Starting phenix.real_space_refine on Thu Feb 22 06:28:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7s_24302/02_2024/7r7s_24302_updated.pdb" } resolution = 4.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.030 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 36 5.49 5 S 180 5.16 5 C 20791 2.51 5 N 5916 2.21 5 O 6316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 65": "NH1" <-> "NH2" Residue "A TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 625": "NH1" <-> "NH2" Residue "A ARG 635": "NH1" <-> "NH2" Residue "A GLU 704": "OE1" <-> "OE2" Residue "A ARG 708": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 741": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "B TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B ASP 431": "OD1" <-> "OD2" Residue "B ASP 438": "OD1" <-> "OD2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 609": "OD1" <-> "OD2" Residue "B ARG 625": "NH1" <-> "NH2" Residue "B ARG 635": "NH1" <-> "NH2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 700": "NH1" <-> "NH2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "C GLU 200": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 625": "NH1" <-> "NH2" Residue "C PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 708": "NH1" <-> "NH2" Residue "C ARG 733": "NH1" <-> "NH2" Residue "C ARG 741": "NH1" <-> "NH2" Residue "C ASP 751": "OD1" <-> "OD2" Residue "C ARG 753": "NH1" <-> "NH2" Residue "C PHE 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 196": "OE1" <-> "OE2" Residue "D TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ASP 354": "OD1" <-> "OD2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ARG 465": "NH1" <-> "NH2" Residue "D GLU 470": "OE1" <-> "OE2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ARG 625": "NH1" <-> "NH2" Residue "D ARG 638": "NH1" <-> "NH2" Residue "D PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 704": "OE1" <-> "OE2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E ASP 564": "OD1" <-> "OD2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E ARG 625": "NH1" <-> "NH2" Residue "E ASP 630": "OD1" <-> "OD2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ASP 107": "OD1" <-> "OD2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "F PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 560": "NH1" <-> "NH2" Residue "F PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 625": "NH1" <-> "NH2" Residue "F ARG 662": "NH1" <-> "NH2" Residue "F PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 708": "NH1" <-> "NH2" Residue "F ARG 733": "NH1" <-> "NH2" Residue "F PHE 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 741": "NH1" <-> "NH2" Residue "F ARG 753": "NH1" <-> "NH2" Residue "I PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 347": "OE1" <-> "OE2" Residue "J PHE 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 347": "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: 33239 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 722, 5680 Classifications: {'peptide': 722} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 681} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 4304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4304 Classifications: {'peptide': 551} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 521} Chain breaks: 4 Chain: "C" Number of atoms: 4272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4272 Classifications: {'peptide': 546} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 516} Chain breaks: 2 Chain: "D" Number of atoms: 5662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 721, 5662 Classifications: {'peptide': 721} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 680} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 5632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 717, 5632 Classifications: {'peptide': 717} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 677} Chain breaks: 4 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 5757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 733, 5757 Classifications: {'peptide': 733} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 692} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 802 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 83 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 758 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 99} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 16.49, per 1000 atoms: 0.50 Number of scatterers: 33239 At special positions: 0 Unit cell: (128.583, 168.147, 176.625, 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 180 16.00 P 36 15.00 O 6316 8.00 N 5916 7.00 C 20791 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.12 Conformation dependent library (CDL) restraints added in 5.6 seconds 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 162 helices and 27 sheets defined 35.9% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 133 through 135 No H-bonds generated for 'chain 'A' and resid 133 through 135' Processing helix chain 'A' and resid 192 through 196 Processing helix chain 'A' and resid 210 through 219 Processing helix chain 'A' and resid 251 through 262 Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 286 through 293 removed outlier: 3.657A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 309 No H-bonds generated for 'chain 'A' and resid 306 through 309' Processing helix chain 'A' and resid 319 through 333 removed outlier: 4.003A pdb=" N ASP A 333 " --> pdb=" O LEU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 384 Processing helix chain 'A' and resid 398 through 401 No H-bonds generated for 'chain 'A' and resid 398 through 401' Processing helix chain 'A' and resid 408 through 424 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 498 Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 501 through 504 No H-bonds generated for 'chain 'A' and resid 501 through 504' Processing helix chain 'A' and resid 525 through 535 removed outlier: 3.751A pdb=" N LYS A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 552 removed outlier: 3.564A pdb=" N LEU A 547 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 550 " --> pdb=" O LEU A 547 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE A 552 " --> pdb=" O THR A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 568 Processing helix chain 'A' and resid 579 through 585 removed outlier: 3.626A pdb=" N ALA A 583 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 584 " --> pdb=" O ASP A 580 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 579 through 585' Processing helix chain 'A' and resid 599 through 609 removed outlier: 3.738A pdb=" N GLN A 603 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 650 through 658 removed outlier: 4.426A pdb=" N ARG A 653 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 654 " --> pdb=" O LYS A 651 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA A 655 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A 656 " --> pdb=" O ARG A 653 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 657 " --> pdb=" O VAL A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 removed outlier: 4.107A pdb=" N ALA A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 712 Processing helix chain 'A' and resid 733 through 741 Processing helix chain 'A' and resid 749 through 757 Processing helix chain 'B' and resid 210 through 223 removed outlier: 4.147A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 251 through 262 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 286 through 293 Processing helix chain 'B' and resid 306 through 309 No H-bonds generated for 'chain 'B' and resid 306 through 309' Processing helix chain 'B' and resid 319 through 334 removed outlier: 4.360A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 384 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 408 through 424 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 476 through 478 No H-bonds generated for 'chain 'B' and resid 476 through 478' Processing helix chain 'B' and resid 483 through 497 removed outlier: 3.611A pdb=" N GLU B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR B 495 " --> pdb=" O GLU B 491 " (cutoff:3.500A) Proline residue: B 496 - end of helix Processing helix chain 'B' and resid 524 through 535 Processing helix chain 'B' and resid 544 through 552 removed outlier: 3.772A pdb=" N MET B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TRP B 551 " --> pdb=" O LEU B 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 568 Processing helix chain 'B' and resid 579 through 583 Processing helix chain 'B' and resid 597 through 609 removed outlier: 3.580A pdb=" N ILE B 601 " --> pdb=" O ASP B 598 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET B 608 " --> pdb=" O LEU B 605 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASP B 609 " --> pdb=" O THR B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 removed outlier: 4.421A pdb=" N ARG B 653 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 677 Processing helix chain 'B' and resid 687 through 711 Processing helix chain 'B' and resid 733 through 741 removed outlier: 3.718A pdb=" N