Starting phenix.real_space_refine on Sat Mar 23 03:30:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/03_2024/7r7t_24304_updated.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 24 5.49 5 S 182 5.16 5 C 22167 2.51 5 N 6282 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 107": "OD1" <-> "OD2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 424": "NH1" <-> "NH2" Residue "A GLU 491": "OE1" <-> "OE2" Residue "A PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 689": "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 "A PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 294": "OE1" <-> "OE2" Residue "F GLU 305": "OE1" <-> "OE2" Residue "F ARG 358": "NH1" <-> "NH2" Residue "F ARG 424": "NH1" <-> "NH2" Residue "F ASP 428": "OD1" <-> "OD2" Residue "F GLU 440": "OE1" <-> "OE2" Residue "F GLU 483": "OE1" <-> "OE2" Residue "F PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 561": "OE1" <-> "OE2" Residue "F ARG 599": "NH1" <-> "NH2" Residue "F ASP 630": "OD1" <-> "OD2" Residue "F TYR 644": "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 "E GLU 34": "OE1" <-> "OE2" Residue "E TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 195": "OE1" <-> "OE2" Residue "E GLU 305": "OE1" <-> "OE2" Residue "E ARG 323": "NH1" <-> "NH2" Residue "E ARG 358": "NH1" <-> "NH2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E PHE 576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 598": "OD1" <-> "OD2" Residue "E ARG 599": "NH1" <-> "NH2" Residue "E ARG 708": "NH1" <-> "NH2" Residue "E ARG 733": "NH1" <-> "NH2" Residue "E ARG 741": "NH1" <-> "NH2" Residue "E PHE 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 753": "NH1" <-> "NH2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 194": "OE1" <-> "OE2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 323": "NH1" <-> "NH2" Residue "D ARG 358": "NH1" <-> "NH2" Residue "D GLU 379": "OE1" <-> "OE2" Residue "D ASP 410": "OD1" <-> "OD2" Residue "D ARG 424": "NH1" <-> "NH2" Residue "D ASP 438": "OD1" <-> "OD2" Residue "D PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 484": "OD1" <-> "OD2" Residue "D TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D GLU 554": "OE1" <-> "OE2" Residue "D ARG 599": "NH1" <-> "NH2" Residue "D ARG 708": "NH1" <-> "NH2" Residue "D ARG 733": "NH1" <-> "NH2" Residue "D GLU 738": "OE1" <-> "OE2" Residue "D ARG 741": "NH1" <-> "NH2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "C TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 196": "OE1" <-> "OE2" Residue "C TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 294": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 358": "NH1" <-> "NH2" Residue "C GLU 417": "OE1" <-> "OE2" Residue "C ARG 424": "NH1" <-> "NH2" Residue "C PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 599": "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 ARG 753": "NH1" <-> "NH2" Residue "C ARG 766": "NH1" <-> "NH2" Residue "C PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 772": "NH1" <-> "NH2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 338": "NH1" <-> "NH2" Residue "B ASP 354": "OD1" <-> "OD2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B ARG 599": "NH1" <-> "NH2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 708": "NH1" <-> "NH2" Residue "B GLU 730": "OE1" <-> "OE2" Residue "B GLU 738": "OE1" <-> "OE2" Residue "B ARG 741": "NH1" <-> "NH2" Residue "B ARG 753": "NH1" <-> "NH2" Residue "B PHE 758": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 280": "OE1" <-> "OE2" Residue "I GLU 347": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35351 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5724 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 688} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5707 Classifications: {'peptide': 725} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 683} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5692 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 685} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5686 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 683} Chain breaks: 3 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: "C" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5736 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 689} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5704 Classifications: {'peptide': 727} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.01, per 1000 atoms: 0.51 Number of scatterers: 35351 At special positions: 0 Unit cell: (132.822, 170.973, 166.734, 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 182 16.00 P 24 15.00 O 6696 8.00 N 6282 7.00 C 