m-10) cc_final: 0.7538 (m-10) REVERT: A 514 TYR cc_start: 0.8733 (m-80) cc_final: 0.8399 (m-80) REVERT: A 600 GLU cc_start: 0.6958 (tp30) cc_final: 0.6741 (tp30) REVERT: A 606 ARG cc_start: 0.7811 (ttm-80) cc_final: 0.7570 (mtm-85) REVERT: A 660 ASN cc_start: 0.7237 (t0) cc_final: 0.7002 (t0) REVERT: A 695 LYS cc_start: 0.7632 (tmtt) cc_final: 0.7338 (tttt) REVERT: A 715 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7298 (mtm180) REVERT: A 744 LYS cc_start: 0.8007 (ptmt) cc_final: 0.7738 (ttpp) REVERT: B 263 ILE cc_start: 0.8782 (tp) cc_final: 0.8523 (tp) REVERT: B 322 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6688 (mm-30) REVERT: B 390 ASN cc_start: 0.7528 (t0) cc_final: 0.7253 (t0) REVERT: B 417 ASP cc_start: 0.7627 (m-30) cc_final: 0.7339 (m-30) REVERT: B 510 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7424 (mtp) REVERT: B 714 ASP cc_start: 0.7792 (m-30) cc_final: 0.7501 (m-30) REVERT: C 329 ASP cc_start: 0.7335 (t0) cc_final: 0.7025 (t0) REVERT: C 332 ASN cc_start: 0.7511 (m110) cc_final: 0.6991 (m110) REVERT: C 664 GLU cc_start: 0.6733 (mt-10) cc_final: 0.6414 (mt-10) REVERT: C 768 TYR cc_start: 0.7803 (t80) cc_final: 0.7311 (t80) REVERT: D 109 ILE cc_start: 0.7765 (mt) cc_final: 0.7513 (mt) REVERT: D 170 LYS cc_start: 0.6426 (mmtt) cc_final: 0.6037 (mmtp) REVERT: D 218 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6205 (mtp85) REVERT: D 231 GLN cc_start: 0.7539 (mp-120) cc_final: 0.7011 (mp-120) REVERT: D 363 GLU cc_start: 0.6008 (mp0) cc_final: 0.5688 (mp0) REVERT: D 497 ASP cc_start: 0.7178 (t0) cc_final: 0.6963 (t0) REVERT: D 548 SER cc_start: 0.7924 (m) cc_final: 0.7652 (p) REVERT: D 704 GLU cc_start: 0.6501 (mp0) cc_final: 0.6160 (mp0) REVERT: E 37 ARG cc_start: 0.6318 (mtp85) cc_final: 0.5512 (tpt90) REVERT: E 267 GLN cc_start: 0.6947 (tp-100) cc_final: 0.6734 (tp-100) REVERT: E 269 THR cc_start: 0.7796 (p) cc_final: 0.6779 (m) REVERT: E 495 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.4923 (pmm) REVERT: E 528 MET cc_start: 0.7880 (mmm) cc_final: 0.7294 (tpp) REVERT: E 532 ILE cc_start: 0.7891 (mm) cc_final: 0.7447 (pt) REVERT: E 664 GLU cc_start: 0.6377 (mm-30) cc_final: 0.5993 (mm-30) REVERT: E 737 MET cc_start: 0.5537 (mmm) cc_final: 0.5240 (mmm) REVERT: F 162 MET cc_start: 0.6777 (mmm) cc_final: 0.6547 (mmm) REVERT: F 375 ASP cc_start: 0.6614 (p0) cc_final: 0.6401 (p0) REVERT: F 417 ASP cc_start: 0.8041 (t70) cc_final: 0.7707 (t0) REVERT: F 419 ARG cc_start: 0.7787 (mtm-85) cc_final: 0.6920 (ttp-170) REVERT: F 420 PHE cc_start: 0.8010 (t80) cc_final: 0.7762 (t80) REVERT: F 430 MET cc_start: 0.6505 (pmm) cc_final: 0.6035 (pmm) REVERT: F 434 ARG cc_start: 0.6120 (ttp80) cc_final: 0.5788 (ttp80) REVERT: F 503 MET cc_start: 0.8246 (mmm) cc_final: 0.7921 (mmm) REVERT: F 564 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7157 (t) REVERT: F 573 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6996 (tm-30) REVERT: F 661 ARG cc_start: 0.6879 (mtm-85) cc_final: 0.6432 (mtm-85) REVERT: F 699 LYS cc_start: 0.8749 (mmtp) cc_final: 0.8354 (mttm) REVERT: F 717 GLU cc_start: 0.8107 (tp30) cc_final: 0.6783 (tp30) outliers start: 71 outliers final: 56 residues processed: 745 average time/residue: 0.5719 time to fit residues: 654.5007 Evaluate side-chains 754 residues out of total 3695 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 693 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 109 ILE Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 523 GLU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 708 ASP Chi-restraints excluded: chain B residue 46 LYS Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 473 LEU Chi-restraints excluded: chain B residue 510 MET Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain C residue 49 CYS Chi-restraints excluded: chain C residue 290 THR Chi-restraints excluded: chain C residue 361 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 523 GLU Chi-restraints excluded: chain C residue 533 GLN Chi-restraints excluded: chain C residue 654 VAL Chi-restraints excluded: chain C residue 701 ASN Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain C residue 740 LEU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 218 ARG Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 255 GLU Chi-restraints excluded: chain D residue 276 VAL Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 406 ASP Chi-restraints excluded: chain D residue 448 LYS Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 541 THR Chi-restraints excluded: chain D residue 654 VAL Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 LYS Chi-restraints excluded: chain E residue 301 ASN Chi-restraints excluded: chain E residue 329 ASP Chi-restraints excluded: chain E residue 383 VAL Chi-restraints excluded: chain E residue 389 THR Chi-restraints excluded: chain E residue 436 VAL Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 563 LYS Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 742 VAL Chi-restraints excluded: chain E residue 769 TYR Chi-restraints excluded: chain F residue 307 VAL Chi-restraints excluded: chain F residue 377 MET Chi-restraints excluded: chain F residue 488 LEU Chi-restraints excluded: chain F residue 513 VAL Chi-restraints excluded: chain F residue 527 LYS Chi-restraints excluded: chain F residue 564 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 438 random chunks: chunk 276 optimal weight: 20.0000 chunk 370 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 320 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 145 optimal weight: 0.5980 chunk 357 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 91 HIS C 426 GLN ** C 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 353 ASN D 533 GLN D 634 ASN E 233 ASN ** E 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 301 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.171305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.135218 restraints weight = 48792.327| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.22 r_work: 0.3464 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 34687 Z= 0.269 Angle : 0.575 9.557 47036 Z= 0.288 Chirality : 0.044 0.210 5455 Planarity : 0.005 0.073 6062 Dihedral : 8.845 176.656 4942 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 2.03 % Allowed : 15.62 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.09 (0.13), residues: 4360 helix: 0.88 (0.13), residues: 1711 sheet: -0.31 (0.21), residues: 640 loop : -0.43 (0.15), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 515 HIS 0.009 0.001 HIS E 285 PHE 0.019 0.001 PHE C 750 TYR 0.020 0.001 TYR C 444 ARG 0.006 0.000 ARG A 365 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10624.67 seconds wall clock time: 190 minutes 44.37 seconds (11444.37 seconds total)