ARG B 741 " --> pdb=" O GLU B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 760 removed outlier: 3.515A pdb=" N ALA B 759 " --> pdb=" O TYR B 755 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 210 through 219 Processing helix chain 'C' and resid 251 through 262 removed outlier: 3.681A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.904A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 309 No H-bonds generated for 'chain 'C' and resid 306 through 309' Processing helix chain 'C' and resid 319 through 333 removed outlier: 4.455A pdb=" N ASP C 333 " --> pdb=" O LEU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 358 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 398 through 402 Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 476 through 478 No H-bonds generated for 'chain 'C' and resid 476 through 478' Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 495 through 498 No H-bonds generated for 'chain 'C' and resid 495 through 498' Processing helix chain 'C' and resid 526 through 535 Processing helix chain 'C' and resid 544 through 551 removed outlier: 3.897A pdb=" N LEU C 548 " --> pdb=" O GLY C 544 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 549 " --> pdb=" O PRO C 545 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N MET C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 568 removed outlier: 3.567A pdb=" N VAL C 559 " --> pdb=" O GLU C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 579 through 587 Processing helix chain 'C' and resid 600 through 610 removed outlier: 3.726A pdb=" N ASP C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLY C 610 " --> pdb=" O THR C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 650 through 659 removed outlier: 4.476A pdb=" N ARG C 653 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N VAL C 654 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ILE C 656 " --> pdb=" O ARG C 653 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA C 659 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 672 through 677 Processing helix chain 'C' and resid 687 through 712 removed outlier: 3.512A pdb=" N ILE C 703 " --> pdb=" O ARG C 700 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG C 709 " --> pdb=" O GLU C 706 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU C 712 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 removed outlier: 4.026A pdb=" N ARG C 741 " --> pdb=" O GLU C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 757 Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.535A pdb=" N ASN D 90 " --> pdb=" O ARG D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 210 through 219 Processing helix chain 'D' and resid 251 through 262 removed outlier: 3.521A pdb=" N ALA D 255 " --> pdb=" O LYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 283 through 295 removed outlier: 6.083A pdb=" N LYS D 288 " --> pdb=" O SER D 284 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 294 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LYS D 295 " --> pdb=" O GLU D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 309 No H-bonds generated for 'chain 'D' and resid 306 through 309' Processing helix chain 'D' and resid 319 through 334 removed outlier: 4.119A pdb=" N ASP D 333 " --> pdb=" O LEU D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 374 through 387 removed outlier: 4.091A pdb=" N LYS D 386 " --> pdb=" O GLN D 382 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ASN D 387 " --> pdb=" O ILE D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 402 Processing helix chain 'D' and resid 408 through 423 Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 476 through 478 No H-bonds generated for 'chain 'D' and resid 476 through 478' Processing helix chain 'D' and resid 483 through 498 removed outlier: 4.549A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 524 through 534 Processing helix chain 'D' and resid 544 through 552 Processing helix chain 'D' and resid 557 through 568 Processing helix chain 'D' and resid 579 through 585 removed outlier: 3.910A pdb=" N ALA D 585 " --> pdb=" O SER D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 606 Processing helix chain 'D' and resid 653 through 658 Processing helix chain 'D' and resid 672 through 677 removed outlier: 3.663A pdb=" N ALA D 676 " --> pdb=" O LEU D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 712 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 757 Processing helix chain 'E' and resid 43 through 49 Processing helix chain 'E' and resid 86 through 92 Processing helix chain 'E' and resid 135 through 138 No H-bonds generated for 'chain 'E' and resid 135 through 138' Processing helix chain 'E' and resid 192 through 196 Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 210 through 219 Processing helix chain 'E' and resid 251 through 261 removed outlier: 3.660A pdb=" N ALA E 255 " --> pdb=" O LYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 286 through 295 removed outlier: 3.914A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 309 No H-bonds generated for 'chain 'E' and resid 306 through 309' Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 355 through 358 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 398 through 402 Processing helix chain 'E' and resid 408 through 425 Processing helix chain 'E' and resid 449 through 457 Processing helix chain 'E' and resid 476 through 478 No H-bonds generated for 'chain 'E' and resid 476 through 478' Processing helix chain 'E' and resid 484 through 497 removed outlier: 4.215A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 500 through 502 No H-bonds generated for 'chain 'E' and resid 500 through 502' Processing helix chain 'E' and resid 524 through 534 removed outlier: 3.781A pdb=" N ALA E 528 " --> pdb=" O LYS E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 552 removed outlier: 3.620A pdb=" N LEU E 548 " --> pdb=" O GLY E 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 557 through 568 Processing helix chain 'E' and resid 579 through 584 Processing helix chain 'E' and resid 600 through 610 removed outlier: 3.658A pdb=" N ASP E 609 " --> pdb=" O LEU E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 658 Processing helix chain 'E' and resid 672 through 678 Processing helix chain 'E' and resid 688 through 712 Processing helix chain 'E' and resid 733 through 741 removed outlier: 3.920A pdb=" N ARG E 741 " --> pdb=" O GLU E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 749 through 760 removed outlier: 5.293A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 86 through 92 Processing helix chain 'F' and resid 210 through 219 Processing helix chain 'F' and resid 251 through 262 Processing helix chain 'F' and resid 271 through 274 No H-bonds generated for 'chain 'F' and resid 271 through 274' Processing helix chain 'F' and resid 286 through 293 removed outlier: 3.886A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 309 No H-bonds generated for 'chain 'F' and resid 306 through 309' Processing helix chain 'F' and resid 319 through 334 removed outlier: 4.239A pdb=" N ASP F 333 " --> pdb=" O LEU F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 397 through 402 Processing helix chain 'F' and resid 408 through 424 Processing helix chain 'F' and resid 442 through 444 No H-bonds generated for 'chain 'F' and resid 442 through 444' Processing helix chain 'F' and resid 449 through 457 Processing helix chain 'F' and resid 476 through 478 No H-bonds generated for 'chain 'F' and resid 476 through 478' Processing helix chain 'F' and resid 483 through 497 removed outlier: 3.686A pdb=" N GLU F 491 " --> pdb=" O ARG F 487 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N TYR F 495 " --> pdb=" O GLU F 491 " (cutoff:3.500A) Proline residue: F 496 - end of helix Processing helix chain 'F' and resid 500 through 505 Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 removed outlier: 4.092A pdb=" N MET F 550 " --> pdb=" O GLU F 546 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TRP F 551 " --> pdb=" O LEU F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 4.204A pdb=" N ARG F 586 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 610 Processing helix chain 'F' and resid 650 through 655 removed outlier: 4.299A pdb=" N ARG F 653 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 654 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA F 655 " --> pdb=" O SER F 652 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 650 through 655' Processing helix chain 'F' and resid 672 through 678 removed outlier: 3.551A pdb=" N LEU F 675 " --> pdb=" O LEU F 672 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 676 " --> pdb=" O GLU F 673 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET F 678 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 687 through 712 Processing helix chain 'F' and resid 733 through 741 Processing helix chain 'F' and resid 749 through 757 Processing helix chain 'I' and resid 273 through 285 removed outlier: 4.070A pdb=" N ALA I 277 " --> pdb=" O PRO I 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU I 278 " --> pdb=" O ALA I 