22167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.83 Conformation dependent library (CDL) restraints added in 5.9 seconds 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8380 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 174 helices and 30 sheets defined 35.5% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.29 Creating SS restraints... Processing helix chain 'A' and resid 43 through 48 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 87 through 90 No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.811A pdb=" N ALA A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 233 No H-bonds generated for 'chain 'A' and resid 230 through 233' Processing helix chain 'A' and resid 252 through 258 removed outlier: 4.402A pdb=" N VAL A 258 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 287 through 295 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 320 through 333 Processing helix chain 'A' and resid 355 through 358 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 381 through 384 No H-bonds generated for 'chain 'A' and resid 381 through 384' Processing helix chain 'A' and resid 397 through 400 No H-bonds generated for 'chain 'A' and resid 397 through 400' Processing helix chain 'A' and resid 408 through 425 Processing helix chain 'A' and resid 449 through 457 Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.867A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 522 through 535 Processing helix chain 'A' and resid 544 through 553 removed outlier: 3.654A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 568 Processing helix chain 'A' and resid 579 through 588 removed outlier: 3.908A pdb=" N ILE A 582 " --> pdb=" O LEU A 579 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 586 " --> pdb=" O ALA A 583 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 587 " --> pdb=" O LYS A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 609 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 661 removed outlier: 4.078A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 678 Processing helix chain 'A' and resid 684 through 711 Processing helix chain 'A' and resid 733 through 741 removed outlier: 4.460A pdb=" N ARG A 741 " --> pdb=" O GLU A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 762 removed outlier: 3.803A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 48 Processing helix chain 'F' and resid 87 through 90 No H-bonds generated for 'chain 'F' and resid 87 through 90' Processing helix chain 'F' and resid 193 through 198 removed outlier: 3.905A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 221 Processing helix chain 'F' and resid 228 through 233 removed outlier: 3.846A pdb=" N ILE F 233 " --> pdb=" O PHE F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 258 removed outlier: 3.660A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 275 removed outlier: 4.070A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 271 through 275' Processing helix chain 'F' and resid 287 through 293 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 320 through 333 Processing helix chain 'F' and resid 376 through 384 Processing helix chain 'F' and resid 408 through 425 Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 449 through 458 removed outlier: 3.803A pdb=" N GLN F 458 " --> pdb=" O TRP F 454 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 492 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 500 through 506 removed outlier: 4.249A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 524 through 534 Processing helix chain 'F' and resid 544 through 552 Processing helix chain 'F' and resid 557 through 568 Processing helix chain 'F' and resid 579 through 586 removed outlier: 3.711A pdb=" N ILE F 582 " --> pdb=" O LEU F 579 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA F 585 " --> pdb=" O ILE F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 601 through 610 Processing helix chain 'F' and resid 650 through 663 removed outlier: 4.035A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 673 through 678 Processing helix chain 'F' and resid 684 through 712 Processing helix chain 'F' and resid 734 through 741 removed outlier: 3.780A pdb=" N GLU F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 749 through 760 Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 86 through 91 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' 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 210 through 221 removed outlier: 4.631A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.505A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 3.564A pdb=" N ALA E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 274 No