274 " (cutoff:3.500A) Processing helix chain 'I' and resid 318 through 328 Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'J' and resid 273 through 286 removed outlier: 4.163A pdb=" N ALA J 277 " --> pdb=" O PRO J 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLU J 278 " --> pdb=" O ALA J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 318 through 328 Processing helix chain 'J' and resid 330 through 334 removed outlier: 3.537A pdb=" N ALA J 333 " --> pdb=" O PRO J 330 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA J 334 " --> pdb=" O ALA J 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 330 through 334' Processing sheet with id= A, first strand: chain 'A' and resid 56 through 59 Processing sheet with id= B, first strand: chain 'A' and resid 144 through 147 removed outlier: 3.662A pdb=" N ARG A 144 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 176 " --> pdb=" O ARG A 144 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 146 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A 174 " --> pdb=" O ILE A 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 151 through 155 Processing sheet with id= D, first strand: chain 'A' and resid 365 through 368 Processing sheet with id= E, first strand: chain 'A' and resid 641 through 645 removed outlier: 6.146A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASP A 577 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 542 " --> pdb=" O ASP A 577 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 365 through 368 removed outlier: 3.651A pdb=" N ILE B 301 " --> pdb=" O ILE B 342 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 346 " --> pdb=" O ILE B 303 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 641 through 645 removed outlier: 6.348A pdb=" N CYS B 572 " --> pdb=" O PHE B 618 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE B 620 " --> pdb=" O CYS B 572 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU B 574 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA B 622 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B 576 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN B 538 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N PHE B 575 " --> pdb=" O ASN B 538 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE B 540 " --> pdb=" O PHE B 575 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP B 577 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE B 542 " --> pdb=" O ASP B 577 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 366 through 368 removed outlier: 6.374A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N ALA C 299 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 8.876A pdb=" N MET C 344 " --> pdb=" O ALA C 299 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 641 through 645 removed outlier: 3.565A pdb=" N LEU C 515 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.975A pdb=" N ILE D 82 " --> pdb=" O ARG D 25 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N CYS D 69 " --> pdb=" O VAL D 57 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 181 through 183 removed outlier: 4.455A pdb=" N VAL D 116 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 145 through 147 removed outlier: 3.664A pdb=" N CYS D 174 " --> pdb=" O ILE D 146 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 344 through 346 removed outlier: 6.892A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ARG D 365 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N TYR D 244 " --> pdb=" O ARG D 365 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL D 367 " --> pdb=" O TYR D 244 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 641 through 645 removed outlier: 3.581A pdb=" N ILE D 643 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASN D 538 " --> pdb=" O VAL D 573 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N PHE D 575 " --> pdb=" O ASN D 538 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE D 540 " --> pdb=" O PHE D 575 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ASP D 577 " --> pdb=" O ILE D 540 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 542 " --> pdb=" O ASP D 577 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.159A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL E 57 " --> pdb=" O CYS E 69 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N CYS E 69 " --> pdb=" O VAL E 57 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.658A pdb=" N ILE E 114 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL E 116 " --> pdb=" O HIS E 183 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 145 through 147 Processing sheet with id= R, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.585A pdb=" N MET E 344 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 346 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 641 through 645 removed outlier: 4.020A pdb=" N TYR E 517 " --> pdb=" O ILE E 643 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 645 " --> pdb=" O TYR E 517 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N PHE E 576 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE E 542 " --> pdb=" O PHE E 575 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASP E 577 " --> pdb=" O ILE E 542 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 28 through 30 removed outlier: 6.578A pdb=" N ILE F 82 " --> pdb=" O ASP F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 38 through 40 removed outlier: 7.562A pdb=" N VAL F 39 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ILE F 70 " --> pdb=" O VAL F 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 116 through 118 Processing sheet with id= W, first strand: chain 'F' and resid 365 through 368 removed outlier: 3.611A pdb=" N ALA F 346 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 620 through 623 removed outlier: 6.441A pdb=" N VAL F 514 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N THR F 623 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N PHE F 516 " --> pdb=" O THR F 623 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N GLN F 641 " --> pdb=" O LEU F 515 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR F 517 " --> pdb=" O GLN F 641 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE F 643 " --> pdb=" O TYR F 517 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'F' and resid 538 through 543 Processing sheet with id= Z, first strand: chain 'I' and resid 337 through 340 removed outlier: 3.596A pdb=" N ARG I 368 " --> pdb=" O VAL I 338 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 299 through 301 removed outlier: 3.510A pdb=" N ARG J 368 " --> pdb=" O VAL J 338 " (cutoff:3.500A) 938 hydrogen bonds defined for protein. 2580 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: 9.84 Time building geometry restraints manager: 13.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 11468 1.37 - 1.51: 8508 1.51 - 1.66: 13527 1.66 - 1.80: 196 1.80 - 1.95: 90 Bond restraints: 33789 Sorted by residual: bond pdb=" C LEU B 222 " pdb=" N PRO B 223 " ideal model delta sigma weight residual 1.335 1.391 -0.056 1.30e-02 5.92e+03 1.86e+01 bond pdb=" C SER E 171 " pdb=" N PRO E 172 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.25e+00 bond pdb=" C ARG C 635 " pdb=" N PRO C 636 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.83e+00 bond pdb=" N PRO F 237 " pdb=" CA PRO F 237 " ideal model delta sigma weight residual 1.465 1.508 -0.043 2.03e-02 2.43e+03 4.44e+00 bond pdb=" CA THR A 475 " pdb=" CB THR A 475 " ideal model delta sigma weight residual 1.530 1.566 -0.036 1.69e-02 3.50e+03 4.43e+00 ... (remaining 33784 not shown) Histogram of bond angle deviations from ideal: 99.10 - 106.23: 1120 106.23 - 113.36: 18241 113.36 - 120.49: 13720 120.49 - 127.62: 12301 127.62 - 134.75: 316 Bond angle restraints: 45698 Sorted by residual: angle pdb=" C ASN A 199 " pdb=" N GLU A 200 " pdb=" CA GLU A 200 " ideal model delta sigma weight residual 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" CA LYS F 236 " pdb=" CB LYS F 236 " pdb=" CG LYS F 236 " ideal model delta sigma weight residual 114.10 125.70 -11.60 2.00e+00 2.50e-01 3.37e+01 angle pdb=" C LEU F 464 " pdb=" N ARG F 465 " pdb=" CA ARG F 465 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.04e+01 angle pdb=" CA ARG D 22 " pdb=" CB ARG D 22 " pdb=" CG ARG D 22 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" C SER E 284 " pdb=" N ASN E 285 " pdb=" CA ASN E 285 " ideal model delta sigma weight residual 121.54 131.90 -10.36 1.91e+00 2.74e-01 2.94e+01 ... (remaining 45693 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.92: 19824 27.92 - 55.84: 1081 55.84 - 83.75: 94 83.75 - 111.67: 7 111.67 - 139.59: 4 Dihedral angle restraints: 21010 sinusoidal: 8878 harmonic: 12132 Sorted by residual: dihedral pdb=" CA PHE I 343 " pdb=" C PHE I 343 " pdb=" N PRO I 344 " pdb=" CA PRO I 344 " ideal model delta harmonic sigma weight residual 180.00 131.54 48.46 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PRO D 237 " pdb=" C PRO D 237 " pdb=" N PRO D 238 " pdb=" CA PRO D 238 " ideal model delta harmonic sigma weight residual -180.00 -131.56 -48.44 0 5.00e+00 4.00e-02 9.39e+01 dihedral pdb=" CA PRO A 237 " pdb=" C PRO A 237 " pdb=" N PRO A 238 " pdb=" CA PRO A 238 " ideal model delta harmonic sigma weight residual -180.00 -132.01 -47.99 0 5.00e+00 4.00e-02 9.21e+01 ... (remaining 21007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 4811 0.106 - 0.213: 320 0.213 - 0.319: 31 0.319 - 0.425: 3 0.425 - 0.532: 2 Chirality restraints: 5167 Sorted by residual: chirality pdb=" CB ILE D 233 " pdb=" CA ILE D 233 " pdb=" CG1 ILE D 233 " pdb=" CG2 ILE D 233 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.06e+00 chirality pdb=" CB ILE E 233 " pdb=" CA ILE E 233 " pdb=" CG1 ILE E 233 " pdb=" CG2 ILE E 233 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.47 2.00e-01 2.50e+01 5.57e+00 chirality pdb=" CB ILE A 151 " pdb=" CA ILE A 151 " pdb=" CG1 ILE A 151 " pdb=" CG2 ILE A 151 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 ... (remaining 5164 not shown) Planarity restraints: 5980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 506 " -0.034 2.00e-02 2.50e+03 3.02e-02 1.60e+01 pdb=" CG PHE B 506 " 0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE B 506 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE B 506 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 506 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 506 " -0.017 2.00e-02 2.50e+03 pdb=" CZ PHE B 506 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 222 " 0.057 5.00e-02 4.00e+02 8.64e-02 1.19e+01 pdb=" N PRO C 223 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE I 343 " -0.057 5.00e-02 4.00e+02 8.62e-02 1.19e+01 pdb=" N PRO I 344 " 0.149 5.00e-02 4.00e+02 pdb=" CA PRO I 344 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO I 344 " -0.047 5.00e-02 4.00e+02 ... (remaining 5977 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9482 2.81 - 3.34: 30609 3.34 - 3.86: 55064 3.86 - 4.38: 61145 4.38 - 4.90: 100748 Nonbonded interactions: 257048 Sorted by model distance: nonbonded pdb=" O VAL E 258 " pdb=" OG1 THR E 262 " model vdw 2.294 2.440 nonbonded pdb=" O LEU B 381 " pdb=" OG1 THR B 385 " model vdw 2.306 2.440 nonbonded pdb=" O PRO C 272 " pdb=" OG SER C 276 " model vdw 2.308 2.440 nonbonded pdb=" O2G AGS F 902 " pdb=" O3A AGS F 902 " model vdw 2.321 2.440 nonbonded pdb=" O CYS F 522 " pdb=" O2B AGS F 902 " model vdw 2.322 2.440 ... (remaining 257043 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 22 through 660 or resid 666 through 767 or resid 901 throu \ gh 902)) selection = (chain 'D' and (resid 22 through 553 or resid 557 through 587 or resid 596 throu \ gh 660 or resid 666 through 767 or resid 901 through 902)) selection = (chain 'E' and (resid 22 through 431 or resid 439 through 553 or resid 557 throu \ gh 587 or resid 596 through 767 or resid 901 through 902)) selection = (chain 'F' and (resid 22 through 553 or resid 557 through 587 or resid 596 throu \ gh 660 or resid 666 through 767 or resid 901 through 902)) } ncs_group { reference = (chain 'B' and (resid 199 through 431 or resid 439 through 588 or resid 597 thro \ ugh 713 or resid 726 through 768 or resid 901 through 902)) selection = (chain 'C' and (resid 199 through 588 or resid 597 through 768 or resid 901 thro \ ugh 902)) } ncs_group { reference = (chain 'I' and resid 267 through 370) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.750 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 79.490 Find NCS groups from input model: 2.470 Set up NCS constraints: 0.180 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 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 : 0.004 0.060 33789 Z= 0.280 Angle : 0.961 16.466 45698 Z= 0.519 Chirality : 0.058 0.532 5167 Planarity : 0.007 0.086 5980 Dihedral : 15.990 139.588 13116 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.26 % Favored : 90.64 % Rotamer: Outliers : 0.03 % Allowed : 0.82 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 4.87 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.11), residues: 4157 helix: -1.77 (0.10), residues: 1626 sheet: -1.33 (0.23), residues: 496 loop : -2.56 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 476 HIS 0.005 0.001 HIS E 406 PHE 0.068 0.002 PHE B 506 TYR 0.020 0.002 TYR F 173 ARG 0.009 0.000 ARG D 453 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 904 time to evaluate : 3.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ILE cc_start: 0.7757 (tp) cc_final: 0.7505 (tp) REVERT: A 296 ASN cc_start: 0.5073 (t0) cc_final: 0.4112 (t0) REVERT: A 379 GLU cc_start: 0.8444 (tt0) cc_final: 0.7661 (tp30) REVERT: A 561 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8627 (tm-30) REVERT: A 564 ASP cc_start: 0.8958 (t0) cc_final: 0.8693 (t0) REVERT: A 577 ASP cc_start: 0.8233 (t0) cc_final: 0.6494 (t70) REVERT: A 607 GLU cc_start: 0.8154 (mm-30) cc_final: 0.6974 (mt-10) REVERT: A 620 ILE cc_start: 0.9214 (mt) cc_final: 0.8954 (pt) REVERT: A 765 SER cc_start: 0.8522 (m) cc_final: 0.8144 (t) REVERT: B 244 TYR cc_start: 0.7660 (p90) cc_final: 0.7297 (p90) REVERT: B 274 ILE cc_start: 0.8283 (tp) cc_final: 0.7764 (tp) REVERT: B 388 MET cc_start: 0.7683 (ppp) cc_final: 0.7042 (ppp) REVERT: B 414 LEU cc_start: 0.8495 (tp) cc_final: 0.8195 (tp) REVERT: B 546 GLU cc_start: 0.8451 (tm-30) cc_final: 0.8233 (tp30) REVERT: B 561 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8141 (tp30) REVERT: B 562 ILE cc_start: 0.9593 (mm) cc_final: 0.9378 (mm) REVERT: B 602 ASN cc_start: 0.8966 (m-40) cc_final: 0.8755 (m-40) REVERT: B 604 ILE cc_start: 0.9369 (mm) cc_final: 0.9144 (mm) REVERT: B 609 ASP cc_start: 0.7918 (t0) cc_final: 0.7264 (t0) REVERT: B 736 PHE cc_start: 0.8212 (m-80) cc_final: 0.7980 (m-80) REVERT: C 274 ILE cc_start: 0.8899 (mm) cc_final: 0.8526 (mm) REVERT: C 302 PHE cc_start: 0.6897 (t80) cc_final: 0.6623 (t80) REVERT: C 315 LYS cc_start: 0.7849 (mtpt) cc_final: 0.7176 (tptt) REVERT: C 364 ASP cc_start: 0.7748 (p0) cc_final: 0.7528 (p0) REVERT: C 562 ILE cc_start: 0.9228 (mm) cc_final: 0.8790 (mm) REVERT: C 564 ASP cc_start: 0.8667 (t0) cc_final: 0.8201 (t0) REVERT: C 603 GLN cc_start: 0.9221 (tp-100) cc_final: 0.8873 (tp-100) REVERT: D 84 MET cc_start: 0.5185 (ptp) cc_final: 0.4912 (ptt) REVERT: D 132 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6827 (mp0) REVERT: D 148 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8197 (ttmm) REVERT: D 239 ARG cc_start: 0.6913 (ttt180) cc_final: 0.6533 (mmt180) REVERT: D 529 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8570 (pttm) REVERT: D 551 TRP cc_start: 0.6190 (t60) cc_final: 0.5812 (t60) REVERT: D 602 ASN cc_start: 0.9120 (t0) cc_final: 0.8568 (t0) REVERT: D 653 ARG cc_start: 0.6708 (pmt170) cc_final: 0.6466 (ppt170) REVERT: E 46 MET cc_start: 0.4833 (mtp) cc_final: 0.4629 (mtt) REVERT: E 219 MET cc_start: 0.7630 (mmt) cc_final: 0.7172 (mmm) REVERT: E 332 MET cc_start: 0.6603 (ttt) cc_final: 0.6042 (ttt) REVERT: E 466 GLU cc_start: 0.6523 (tm-30) cc_final: 0.6243 (tm-30) REVERT: E 602 ASN cc_start: 0.9235 (m-40) cc_final: 0.8773 (t0) REVERT: E 628 ILE cc_start: 0.7896 (pt) cc_final: 0.7578 (mt) REVERT: E 690 ILE cc_start: 0.8140 (mm) cc_final: 0.7912 (mp) REVERT: F 194 GLU cc_start: 0.7810 (tt0) cc_final: 0.7277 (mp0) REVERT: F 269 ILE cc_start: 0.8658 (mm) cc_final: 0.8442 (mt) REVERT: F 351 ASN cc_start: 0.8420 (p0) cc_final: 0.6475 (p0) REVERT: F 411 LEU cc_start: 0.8458 (tp) cc_final: 0.8001 (tp) REVERT: F 560 ARG cc_start: 0.8486 (mtt180) cc_final: 0.7902 (mtt-85) REVERT: F 607 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7962 (mm-30) REVERT: I 332 MET cc_start: 0.2924 (mmp) cc_final: 0.2581 (mmm) REVERT: J 341 THR cc_start: 0.5620 (p) cc_final: 0.4949 (p) REVERT: J 365 ILE cc_start: 0.5972 (mt) cc_final: 0.5624 (mt) outliers start: 1 outliers final: 0 residues processed: 905 average time/residue: 0.5150 time to fit residues: 715.6613 Evaluate side-chains 515 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 352 optimal weight: 8.9990 chunk 316 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 213 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 327 optimal weight: 9.9990 chunk 126 optimal weight: 0.6980 chunk 199 optimal weight: 8.9990 chunk 243 optimal weight: 0.0170 chunk 379 optimal weight: 8.9990 overall best weight: 2.3022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 GLN B 285 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 327 GLN D 36 ASN D 285 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS E 36 ASN E 494 GLN E 538 ASN F 494 GLN ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33789 Z= 0.241 Angle : 0.692 14.048 45698 Z= 0.358 Chirality : 0.046 0.297 5167 Planarity : 0.006 0.109 5980 Dihedral : 9.769 133.904 4798 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 16.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.89 % Favored : 92.06 % Rotamer: Outliers : 0.08 % Allowed : 6.23 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 3.10 % 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: -2.20 (0.13), residues: 4157 helix: -0.49 (0.12), residues: 1632 sheet: -1.30 (0.23), residues: 514 loop : -2.36 (0.13), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 454 HIS 0.005 0.001 HIS A 404 PHE 0.033 0.002 PHE B 506 TYR 0.014 0.001 TYR F 173 ARG 0.011 0.001 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 623 time to evaluate : 4.