H-bonds generated for 'chain 'E' and resid 271 through 274' Processing helix chain 'E' and resid 287 through 295 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 320 through 332 Processing helix chain 'E' and resid 374 through 384 Processing helix chain 'E' and resid 397 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 483 through 498 removed outlier: 4.696A 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 506 removed outlier: 3.694A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 534 Processing helix chain 'E' and resid 544 through 552 Processing helix chain 'E' and resid 556 through 568 removed outlier: 3.957A pdb=" N VAL E 559 " --> pdb=" O GLU E 556 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU E 561 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 586 Processing helix chain 'E' and resid 601 through 609 removed outlier: 3.509A pdb=" N LEU E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 628 No H-bonds generated for 'chain 'E' and resid 626 through 628' Processing helix chain 'E' and resid 631 through 634 No H-bonds generated for 'chain 'E' and resid 631 through 634' Processing helix chain 'E' and resid 650 through 661 Processing helix chain 'E' and resid 679 through 681 No H-bonds generated for 'chain 'E' and resid 679 through 681' Processing helix chain 'E' and resid 684 through 712 removed outlier: 3.548A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) Processing helix chain 'E' and resid 733 through 741 Processing helix chain 'E' and resid 749 through 761 Processing helix chain 'D' and resid 43 through 48 removed outlier: 3.625A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 48' Processing helix chain 'D' and resid 86 through 91 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 210 through 221 removed outlier: 4.549A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 233 removed outlier: 3.683A pdb=" N PHE D 230 " --> pdb=" O PRO D 227 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 231 " --> pdb=" O ALA D 228 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 233 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 258 Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 287 through 294 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 320 through 334 Processing helix chain 'D' and resid 355 through 358 Processing helix chain 'D' and resid 374 through 386 Processing helix chain 'D' and resid 398 through 402 removed outlier: 3.649A pdb=" N GLU D 402 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 425 Processing helix chain 'D' and resid 439 through 442 No H-bonds generated for 'chain 'D' and resid 439 through 442' Processing helix chain 'D' and resid 449 through 457 Processing helix chain 'D' and resid 483 through 498 removed outlier: 3.550A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 4.364A 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 500 through 506 removed outlier: 3.765A pdb=" N PHE D 506 " --> pdb=" O PHE D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 Processing helix chain 'D' and resid 544 through 553 Processing helix chain 'D' and resid 558 through 568 Processing helix chain 'D' and resid 580 through 585 Processing helix chain 'D' and resid 599 through 609 Processing helix chain 'D' and resid 653 through 659 Processing helix chain 'D' and resid 684 through 712 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 749 through 761 Processing helix chain 'C' and resid 43 through 49 removed outlier: 4.089A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 135 through 138 No H-bonds generated for 'chain 'C' and resid 135 through 138' Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 210 through 221 removed outlier: 4.739A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 233 removed outlier: 3.581A pdb=" N LYS C 231 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE C 233 " --> pdb=" O PHE C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 258 Processing helix chain 'C' and resid 271 through 275 Processing helix chain 'C' and resid 287 through 294 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 Processing helix chain 'C' and resid 374 through 384 Processing helix chain 'C' and resid 398 through 401 No H-bonds generated for 'chain 'C' and resid 398 through 401' Processing helix chain 'C' and resid 408 through 425 Processing helix chain 'C' and resid 449 through 457 Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 494 through 498 Processing helix chain 'C' and resid 501 through 504 No H-bonds generated for 'chain 'C' and resid 501 through 504' Processing helix chain 'C' and resid 524 through 534 removed outlier: 3.849A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 