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7440 (tt0) REVERT: A 274 ILE cc_start: 0.8084 (tp) cc_final: 0.7784 (tp) REVERT: A 379 GLU cc_start: 0.8345 (tt0) cc_final: 0.8130 (tp30) REVERT: A 575 PHE cc_start: 0.6969 (t80) cc_final: 0.6414 (t80) REVERT: A 582 ILE cc_start: 0.9090 (mp) cc_final: 0.8745 (mt) REVERT: A 607 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7021 (mt-10) REVERT: A 642 LEU cc_start: 0.8992 (mp) cc_final: 0.8430 (pt) REVERT: A 673 GLU cc_start: 0.8383 (pm20) cc_final: 0.8154 (pp20) REVERT: A 765 SER cc_start: 0.8571 (m) cc_final: 0.8275 (t) REVERT: B 274 ILE cc_start: 0.8367 (tp) cc_final: 0.7985 (tp) REVERT: B 546 GLU cc_start: 0.8595 (tm-30) cc_final: 0.8331 (tp30) REVERT: B 551 TRP cc_start: 0.6291 (t60) cc_final: 0.5924 (t60) REVERT: B 602 ASN cc_start: 0.9169 (m-40) cc_final: 0.8772 (m-40) REVERT: C 230 PHE cc_start: 0.7591 (t80) cc_final: 0.7349 (t80) REVERT: C 315 LYS cc_start: 0.8017 (mtpt) cc_final: 0.7110 (tptt) REVERT: C 348 ASN cc_start: 0.8256 (p0) cc_final: 0.8029 (t0) REVERT: C 364 ASP cc_start: 0.7795 (p0) cc_final: 0.7531 (p0) REVERT: C 489 LEU cc_start: 0.8617 (mm) cc_final: 0.8302 (mm) REVERT: C 549 THR cc_start: 0.7448 (p) cc_final: 0.7204 (p) REVERT: C 564 ASP cc_start: 0.9058 (t0) cc_final: 0.8707 (t0) REVERT: D 88 VAL cc_start: 0.6422 (t) cc_final: 0.6195 (t) REVERT: D 132 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6710 (mp0) REVERT: D 148 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8062 (ttmm) REVERT: D 411 LEU cc_start: 0.8643 (mp) cc_final: 0.8394 (mp) REVERT: D 550 MET cc_start: 0.7608 (ptp) cc_final: 0.7396 (ptp) REVERT: D 602 ASN cc_start: 0.9093 (t0) cc_final: 0.8556 (t0) REVERT: E 46 MET cc_start: 0.4436 (mtp) cc_final: 0.3565 (ttm) REVERT: E 244 TYR cc_start: 0.8201 (p90) cc_final: 0.7801 (p90) REVERT: E 302 PHE cc_start: 0.7100 (t80) cc_final: 0.6743 (t80) REVERT: E 332 MET cc_start: 0.6909 (ttt) cc_final: 0.6383 (ttt) REVERT: E 427 MET cc_start: 0.7843 (ppp) cc_final: 0.7246 (ppp) REVERT: E 508 MET cc_start: 0.5159 (ttm) cc_final: 0.4647 (ttm) REVERT: E 602 ASN cc_start: 0.9221 (m-40) cc_final: 0.8847 (t0) REVERT: E 695 CYS cc_start: 0.7890 (m) cc_final: 0.7287 (m) REVERT: F 173 TYR cc_start: 0.7514 (p90) cc_final: 0.7311 (p90) REVERT: F 194 GLU cc_start: 0.7961 (tt0) cc_final: 0.7376 (mp0) REVERT: F 205 ASP cc_start: 0.7112 (t0) cc_final: 0.6759 (t0) REVERT: F 411 LEU cc_start: 0.8641 (tp) cc_final: 0.8348 (tp) REVERT: F 508 MET cc_start: 0.6617 (mmm) cc_final: 0.6062 (tpp) REVERT: F 560 ARG cc_start: 0.8638 (mtt180) cc_final: 0.8409 (mtt-85) REVERT: F 580 ASP cc_start: 0.7822 (m-30) cc_final: 0.7299 (m-30) REVERT: F 615 LYS cc_start: 0.7785 (mtpt) cc_final: 0.7518 (mtmm) REVERT: I 332 MET cc_start: 0.2861 (mmp) cc_final: 0.2629 (mmm) REVERT: I 366 VAL cc_start: 0.4161 (t) cc_final: 0.3841 (m) outliers start: 3 outliers final: 2 residues processed: 626 average time/residue: 0.4927 time to fit residues: 484.9637 Evaluate side-chains 438 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 436 time to evaluate : 4.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 210 optimal weight: 20.0000 chunk 117 optimal weight: 1.9990 chunk 315 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 380 optimal weight: 20.0000 chunk 410 optimal weight: 0.6980 chunk 338 optimal weight: 10.0000 chunk 377 optimal weight: 8.9990 chunk 129 optimal weight: 10.0000 chunk 305 optimal weight: 9.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 ASN ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 660 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 33789 Z= 0.369 Angle : 0.795 10.982 45698 Z= 0.413 Chirality : 0.047 0.196 5167 Planarity : 0.006 0.075 5980 Dihedral : 9.920 138.589 4798 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.62 % Favored : 90.28 % Rotamer: Outliers : 0.11 % Allowed : 7.48 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.13), residues: 4157 helix: -0.42 (0.12), residues: 1631 sheet: -1.44 (0.22), residues: 519 loop : -2.37 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP F 551 HIS 0.010 0.001 HIS D 735 PHE 0.028 0.002 PHE E 265 TYR 0.025 0.002 TYR F 143 ARG 0.011 0.001 ARG C 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 560 time to evaluate : 3.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 GLU cc_start: 0.8621 (tt0) cc_final: 0.8361 (tp30) REVERT: A 442 MET cc_start: 0.6879 (mpp) cc_final: 0.6172 (mmt) REVERT: A 505 LYS cc_start: 0.7922 (mptt) cc_final: 0.7644 (mmmm) REVERT: A 575 PHE cc_start: 0.7186 (t80) cc_final: 0.6677 (t80) REVERT: A 642 LEU cc_start: 0.8984 (mp) cc_final: 0.8630 (pt) REVERT: B 244 TYR cc_start: 0.7912 (p90) cc_final: 0.6999 (p90) REVERT: B 274 ILE cc_start: 0.8541 (tp) cc_final: 0.8220 (tp) REVERT: B 388 MET cc_start: 0.8350 (ptm) cc_final: 0.7294 (ppp) REVERT: B 517 TYR cc_start: 0.7859 (p90) cc_final: 0.7659 (p90) REVERT: B 602 ASN cc_start: 0.9111 (m-40) cc_final: 0.8836 (m-40) REVERT: C 348 ASN cc_start: 0.8660 (p0) cc_final: 0.8143 (t0) REVERT: C 364 ASP cc_start: 0.8008 (p0) cc_final: 0.7676 (m-30) REVERT: C 388 MET cc_start: 0.7462 (ptp) cc_final: 0.5776 (ppp) REVERT: C 402 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7447 (mt-10) REVERT: C 564 ASP cc_start: 0.9008 (t0) cc_final: 0.8507 (t0) REVERT: C 602 ASN cc_start: 0.9164 (m110) cc_final: 0.8372 (t0) REVERT: C 603 GLN cc_start: 0.9431 (tp-100) cc_final: 0.9148 (tp-100) REVERT: D 132 GLU cc_start: 0.7420 (mm-30) cc_final: 0.6805 (pm20) REVERT: D 291 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7591 (tp30) REVERT: D 560 ARG cc_start: 0.8520 (ttm170) cc_final: 0.8200 (ttp-170) REVERT: D 602 ASN cc_start: 0.9227 (t0) cc_final: 0.8606 (t0) REVERT: D 678 MET cc_start: 0.6769 (ttt) cc_final: 0.6442 (ttm) REVERT: E 46 MET cc_start: 0.4606 (mtp) cc_final: 0.3808 (ttm) REVERT: E 110 TYR cc_start: 0.6836 (m-10) cc_final: 0.6435 (t80) REVERT: E 219 MET cc_start: 0.8112 (mmm) cc_final: 0.7827 (mmm) REVERT: E 427 MET cc_start: 0.8153 (ppp) cc_final: 0.7549 (ppp) REVERT: E 602 ASN cc_start: 0.9320 (m-40) cc_final: 0.8596 (t0) REVERT: F 52 PHE cc_start: 0.6139 (m-80) cc_final: 0.5483 (m-80) REVERT: F 158 MET cc_start: 0.8149 (tmm) cc_final: 0.7896 (tmm) REVERT: F 205 ASP cc_start: 0.7601 (t0) cc_final: 0.7160 (t0) REVERT: F 560 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8399 (mtt-85) REVERT: F 561 GLU cc_start: 0.9056 (tp30) cc_final: 0.8801 (mt-10) REVERT: F 564 ASP cc_start: 0.9115 (m-30) cc_final: 0.8912 (m-30) REVERT: F 578 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7358 (mp0) REVERT: F 606 THR cc_start: 0.8784 (m) cc_final: 0.8480 (p) REVERT: I 332 MET cc_start: 0.2931 (mmp) cc_final: 0.2597 (mmm) REVERT: I 366 VAL cc_start: 0.4388 (t) cc_final: 0.4178 (t) outliers start: 4 outliers final: 1 residues processed: 563 average time/residue: 0.4809 time to fit residues: 425.8829 Evaluate side-chains 424 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 3.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 375 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 197 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 0.5980 chunk 255 optimal weight: 0.0870 chunk 381 optimal weight: 0.7980 chunk 404 optimal weight: 1.9990 chunk 199 optimal weight: 0.4980 chunk 361 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN A 602 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 ASN C 406 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 616 ASN D 285 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN D 660 ASN ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 603 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33789 Z= 0.182 Angle : 0.660 13.847 45698 Z= 0.334 Chirality : 0.046 0.250 5167 Planarity : 0.006 0.099 5980 Dihedral : 9.534 133.188 4798 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.23 % Favored : 91.75 % Rotamer: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.13), residues: 4157 helix: -0.10 (0.13), residues: 1630 sheet: -1.43 (0.22), residues: 512 loop : -2.22 (0.14), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 551 HIS 0.006 0.001 HIS E 499 PHE 0.026 0.002 PHE F 266 TYR 0.025 0.001 TYR E 495 ARG 0.011 0.000 ARG F 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 582 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 379 GLU cc_start: 0.8546 (tt0) cc_final: 0.8276 (tp30) REVERT: A 397 GLU cc_start: 0.7913 (mp0) cc_final: 0.7234 (mp0) REVERT: A 442 MET cc_start: 0.6930 (mpp) cc_final: 0.6153 (mmt) REVERT: A 575 PHE cc_start: 0.6984 (t80) cc_final: 0.6467 (t80) REVERT: A 582 ILE cc_start: 0.9378 (mp) cc_final: 0.9118 (mt) REVERT: A 604 ILE cc_start: 0.9153 (mm) cc_final: 0.8860 (mm) REVERT: A 642 LEU cc_start: 0.8886 (mp) cc_final: 0.8378 (pt) REVERT: B 274 ILE cc_start: 0.8478 (tp) cc_final: 0.8158 (tp) REVERT: B 332 MET cc_start: 0.8032 (ppp) cc_final: 0.7553 (ppp) REVERT: B 388 MET cc_start: 0.8308 (ptm) cc_final: 0.7351 (ppp) REVERT: B 508 MET cc_start: 0.5370 (mmt) cc_final: 0.4794 (mmm) REVERT: B 602 ASN cc_start: 0.8988 (m-40) cc_final: 0.8676 (m-40) REVERT: C 348 ASN cc_start: 0.8365 (p0) cc_final: 0.7918 (t0) REVERT: C 388 MET cc_start: 0.7011 (ptp) cc_final: 0.5607 (ppp) REVERT: C 489 LEU cc_start: 0.8634 (mm) cc_final: 0.8262 (mm) REVERT: C 564 ASP cc_start: 0.8777 (t0) cc_final: 0.8398 (t0) REVERT: C 602 ASN cc_start: 0.8874 (m110) cc_final: 0.8274 (t0) REVERT: D 132 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6695 (pm20) REVERT: D 411 LEU cc_start: 0.8661 (mp) cc_final: 0.8381 (mp) REVERT: D 602 ASN cc_start: 0.8903 (t0) cc_final: 0.8660 (t0) REVERT: D 678 MET cc_start: 0.6621 (ttt) cc_final: 0.6359 (ttm) REVERT: E 110 TYR cc_start: 0.6839 (m-10) cc_final: 0.6396 (t80) REVERT: E 140 LEU cc_start: 0.7922 (pp) cc_final: 0.7463 (mt) REVERT: E 427 MET cc_start: 0.8010 (ppp) cc_final: 0.7441 (ppp) REVERT: E 690 ILE cc_start: 0.7833 (mp) cc_final: 0.7198 (mp) REVERT: F 52 PHE cc_start: 0.6140 (m-80) cc_final: 0.5516 (m-80) REVERT: F 194 GLU cc_start: 0.8104 (tt0) cc_final: 0.7425 (mp0) REVERT: F 205 ASP cc_start: 0.7397 (t0) cc_final: 0.6948 (t0) REVERT: F 212 GLN cc_start: 0.8737 (mp10) cc_final: 0.8046 (mp10) REVERT: F 303 ILE cc_start: 0.9133 (pt) cc_final: 0.8929 (pt) REVERT: F 468 VAL cc_start: 0.9037 (p) cc_final: 0.8771 (p) REVERT: F 560 ARG cc_start: 0.8685 (mtt180) cc_final: 0.8318 (mtt-85) REVERT: I 332 MET cc_start: 0.2882 (mmp) cc_final: 0.2619 (mmm) outliers start: 4 outliers final: 0 residues processed: 585 average time/residue: 0.4881 time to fit residues: 462.3024 Evaluate side-chains 433 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 433 time to evaluate : 3.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 336 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 300 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 chunk 279 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 206 optimal weight: 9.9990 chunk 362 optimal weight: 8.9990 chunk 101 optimal weight: 0.0470 overall best weight: 4.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 558 ASN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN D 285 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 226 HIS ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 33789 Z= 0.344 Angle : 0.747 11.282 45698 Z= 0.387 Chirality : 0.047 0.225 5167 Planarity : 0.006 0.083 5980 Dihedral : 9.687 137.216 4798 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 24.04 Ramachandran Plot: Outliers : 0.07 % Allowed : 10.01 % Favored : 89.92 % Rotamer: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 2.21 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.13), residues: 4157 helix: -0.27 (0.13), residues: 1605 sheet: -1.54 (0.22), residues: 522 loop : -2.20 (0.14), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP C 551 HIS 0.008 0.001 HIS A 404 PHE 0.026 0.002 PHE E 265 TYR 0.033 0.002 TYR D 517 ARG 0.009 0.001 ARG C 653 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 519 time to evaluate : 3.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 218 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7601 (tt0) REVERT: A 304 ASP cc_start: 0.7281 (p0) cc_final: 0.6823 (p0) REVERT: A 379 GLU cc_start: 0.8635 (tt0) cc_final: 0.8355 (tp30) REVERT: A 397 GLU cc_start: 0.8198 (mp0) cc_final: 0.7533 (mp0) REVERT: A 564 ASP cc_start: 0.9126 (t0) cc_final: 0.8902 (t0) REVERT: A 575 PHE cc_start: 0.7159 (t80) cc_final: 0.6417 (t80) REVERT: A 630 ASP cc_start: 0.8503 (m-30) cc_final: 0.8292 (m-30) REVERT: A 642 LEU cc_start: 0.8908 (mp) cc_final: 0.8601 (pt) REVERT: B 274 ILE cc_start: 0.8533 (tp) cc_final: 0.8307 (tp) REVERT: B 332 MET cc_start: 0.8244 (ppp) cc_final: 0.7706 (ppp) REVERT: B 564 ASP cc_start: 0.8756 (m-30) cc_final: 0.8435 (m-30) REVERT: B 602 ASN cc_start: 0.9193 (m-40) cc_final: 0.8966 (m-40) REVERT: C 348 ASN cc_start: 0.8515 (p0) cc_final: 0.8038 (t0) REVERT: C 402 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7122 (pt0) REVERT: C 449 MET cc_start: 0.8213 (mmm) cc_final: 0.7999 (mpp) REVERT: C 466 GLU cc_start: 0.7049 (pp20) cc_final: 0.6784 (tm-30) REVERT: C 489 LEU cc_start: 0.8642 (mm) cc_final: 0.8366 (mm) REVERT: C 549 THR cc_start: 0.7575 (p) cc_final: 0.7277 (p) REVERT: C 551 TRP cc_start: 0.6340 (t60) cc_final: 0.4939 (t-100) REVERT: C 564 ASP cc_start: 0.8836 (t0) cc_final: 0.8444 (t0) REVERT: C 602 ASN cc_start: 0.9027 (m-40) cc_final: 0.8461 (t0) REVERT: D 89 ARG cc_start: 0.7893 (ttm110) cc_final: 0.7255 (tmm-80) REVERT: D 132 GLU cc_start: 0.7640 (mm-30) cc_final: 0.6926 (pm20) REVERT: D 411 LEU cc_start: 0.8790 (mp) cc_final: 0.8565 (mp) REVERT: D 449 MET cc_start: 0.6494 (tmm) cc_final: 0.6231 (tmm) REVERT: D 568 GLN cc_start: 0.8076 (pp30) cc_final: 0.7697 (tm-30) REVERT: D 602 ASN cc_start: 0.9008 (t0) cc_final: 0.8803 (t0) REVERT: E 110 TYR cc_start: 0.6859 (m-10) cc_final: 0.6443 (t80) REVERT: E 140 LEU cc_start: 0.8009 (pp) cc_final: 0.7532 (mt) REVERT: E 427 MET cc_start: 0.8238 (ppp) cc_final: 0.7606 (ppp) REVERT: E 508 MET cc_start: 0.5349 (tpt) cc_final: 0.5107 (tpt) REVERT: F 52 PHE cc_start: 0.6622 (m-80) cc_final: 0.6093 (m-80) REVERT: F 173 TYR cc_start: 0.7032 (p90) cc_final: 0.6785 (p90) REVERT: F 205 ASP cc_start: 0.7546 (t0) cc_final: 0.7146 (t0) REVERT: F 565 LYS cc_start: 0.9094 (mtmm) cc_final: 0.8848 (mttt) REVERT: F 580 ASP cc_start: 0.7925 (m-30) cc_final: 0.7691 (m-30) REVERT: J 332 MET cc_start: 0.1740 (ttt) cc_final: 0.1526 (ttt) outliers start: 0 outliers final: 0 residues processed: 519 average time/residue: 0.4669 time to fit residues: 386.4806 Evaluate side-chains 387 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 135 optimal weight: 0.0870 chunk 363 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 237 optimal weight: 0.0970 chunk 99 optimal weight: 8.9990 chunk 404 optimal weight: 30.0000 chunk 335 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 33 optimal weight: 0.0050 chunk 133 optimal weight: 2.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.7972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 603 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 490 GLN C 494 GLN C 602 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN D 285 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN D 660 ASN F 183 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33789 Z= 0.181 Angle : 0.657 11.753 45698 Z= 0.333 Chirality : 0.046 0.221 5167 Planarity : 0.005 0.073 5980 Dihedral : 9.327 129.365 4798 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.64 % Favored : 91.32 % Rotamer: Outliers : 0.08 % Allowed : 2.55 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.13), residues: 4157 helix: -0.02 (0.13), residues: 1629 sheet: -1.39 (0.22), residues: 520 loop : -2.18 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 551 HIS 0.003 0.001 HIS C 226 PHE 0.052 0.002 PHE C 267 TYR 0.017 0.001 TYR D 517 ARG 0.012 0.000 ARG F 465 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 554 time to evaluate : 4.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 397 GLU cc_start: 0.7899 (mp0) cc_final: 0.7262 (mp0) REVERT: A 575 PHE cc_start: 0.6932 (t80) cc_final: 0.6613 (t80) REVERT: A 577 ASP cc_start: 0.7025 (t70) cc_final: 0.6624 (t70) REVERT: A 582 ILE cc_start: 0.9503 (mp) cc_final: 0.9160 (mt) REVERT: A 642 LEU cc_start: 0.8784 (mp) cc_final: 0.8462 (pt) REVERT: A 709 ARG cc_start: 0.7133 (tmt-80) cc_final: 0.6868 (tpt90) REVERT: B 274 ILE cc_start: 0.8559 (tp) cc_final: 0.8213 (tp) REVERT: B 332 MET cc_start: 0.8155 (ppp) cc_final: 0.7690 (ppp) REVERT: B 388 MET cc_start: 0.8256 (ptm) cc_final: 0.6906 (ppp) REVERT: B 740 MET cc_start: 0.7935 (tpp) cc_final: 0.7584 (tpp) REVERT: C 216 ILE cc_start: 0.8695 (mm) cc_final: 0.8459 (tp) REVERT: C 348 ASN cc_start: 0.8790 (p0) cc_final: 0.7829 (t0) REVERT: C 388 MET cc_start: 0.7156 (ptp) cc_final: 0.5733 (ppp) REVERT: C 402 GLU cc_start: 0.7515 (mt-10) cc_final: 0.6872 (pt0) REVERT: C 489 LEU cc_start: 0.8553 (mm) cc_final: 0.8279 (mm) REVERT: C 551 TRP cc_start: 0.6270 (t60) cc_final: 0.5026 (t-100) REVERT: C 564 ASP cc_start: 0.8793 (t0) cc_final: 0.8374 (t0) REVERT: C 602 ASN cc_start: 0.8854 (m110) cc_final: 0.8244 (t0) REVERT: D 89 ARG cc_start: 0.7603 (ttm110) cc_final: 0.7174 (tmm-80) REVERT: D 132 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6724 (pm20) REVERT: D 411 LEU cc_start: 0.8661 (mp) cc_final: 0.8447 (mp) REVERT: D 602 ASN cc_start: 0.8872 (t0) cc_final: 0.8603 (t0) REVERT: D 678 MET cc_start: 0.6470 (ttt) cc_final: 0.6212 (ttm) REVERT: E 83 ARG cc_start: 0.5814 (mtp180) cc_final: 0.5534 (mtm-85) REVERT: E 140 LEU cc_start: 0.7898 (pp) cc_final: 0.7440 (mt) REVERT: E 427 MET cc_start: 0.8148 (ppp) cc_final: 0.7590 (ppp) REVERT: E 690 ILE cc_start: 0.7838 (mp) cc_final: 0.7293 (mp) REVERT: F 52 PHE cc_start: 0.6240 (m-80) cc_final: 0.5613 (m-80) REVERT: F 194 GLU cc_start: 0.8114 (tt0) cc_final: 0.7862 (tt0) REVERT: F 205 ASP cc_start: 0.7312 (t0) cc_final: 0.7032 (t0) REVERT: F 303 ILE cc_start: 0.9269 (pt) cc_final: 0.9052 (pt) REVERT: F 560 ARG cc_start: 0.8380 (mpt-90) cc_final: 0.7893 (mpp80) REVERT: F 562 ILE cc_start: 0.8909 (pt) cc_final: 0.8589 (pt) REVERT: F 564 ASP cc_start: 0.9010 (m-30) cc_final: 0.8638 (m-30) REVERT: F 580 ASP cc_start: 0.7923 (m-30) cc_final: 0.7563 (m-30) REVERT: I 332 MET cc_start: 0.3267 (mmt) cc_final: 0.2964 (mmm) REVERT: J 332 MET cc_start: 0.1852 (ttt) cc_final: 0.1555 (ttt) outliers start: 3 outliers final: 1 residues processed: 557 average time/residue: 0.4733 time to fit residues: 423.9648 Evaluate side-chains 407 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 4.