552 Processing helix chain 'C' and resid 556 through 568 Processing helix chain 'C' and resid 579 through 587 removed outlier: 3.531A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 Processing helix chain 'C' and resid 650 through 660 removed outlier: 4.277A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN C 660 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 712 removed outlier: 4.073A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 733 through 741 Processing helix chain 'C' and resid 749 through 762 removed outlier: 3.694A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 130 through 133 No H-bonds generated for 'chain 'B' and resid 130 through 133' Processing helix chain 'B' and resid 135 through 138 No H-bonds generated for 'chain 'B' and resid 135 through 138' Processing helix chain 'B' and resid 194 through 197 No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 210 through 220 removed outlier: 4.186A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'B' and resid 251 through 258 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 288 through 295 removed outlier: 3.554A pdb=" N GLU B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYS B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) 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 320 through 332 Processing helix chain 'B' and resid 374 through 385 Processing helix chain 'B' and resid 398 through 401 No H-bonds generated for 'chain 'B' and resid 398 through 401' Processing helix chain 'B' and resid 408 through 425 Processing helix chain 'B' and resid 449 through 457 Processing helix chain 'B' and resid 483 through 493 removed outlier: 3.672A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 527 through 533 Processing helix chain 'B' and resid 544 through 552 Processing helix chain 'B' and resid 558 through 568 Processing helix chain 'B' and resid 579 through 587 Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 650 through 661 Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.678A pdb=" N ALA B 676 " --> pdb=" O GLU B 673 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS B 677 " --> pdb=" O PHE B 674 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N MET B 678 " --> pdb=" O LEU B 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 673 through 678' Processing helix chain 'B' and resid 684 through 712 Processing helix chain 'B' and resid 739 through 742 Processing helix chain 'B' and resid 749 through 762 Processing helix chain 'I' and resid 276 through 286 Processing helix chain 'I' and resid 318 through 328 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.595A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 365 through 368 Processing sheet with id= C, first strand: chain 'A' and resid 513 through 517 removed outlier: 8.399A pdb=" N VAL A 514 " --> pdb=" O VAL A 617 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE A 619 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N PHE A 516 " --> pdb=" O ILE A 619 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY A 621 " --> pdb=" O PHE A 516 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N CYS A 572 " --> pdb=" O PHE A 618 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N ILE A 620 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 574 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA A 622 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE A 576 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'F' and resid 66 through 69 Processing sheet with id= E, first strand: chain 'F' and resid 151 through 153 removed outlier: 3.984A pdb=" N PHE F 152 " --> pdb=" O PHE F 163 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE F 163 " --> pdb=" O PHE F 152 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'F' and resid 365 through 368 removed outlier: 6.306A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 641 through 645 removed outlier: 4.098A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N VAL F 514 " --> pdb=" O VAL F 617 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ILE F 619 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N PHE F 516 " --> pdb=" O ILE F 619 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLY F 621 " --> pdb=" O PHE F 516 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N GLY F 518 " --> pdb=" O GLY F 621 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N THR F 623 " --> pdb=" O GLY F 518 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS F 572 " --> pdb=" O PHE F 618 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE F 620 " --> pdb=" O CYS F 572 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU F 574 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ALA F 622 " --> pdb=" O LEU F 574 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N PHE F 576 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 81 through 83 removed outlier: 7.756A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL E 39 " --> pdb=" O ILE E 70 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 41 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 181 through 183 removed outlier: 3.840A pdb=" N GLU E 167 " --> pdb=" O HIS E 115 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU E 117 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL E 165 " --> pdb=" O LEU E 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.578A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 365 through 368 removed outlier: 3.520A pdb=" N LEU E 242 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR E 244 " --> pdb=" O VAL E 367 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL E 343 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N LEU E 243 " --> pdb=" O VAL E 343 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA E 345 " --> pdb=" O LEU E 243 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 641 through 645 removed outlier: 7.223A pdb=" N ILE E 619 " --> pdb=" O VAL E 514 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N PHE E 516 " --> pdb=" O ILE E 619 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLY E 621 " --> pdb=" O PHE E 516 " (cutoff:3.500A) removed outlier: 8.938A pdb=" N GLY E 518 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN E 538 " --> pdb=" O VAL E 573 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N PHE E 575 " --> pdb=" O ASN E 538 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE E 540 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 27 through 30 Processing sheet with id= N, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.310A pdb=" N ILE D 70 " --> pdb=" O VAL D 39 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU D 41 " --> pdb=" O ILE D 70 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU D 72 " --> pdb=" O LEU D 41 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 57 through 60 removed outlier: 3.680A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.640A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 240 through 244 removed outlier: 8.904A pdb=" N ILE D 241 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL D 343 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LEU D 243 " --> pdb=" O VAL D 343 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA D 345 " --> pdb=" O LEU D 243 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 538 through 542 removed outlier: 4.074A pdb=" N ASP D 577 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP D 640 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU D 515 " --> pdb=" O ASP D 640 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N LEU D 642 " --> pdb=" O LEU D 515 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N TYR D 517 " --> pdb=" O LEU D 642 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR D 644 " --> pdb=" O TYR D 517 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 81 through 84 removed outlier: 7.963A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 100 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 181 through 183 removed outlier: 6.459A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.551A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 365 through 368 removed outlier: 3.961A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 367 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR C 244 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 343 " --> pdb=" O ILE C 241 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU C 243 " --> pdb=" O VAL C 343 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA C 345 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 641 through 644 removed outlier: 4.231A pdb=" N GLN C 641 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU C 515 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ILE C 619 " --> pdb=" O VAL C 514 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE C 516 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY C 621 " --> pdb=" O PHE C 516 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 81 through 84 removed outlier: 7.669A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 181 through 183 removed outlier: 3.753A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'B' and resid 145 through 147 Processing sheet with id= AA, first strand: chain 'B' and resid 365 through 368 removed outlier: 6.128A pdb=" N