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 389 optimal weight: 0.0770 chunk 45 optimal weight: 10.0000 chunk 230 optimal weight: 0.0370 chunk 295 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 340 optimal weight: 30.0000 chunk 225 optimal weight: 0.1980 chunk 402 optimal weight: 4.9990 chunk 252 optimal weight: 8.9990 chunk 245 optimal weight: 20.0000 chunk 186 optimal weight: 40.0000 overall best weight: 2.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 HIS B 602 ASN C 494 GLN C 499 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 764 GLN D 285 ASN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33789 Z= 0.213 Angle : 0.672 11.227 45698 Z= 0.344 Chirality : 0.046 0.273 5167 Planarity : 0.005 0.087 5980 Dihedral : 9.209 131.506 4798 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.26 % Favored : 90.71 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.77 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 4157 helix: -0.03 (0.13), residues: 1623 sheet: -1.35 (0.22), residues: 531 loop : -2.13 (0.14), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 551 HIS 0.005 0.001 HIS D 317 PHE 0.032 0.002 PHE A 552 TYR 0.037 0.002 TYR F 173 ARG 0.011 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 523 time to evaluate : 3.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 397 GLU cc_start: 0.8146 (mp0) cc_final: 0.7489 (mp0) REVERT: A 442 MET cc_start: 0.6708 (mpp) cc_final: 0.5866 (tpp) REVERT: A 564 ASP cc_start: 0.9124 (t0) cc_final: 0.8909 (t0) REVERT: A 575 PHE cc_start: 0.7086 (t80) cc_final: 0.6638 (t80) REVERT: A 577 ASP cc_start: 0.7274 (t70) cc_final: 0.6805 (t70) REVERT: A 582 ILE cc_start: 0.9518 (mp) cc_final: 0.9179 (mt) REVERT: A 642 LEU cc_start: 0.8818 (mp) cc_final: 0.8581 (pt) REVERT: A 709 ARG cc_start: 0.7151 (tmt-80) cc_final: 0.6573 (tpt90) REVERT: B 274 ILE cc_start: 0.8565 (tp) cc_final: 0.8328 (tp) REVERT: B 316 THR cc_start: 0.8089 (p) cc_final: 0.7879 (p) REVERT: B 332 MET cc_start: 0.8135 (ppp) cc_final: 0.7798 (ppp) REVERT: B 388 MET cc_start: 0.8236 (ptm) cc_final: 0.6677 (ppp) REVERT: B 508 MET cc_start: 0.5976 (mmt) cc_final: 0.5395 (mmm) REVERT: B 564 ASP cc_start: 0.8843 (m-30) cc_final: 0.8353 (m-30) REVERT: B 602 ASN cc_start: 0.9109 (m110) cc_final: 0.8902 (m-40) REVERT: B 740 MET cc_start: 0.8027 (tpp) cc_final: 0.7705 (tpp) REVERT: C 216 ILE cc_start: 0.8713 (mm) cc_final: 0.8491 (tp) REVERT: C 348 ASN cc_start: 0.8673 (p0) cc_final: 0.7787 (t0) REVERT: C 388 MET cc_start: 0.7357 (ptp) cc_final: 0.5736 (ppp) REVERT: C 402 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6819 (pt0) REVERT: C 489 LEU cc_start: 0.8597 (mm) cc_final: 0.8337 (mm) REVERT: C 549 THR cc_start: 0.7596 (p) cc_final: 0.7385 (p) REVERT: C 551 TRP cc_start: 0.6202 (t60) cc_final: 0.5017 (t-100) REVERT: C 564 ASP cc_start: 0.8794 (t0) cc_final: 0.8373 (t0) REVERT: C 602 ASN cc_start: 0.8836 (m110) cc_final: 0.8133 (t0) REVERT: D 132 GLU cc_start: 0.7484 (mm-30) cc_final: 0.6717 (pm20) REVERT: D 529 LYS cc_start: 0.8983 (ptpp) cc_final: 0.8755 (pttm) REVERT: D 564 ASP cc_start: 0.8100 (m-30) cc_final: 0.7500 (m-30) REVERT: D 568 GLN cc_start: 0.8085 (pp30) cc_final: 0.7600 (tm-30) REVERT: D 602 ASN cc_start: 0.8870 (t0) cc_final: 0.8639 (t0) REVERT: E 83 ARG cc_start: 0.6006 (mtp180) cc_final: 0.5672 (mtm-85) REVERT: E 427 MET cc_start: 0.8184 (ppp) cc_final: 0.7619 (ppp) REVERT: E 690 ILE cc_start: 0.7723 (mp) cc_final: 0.7187 (mp) REVERT: F 52 PHE cc_start: 0.6262 (m-80) cc_final: 0.5591 (m-80) REVERT: F 194 GLU cc_start: 0.8113 (tt0) cc_final: 0.7702 (tt0) REVERT: F 449 MET cc_start: 0.7295 (tmm) cc_final: 0.7018 (tmm) REVERT: F 484 ASP cc_start: 0.6881 (p0) cc_final: 0.6454 (p0) REVERT: F 560 ARG cc_start: 0.8539 (mpt-90) cc_final: 0.8160 (mpt-90) REVERT: F 561 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8857 (mt-10) REVERT: F 564 ASP cc_start: 0.9028 (m-30) cc_final: 0.8718 (m-30) REVERT: F 580 ASP cc_start: 0.7932 (m-30) cc_final: 0.7620 (m-30) REVERT: F 604 ILE cc_start: 0.9519 (pt) cc_final: 0.9238 (pt) REVERT: I 332 MET cc_start: 0.3291 (mmt) cc_final: 0.2978 (mmm) REVERT: J 332 MET cc_start: 0.0813 (ttt) cc_final: 0.0490 (ttt) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.4668 time to fit residues: 393.7771 Evaluate side-chains 396 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 4.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 249 optimal weight: 9.9990 chunk 160 optimal weight: 0.0870 chunk 240 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 256 optimal weight: 30.0000 chunk 274 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 316 optimal weight: 10.0000 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 499 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 680 ASN C 764 GLN ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN E 296 ASN F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33789 Z= 0.205 Angle : 0.668 11.088 45698 Z= 0.342 Chirality : 0.046 0.282 5167 Planarity : 0.005 0.081 5980 Dihedral : 9.135 130.706 4798 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.29 % Favored : 90.69 % Rotamer: Outliers : 0.03 % Allowed : 1.59 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 4157 helix: -0.00 (0.13), residues: 1631 sheet: -1.29 (0.22), residues: 524 loop : -2.11 (0.14), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP C 476 HIS 0.008 0.001 HIS C 499 PHE 0.032 0.002 PHE B 506 TYR 0.024 0.001 TYR F 173 ARG 0.023 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 515 time to evaluate : 4.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 442 MET cc_start: 0.6758 (mpp) cc_final: 0.5924 (tpp) REVERT: A 540 ILE cc_start: 0.8892 (tp) cc_final: 0.8584 (tp) REVERT: A 575 PHE cc_start: 0.7063 (t80) cc_final: 0.6160 (t80) REVERT: A 577 ASP cc_start: 0.7310 (t70) cc_final: 0.6644 (t70) REVERT: A 582 ILE cc_start: 0.9489 (mp) cc_final: 0.9143 (mt) REVERT: A 642 LEU cc_start: 0.8820 (mp) cc_final: 0.8580 (pt) REVERT: A 709 ARG cc_start: 0.7224 (tmt-80) cc_final: 0.6670 (tpt90) REVERT: B 274 ILE cc_start: 0.8559 (tp) cc_final: 0.8316 (tp) REVERT: B 316 THR cc_start: 0.8206 (p) cc_final: 0.7908 (p) REVERT: B 332 MET cc_start: 0.7965 (ppp) cc_final: 0.7671 (ppp) REVERT: B 388 MET cc_start: 0.8194 (ptm) cc_final: 0.6793 (ppp) REVERT: B 508 MET cc_start: 0.6602 (mmm) cc_final: 0.6157 (mmm) REVERT: B 564 ASP cc_start: 0.8836 (m-30) cc_final: 0.8330 (m-30) REVERT: B 572 CYS cc_start: 0.5578 (p) cc_final: 0.5283 (p) REVERT: B 602 ASN cc_start: 0.9226 (m110) cc_final: 0.8888 (m-40) REVERT: C 348 ASN cc_start: 0.8782 (p0) cc_final: 0.7738 (t0) REVERT: C 349 ARG cc_start: 0.8340 (tpm170) cc_final: 0.8057 (mmm160) REVERT: C 388 MET cc_start: 0.7368 (ptp) cc_final: 0.5752 (ppp) REVERT: C 402 GLU cc_start: 0.7742 (mt-10) cc_final: 0.6966 (pt0) REVERT: C 549 THR cc_start: 0.7589 (p) cc_final: 0.7363 (p) REVERT: C 551 TRP cc_start: 0.6400 (t60) cc_final: 0.5191 (t-100) REVERT: C 564 ASP cc_start: 0.8791 (t0) cc_final: 0.8367 (t0) REVERT: C 602 ASN cc_start: 0.8882 (m110) cc_final: 0.8148 (t0) REVERT: D 132 GLU cc_start: 0.7488 (mm-30) cc_final: 0.6723 (pm20) REVERT: D 449 MET cc_start: 0.7093 (ptt) cc_final: 0.6883 (tmm) REVERT: D 508 MET cc_start: 0.4646 (mmt) cc_final: 0.3896 (mtp) REVERT: D 568 GLN cc_start: 0.8055 (pp30) cc_final: 0.7628 (tm-30) REVERT: D 602 ASN cc_start: 0.8921 (t0) cc_final: 0.8658 (t0) REVERT: E 83 ARG cc_start: 0.5884 (mtp180) cc_final: 0.5679 (mtm-85) REVERT: E 427 MET cc_start: 0.8064 (ppp) cc_final: 0.7504 (ppp) REVERT: E 549 THR cc_start: 0.8145 (p) cc_final: 0.7916 (p) REVERT: E 690 ILE cc_start: 0.7720 (mp) cc_final: 0.7483 (mp) REVERT: F 52 PHE cc_start: 0.6264 (m-80) cc_final: 0.5621 (m-80) REVERT: F 194 GLU cc_start: 0.8195 (tt0) cc_final: 0.7755 (tt0) REVERT: F 484 ASP cc_start: 0.7199 (p0) cc_final: 0.6739 (p0) REVERT: F 560 ARG cc_start: 0.8515 (mpt-90) cc_final: 0.8088 (mpt-90) REVERT: F 561 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8900 (mt-10) REVERT: F 562 ILE cc_start: 0.8908 (pt) cc_final: 0.8635 (pt) REVERT: F 564 ASP cc_start: 0.8992 (m-30) cc_final: 0.8630 (m-30) REVERT: F 580 ASP cc_start: 0.7928 (m-30) cc_final: 0.7652 (m-30) REVERT: F 606 THR cc_start: 0.8610 (m) cc_final: 0.8285 (p) REVERT: I 332 MET cc_start: 0.3297 (mmt) cc_final: 0.2980 (mmm) REVERT: J 332 MET cc_start: 0.0819 (ttt) cc_final: 0.0505 (ttt) outliers start: 1 outliers final: 0 residues processed: 516 average time/residue: 0.4529 time to fit residues: 378.8864 Evaluate side-chains 400 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 4.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 366 optimal weight: 6.9990 chunk 385 optimal weight: 1.9990 chunk 352 optimal weight: 5.9990 chunk 375 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 339 optimal weight: 0.2980 chunk 355 optimal weight: 0.9990 chunk 374 optimal weight: 6.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 680 ASN J 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33789 Z= 0.204 Angle : 0.681 11.001 45698 Z= 0.347 Chirality : 0.046 0.277 5167 Planarity : 0.005 0.076 5980 Dihedral : 9.024 130.651 4798 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.60 % Favored : 90.38 % Rotamer: Outliers : 0.03 % Allowed : 0.62 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % 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: -1.71 (0.13), residues: 4157 helix: -0.02 (0.13), residues: 1640 sheet: -1.28 (0.22), residues: 527 loop : -2.07 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 476 HIS 0.003 0.001 HIS D 735 PHE 0.043 0.002 PHE C 267 TYR 0.022 0.002 TYR F 173 ARG 0.012 0.000 ARG B 662 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 517 time to evaluate : 3.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 307 ASP cc_start: 0.7039 (t0) cc_final: 0.6830 (t0) REVERT: A 442 MET cc_start: 0.6790 (mpp) cc_final: 0.5844 (tpp) REVERT: A 540 ILE cc_start: 0.8943 (tp) cc_final: 0.8688 (tp) REVERT: A 582 ILE cc_start: 0.9513 (mp) cc_final: 0.9144 (mt) REVERT: A 602 ASN cc_start: 0.9212 (m-40) cc_final: 0.8600 (t0) REVERT: A 642 LEU cc_start: 0.8806 (mp) cc_final: 0.8526 (pt) REVERT: B 274 ILE cc_start: 0.8565 (tp) cc_final: 0.8341 (tp) REVERT: B 388 MET cc_start: 0.8200 (ptm) cc_final: 0.6793 (ppp) REVERT: B 564 ASP cc_start: 0.8888 (m-30) cc_final: 0.8393 (m-30) REVERT: B 602 ASN cc_start: 0.9198 (m110) cc_final: 0.8912 (m-40) REVERT: C 388 MET cc_start: 0.7369 (ptp) cc_final: 0.5765 (ppp) REVERT: C 402 GLU cc_start: 0.7732 (mt-10) cc_final: 0.7055 (pt0) REVERT: C 489 LEU cc_start: 0.8635 (mm) cc_final: 0.8332 (mm) REVERT: C 551 TRP cc_start: 0.6308 (t60) cc_final: 0.5114 (t-100) REVERT: C 564 ASP cc_start: 0.8795 (t0) cc_final: 0.8350 (t0) REVERT: C 602 ASN cc_start: 0.8872 (m110) cc_final: 0.8293 (t0) REVERT: C 695 CYS cc_start: 0.6727 (t) cc_final: 0.6513 (t) REVERT: D 84 MET cc_start: 0.5326 (ppp) cc_final: 0.5112 (ppp) REVERT: D 132 GLU cc_start: 0.7503 (mm-30) cc_final: 0.6723 (pm20) REVERT: D 508 MET cc_start: 0.3681 (mmt) cc_final: 0.3441 (mtp) REVERT: D 568 GLN cc_start: 0.8058 (pp30) cc_final: 0.7632 (tm-30) REVERT: D 602 ASN cc_start: 0.8927 (t0) cc_final: 0.8668 (t0) REVERT: E 83 ARG cc_start: 0.5869 (mtp180) cc_final: 0.5661 (mtm-85) REVERT: E 427 MET cc_start: 0.8034 (ppp) cc_final: 0.7474 (ppp) REVERT: F 52 PHE cc_start: 0.6195 (m-80) cc_final: 0.5453 (m-80) REVERT: F 194 GLU cc_start: 0.8092 (tt0) cc_final: 0.7776 (tt0) REVERT: F 205 ASP cc_start: 0.7231 (t0) cc_final: 0.7025 (t0) REVERT: F 484 ASP cc_start: 0.7280 (p0) cc_final: 0.6816 (p0) REVERT: F 508 MET cc_start: 0.5361 (mmt) cc_final: 0.4458 (mmt) REVERT: F 558 ASN cc_start: 0.7721 (t0) cc_final: 0.7098 (t0) REVERT: F 560 ARG cc_start: 0.8518 (mpt-90) cc_final: 0.8144 (mpt-90) REVERT: F 562 ILE cc_start: 0.8963 (pt) cc_final: 0.8626 (pt) REVERT: F 564 ASP cc_start: 0.9004 (m-30) cc_final: 0.8622 (m-30) REVERT: I 332 MET cc_start: 0.3269 (mmt) cc_final: 0.2983 (mmm) REVERT: J 332 MET cc_start: 0.0985 (ttt) cc_final: 0.0672 (ttt) outliers start: 1 outliers final: 0 residues processed: 517 average time/residue: 0.4491 time to fit residues: 375.5615 Evaluate side-chains 406 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 3.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 246 optimal weight: 10.0000 chunk 397 optimal weight: 50.0000 chunk 242 optimal weight: 2.9990 chunk 188 optimal weight: 30.0000 chunk 275 optimal weight: 0.0670 chunk 416 optimal weight: 40.0000 chunk 383 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 256 optimal weight: 30.0000 chunk 203 optimal weight: 7.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN C 406 HIS ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 558 ASN E 421 GLN ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 33789 Z= 0.330 Angle : 0.775 10.864 45698 Z= 0.400 Chirality : 0.048 0.312 5167 Planarity : 0.006 0.076 5980 Dihedral : 9.278 135.853 4798 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 25.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.78 % Favored : 89.17 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.13), residues: 4157 helix: -0.36 (0.13), residues: 1631 sheet: -1.33 (0.22), residues: 513 loop : -2.18 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C 476 HIS 0.007 0.002 HIS D 735 PHE 0.034 0.002 PHE C 267 TYR 0.022 0.002 TYR D 517 ARG 0.014 0.001 ARG B 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8314 Ramachandran restraints generated. 4157 Oldfield, 0 Emsley, 4157 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 3.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 ASP cc_start: 0.7170 (t0) cc_final: 0.6804 (t0) REVERT: A 442 MET cc_start: 0.6979 (mpp) cc_final: 0.6301 (tpp) REVERT: A 540 ILE cc_start: 0.8960 (tp) cc_final: 0.8708 (tp) REVERT: A 564 ASP cc_start: 0.9150 (t0) cc_final: 0.8949 (t0) REVERT: A 582 ILE cc_start: 0.9516 (mp) cc_final: 0.9033 (tt) REVERT: A 642 LEU cc_start: 0.8911 (mp) cc_final: 0.8565 (pt) REVERT: A 709 ARG cc_start: 0.7521 (tpt90) cc_final: 0.7107 (tpt90) REVERT: B 274 ILE cc_start: 0.8633 (tp) cc_final: 0.8407 (tp) REVERT: B 316 THR cc_start: 0.8235 (p) cc_final: 0.7992 (p) REVERT: B 388 MET cc_start: 0.8219 (ptm) cc_final: 0.6712 (ppp) REVERT: B 564 ASP cc_start: 0.9034 (m-30) cc_final: 0.8512 (m-30) REVERT: B 572 CYS cc_start: 0.5806 (p) cc_final: 0.5566 (p) REVERT: B 602 ASN cc_start: 0.9333 (m-40) cc_final: 0.9028 (m-40) REVERT: C 388 MET cc_start: 0.7238 (ptp) cc_final: 0.5845 (ppp) REVERT: C 489 LEU cc_start: 0.8648 (mm) cc_final: 0.8364 (mm) REVERT: C 549 THR cc_start: 0.7699 (p) cc_final: 0.7474 (p) REVERT: C 551 TRP cc_start: 0.6421 (t60) cc_final: 0.5929 (t60) REVERT: C 564 ASP cc_start: 0.8838 (t0) cc_final: 0.8426 (t0) REVERT: C 602 ASN cc_start: 0.8944 (m110) cc_final: 0.8253 (t0) REVERT: C 695 CYS cc_start: 0.6707 (t) cc_final: 0.6497 (t) REVERT: D 84 MET cc_start: 0.5202 (ppp) cc_final: 0.4950 (ppp) REVERT: D 564 ASP cc_start: 0.8153 (m-30) cc_final: 0.7558 (m-30) REVERT: D 568 GLN cc_start: 0.8068 (pp30) cc_final: 0.7719 (tm-30) REVERT: D 678 MET cc_start: 0.6995 (ttm) cc_final: 0.6750 (ttp) REVERT: E 84 MET cc_start: 0.4028 (ptt) cc_final: 0.3824 (ptt) REVERT: E 140 LEU cc_start: 0.7949 (pp) cc_final: 0.7479 (mt) REVERT: E 427 MET cc_start: 0.8183 (ppp) cc_final: 0.7546 (ppp) REVERT: E 558 ASN cc_start: 0.9425 (m110) cc_final: 0.8996 (t0) REVERT: F 304 ASP cc_start: 0.6512 (t0) cc_final: 0.5553 (t0) REVERT: F 542 ILE cc_start: 0.9496 (mp) cc_final: 0.9120 (tp) REVERT: F 560 ARG cc_start: 0.8479 (mpt-90) cc_final: 0.8085 (mpt-90) REVERT: F 561 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8940 (mt-10) REVERT: F 564 ASP cc_start: 0.9033 (m-30) cc_final: 0.8723 (m-30) REVERT: F 580 ASP cc_start: 0.8019 (m-30) cc_final: 0.7180 (m-30) REVERT: F 606 THR cc_start: 0.8737 (m) cc_final: 0.8397 (p) REVERT: I 332 MET cc_start: 0.3581 (mmt) cc_final: 0.3189 (mmm) REVERT: J 300 ILE cc_start: 0.7829 (mm) cc_final: 0.7612 (tp) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.4546 time to fit residues: 366.1975 Evaluate side-chains 379 residues out of total 3570 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 418 random chunks: chunk 263 optimal weight: 20.0000 chunk 353 optimal weight: 10.0000 chunk 101 optimal weight: 0.0980 chunk 305 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 332 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 341 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 GLN C 406 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 680 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 558 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 183 HIS ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 460 ASN F 680 ASN ** F 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.099332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075432 restraints weight = 129486.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.076837 restraints weight = 88789.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.077934 restraints weight = 66027.252| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33789 Z= 0.219 Angle : 0.715 13.686 45698 Z= 0.366 Chirality : 0.048 0.476 5167 Planarity : 0.005 0.072 5980 Dihedral : 9.075 131.723 4798 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.62 % Favored : 90.33 % Rotamer: Outliers : 0.06 % Allowed : 0.34 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.65 % Cis-general : 0.00 % Twisted Proline : 1.33 % Twisted General : 0.03 % 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: -1.87 (0.13), residues: 4157 helix: -0.18 (0.13), residues: 1638 sheet: -1.33 (0.22), residues: 520 loop : -2.15 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 551 HIS 0.005 0.001 HIS B 406 PHE 0.036 0.002 PHE B 506 TYR 0.020 0.002 TYR A 495 ARG 0.022 0.001 ARG E 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7769.17 seconds wall clock time: 141 minutes 24.38 seconds (8484.38 seconds total)