VAL B 343 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N LEU B 243 " --> pdb=" O VAL B 343 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ALA B 345 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 619 through 623 removed outlier: 4.052A pdb=" N GLY B 518 " --> pdb=" O THR B 623 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLN B 641 " --> pdb=" O LEU B 515 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N TYR B 517 " --> pdb=" O GLN B 641 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 643 " --> pdb=" O TYR B 517 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 539 through 542 removed outlier: 6.124A pdb=" N VAL B 573 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE B 542 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE B 575 " --> pdb=" O ILE B 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'I' and resid 338 through 340 998 hydrogen bonds defined for protein. 2835 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: 13.35 Time building geometry restraints manager: 14.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10998 1.34 - 1.46: 5221 1.46 - 1.58: 19400 1.58 - 1.70: 36 1.70 - 1.82: 292 Bond restraints: 35947 Sorted by residual: bond pdb=" C PRO F 237 " pdb=" N PRO F 238 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.59e+00 bond pdb=" C PRO C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C SER A 171 " pdb=" N PRO A 172 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.53e+00 bond pdb=" C PRO E 237 " pdb=" N PRO E 238 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.21e+00 bond pdb=" CB ASP B 669 " pdb=" CG ASP B 669 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.99e+00 ... (remaining 35942 not shown) Histogram of bond angle deviations from ideal: 97.71 - 105.84: 1014 105.84 - 113.97: 20425 113.97 - 122.10: 19957 122.10 - 130.23: 7034 130.23 - 138.36: 163 Bond angle restraints: 48593 Sorted by residual: angle pdb=" N VAL A 399 " pdb=" CA VAL A 399 " pdb=" C VAL A 399 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N GLU A 261 " pdb=" CA GLU A 261 " pdb=" C GLU A 261 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" CA LEU F 548 " pdb=" CB LEU F 548 " pdb=" CG LEU F 548 " ideal model delta sigma weight residual 116.30 135.03 -18.73 3.50e+00 8.16e-02 2.86e+01 angle pdb=" C LYS D 614 " pdb=" N LYS D 615 " pdb=" CA LYS D 615 " ideal model delta sigma weight residual 121.54 131.76 -10.22 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS B 63 " pdb=" N ARG B 64 " pdb=" CA ARG B 64 " ideal model delta sigma weight residual 122.08 129.90 -7.82 1.47e+00 4.63e-01 2.83e+01 ... (remaining 48588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 21736 35.20 - 70.41: 496 70.41 - 105.61: 35 105.61 - 140.81: 11 140.81 - 176.01: 3 Dihedral angle restraints: 22281 sinusoidal: 9388 harmonic: 12893 Sorted by residual: dihedral pdb=" CA ARG B 22 " pdb=" C ARG B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 -134.13 -45.87 0 5.00e+00 4.00e-02 8.41e+01 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 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 dihedral pdb=" CA ILE A 114 " pdb=" C ILE A 114 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta harmonic sigma weight residual 180.00 -139.48 -40.52 0 5.00e+00 4.00e-02 6.57e+01 ... (remaining 22278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4698 0.087 - 0.174: 713 0.174 - 0.260: 50 0.260 - 0.347: 5 0.347 - 0.434: 4 Chirality restraints: 5470 Sorted by residual: chirality pdb=" CB VAL D 407 " pdb=" CA VAL D 407 " pdb=" CG1 VAL D 407 " pdb=" CG2 VAL D 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL A 407 " pdb=" CA VAL A 407 " pdb=" CG1 VAL A 407 " pdb=" CG2 VAL A 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB VAL F 407 " pdb=" CA VAL F 407 " pdb=" CG1 VAL F 407 " pdb=" CG2 VAL F 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 5467 not shown) Planarity restraints: 6370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 22 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ARG B 22 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG B 22 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B 23 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 169 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO D 170 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 271 " -0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO B 272 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.049 5.00e-02 4.00e+02 ... (remaining 6367 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9566 2.81 - 3.33: 32445 3.33 - 3.85: 59814 3.85 - 4.38: 66858 4.38 - 4.90: 108566 Nonbonded interactions: 277249 Sorted by model distance: nonbonded pdb=" O CYS D 522 " pdb=" OG1 THR D 525 " model vdw 2.286 2.440 nonbonded pdb=" O PRO D 272 " pdb=" OG SER D 276 " model vdw 2.295 2.440 nonbonded pdb=" OG1 THR C 448 " pdb=" OD1 ASP C 450 " model vdw 2.302 2.440 nonbonded pdb=" OG SER D 702 " pdb=" O PRO D 727 " model vdw 2.323 2.440 nonbonded pdb=" O LEU B 381 " pdb=" OG1 THR B 385 " model vdw 2.325 2.440 ... (remaining 277244 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 24 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 432 or resid 439 through 587 or \ resid 598 through 763 or resid 901 through 902)) selection = (chain 'B' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 587 or resid 598 through 763 or resid 901 thr \ ough 902)) selection = (chain 'C' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 587 or resid 598 through 763 or resid 901 thr \ ough 902)) selection = (chain 'D' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 432 or resid 439 through 587 or resid 598 thr \ ough 763 or resid 901 through 902)) selection = (chain 'E' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 432 or resid 439 through 587 or resid 598 thr \ ough 763 or resid 901 through 902)) selection = (chain 'F' and (resid 24 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 763 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.110 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 92.710 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 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 35947 Z= 0.279 Angle : 1.024 18.726 48593 Z= 0.537 Chirality : 0.059 0.434 5470 Planarity : 0.008 0.101 6370 Dihedral : 15.884 176.014 13901 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.11), residues: 4424 helix: -2.17 (0.10), residues: 1687 sheet: -0.69 (0.22), residues: 550 loop : -2.36 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 454 HIS 0.008 0.001 HIS A 115 PHE 0.037 0.002 PHE C 363 TYR 0.014 0.002 TYR A 134 ARG 0.010 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 932 time to evaluate : 4.332 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: 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 200 GLU cc_start: 0.8974 (pm20) cc_final: 0.8693 (mp0) REVERT: A 218 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8199 (tt0) REVERT: A 241 ILE cc_start: 0.9442 (mm) cc_final: 0.9081 (tp) REVERT: A 274 ILE cc_start: 0.9597 (mm) cc_final: 0.9328 (tp) REVERT: A 300 ILE cc_start: 0.9585 (mt) cc_final: 0.9320 (tp) REVERT: A 360 PHE cc_start: 0.7711 (m-10) cc_final: 0.5522 (m-80) REVERT: A 365 ARG cc_start: 0.9339 (tpt90) cc_final: 0.8751 (mmm160) REVERT: A 388 MET cc_start: 0.7763 (ppp) cc_final: 0.7214 (ppp) REVERT: A 562 ILE cc_start: 0.9676 (mm) cc_final: 0.9383 (mt) REVERT: A 565 LYS cc_start: 0.8882 (pttt) cc_final: 0.8088 (pttm) REVERT: A 567 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8201 (ttp80) REVERT: A 603 GLN cc_start: 0.9577 (mm-40) cc_final: 0.9190 (mm-40) REVERT: A 607 GLU cc_start: 0.9170 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 700 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7943 (tmt170) REVERT: A 757 MET cc_start: 0.8598 (mtp) cc_final: 0.8273 (mmp) REVERT: F 55 ASP cc_start: 0.8555 (m-30) cc_final: 0.8354 (t0) REVERT: F 220 VAL cc_start: 0.9177 (t) cc_final: 0.8864 (m) REVERT: F 304 ASP cc_start: 0.8873 (t0) cc_final: 0.8609 (t0) REVERT: F 305 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8376 (mm-30) REVERT: F 352 SER cc_start: 0.9466 (t) cc_final: 0.9233 (p) REVERT: F 368 ASP cc_start: 0.8996 (p0) cc_final: 0.8773 (t0) REVERT: F 369 ILE cc_start: 0.9667 (mm) cc_final: 0.9402 (tp) REVERT: F 381 LEU cc_start: 0.9613 (tp) cc_final: 0.9343 (tp) REVERT: F 420 LEU cc_start: 0.9428 (tp) cc_final: 0.8641 (tp) REVERT: F 423 ILE cc_start: 0.9280 (mt) cc_final: 0.9019 (mt) REVERT: F 440 GLU cc_start: 0.7886 (mp0) cc_final: 0.7433 (tm-30) REVERT: F 449 MET cc_start: 0.8450 (pmm) cc_final: 0.7854 (ppp) REVERT: F 450 ASP cc_start: 0.8616 (t70) cc_final: 0.8401 (p0) REVERT: F 478 ASP cc_start: 0.8556 (p0) cc_final: 0.7901 (t70) REVERT: F 498 GLU cc_start: 0.8965 (tt0) cc_final: 0.8765 (mp0) REVERT: F 508 MET cc_start: 0.6334 (ttm) cc_final: 0.5266 (ttm) REVERT: F 541 SER cc_start: 0.9122 (p) cc_final: 0.8809 (t) REVERT: F 551 TRP cc_start: 0.7767 (t60) cc_final: 0.7396 (t60) REVERT: F 599 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8667 (ttm110) REVERT: F 639 LEU cc_start: 0.8364 (mp) cc_final: 0.7930 (tt) REVERT: F 642 LEU cc_start: 0.8236 (mt) cc_final: 0.8018 (mt) REVERT: F 765 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7697 (tmm160) REVERT: E 164 LYS cc_start: 0.7981 (tttp) cc_final: 0.7646 (mtmt) REVERT: E 253 LEU cc_start: 0.9244 (mp) cc_final: 0.8891 (mp) REVERT: E 273 GLU cc_start: 0.8991 (mp0) cc_final: 0.8237 (tm-30) REVERT: E 291 GLU cc_start: 0.8978 (mp0) cc_final: 0.8605 (mp0) REVERT: E 309 ILE cc_start: 0.9568 (mt) cc_final: 0.9303 (mp) REVERT: E 344 MET cc_start: 0.9394 (mtt) cc_final: 0.8918 (mtt) REVERT: E 462 SER cc_start: 0.8245 (p) cc_final: 0.8011 (t) REVERT: E 468 VAL cc_start: 0.8926 (m) cc_final: 0.8652 (p) REVERT: E 540 ILE cc_start: 0.9001 (mt) cc_final: 0.8795 (mm) REVERT: E 542 ILE cc_start: 0.9529 (mm) cc_final: 0.9307 (mp) REVERT: E 543 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8912 (mmtm) REVERT: E 563 PHE cc_start: 0.9378 (m-80) cc_final: 0.9140 (m-80) REVERT: E 584 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8193 (mttm) REVERT: E 607 GLU cc_start: 0.9561 (mm-30) cc_final: 0.8946 (mm-30) REVERT: E 678 MET cc_start: 0.9124 (mpp) cc_final: 0.8647 (mpp) REVERT: D 241 ILE cc_start: 0.9111 (mp) cc_final: 0.8886 (mm) REVERT: D 244 TYR cc_start: 0.7928 (p90) cc_final: 0.7238 (p90) REVERT: D 329 LEU cc_start: 0.9417 (mt) cc_final: 0.9157 (mt) REVERT: D 357 LEU cc_start: 0.9415 (tp) cc_final: 0.8881 (tp) REVERT: D 360 PHE cc_start: 0.8644 (m-80) cc_final: 0.8318 (m-10) REVERT: D 388 MET cc_start: 0.8971 (ppp) cc_final: 0.8722 (ppp) REVERT: D 415 CYS cc_start: 0.9443 (m) cc_final: 0.9128 (p) REVERT: D 417 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8698 (tm-30) REVERT: D 464 LEU cc_start: 0.8951 (tp) cc_final: 0.8588 (tp) REVERT: D 515 LEU cc_start: 0.9521 (tp) cc_final: 0.9297 (tp) REVERT: D 542 ILE cc_start: 0.9613 (mm) cc_final: 0.9346 (mp) REVERT: D 560 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7946 (mmm-85) REVERT: D 574 LEU cc_start: 0.9647 (mm) cc_final: 0.9440 (mm) REVERT: C 84 MET cc_start: 0.6112 (ptp) cc_final: 0.5587 (ppp) REVERT: C 275 MET cc_start: 0.9458 (mmm) cc_final: 0.9251 (mmm) REVERT: C 305 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8820 (mm-30) REVERT: C 336 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8534 (mmtm) REVERT: C 449 MET cc_start: 0.8782 (ttm) cc_final: 0.8197 (mtp) REVERT: C 560 ARG cc_start: 0.9205 (mtp180) cc_final: 0.8896 (mtp85) REVERT: C 607 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8415 (mt-10) REVERT: C 623 THR cc_start: 0.9319 (m) cc_final: 0.9091 (m) REVERT: C 662 ARG cc_start: 0.9523 (mpt180) cc_final: 0.9247 (mpp-170) REVERT: C 689 GLU cc_start: 0.9150 (tt0) cc_final: 0.8787 (mt-10) REVERT: C 740 MET cc_start: 0.8530 (ptt) cc_final: 0.8291 (ptt) REVERT: C 756 GLU cc_start: 0.9387 (mp0) cc_final: 0.9158 (tm-30) REVERT: B 138 TYR cc_start: 0.3554 (t80) cc_final: 0.3017 (t80) REVERT: B 246 PRO cc_start: 0.8943 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: B 375 THR cc_start: 0.9028 (p) cc_final: 0.8717 (t) REVERT: B 379 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9087 (mm-30) REVERT: B 407 VAL cc_start: 0.9196 (t) cc_final: 0.8930 (p) REVERT: B 417 GLU cc_start: 0.9453 (tp30) cc_final: 0.8936 (tm-30) REVERT: B 465 ARG cc_start: 0.8874 (ptt-90) cc_final: 0.8016 (ptt-90) REVERT: B 565 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8422 (tppt) REVERT: B 611 MET cc_start: 0.7448 (tpt) cc_final: 0.6720 (tpt) REVERT: B 643 ILE cc_start: 0.9335 (mm) cc_final: 0.8702 (mt) outliers start: 0 outliers final: 0 residues processed: 932 average time/residue: 0.5390 time to fit residues: 779.0524 Evaluate side-chains 574 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 30.0000 chunk 335 optimal weight: 8.9990 chunk 186 optimal weight: 0.0060 chunk 114 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 211 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 402 optimal weight: 20.0000 overall best weight: 5.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN F 384 HIS ** F 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 558 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 384 HIS ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 533 ASN C 602 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35947 Z= 0.331 Angle : 0.802 9.648 48593 Z= 0.406 Chirality : 0.047 0.333 5470 Planarity : 0.006 0.070 6370 Dihedral : 10.402 177.532 4987 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 21.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.16 % Allowed : 6.52 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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: -2.11 (0.12), residues: 4424 helix: -0.78 (0.12), residues: 1699 sheet: -0.71 (0.22), residues: 561 loop : -2.11 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 476 HIS 0.008 0.002 HIS F 499 PHE 0.045 0.002 PHE F 563 TYR 0.025 0.002 TYR A 244 ARG 0.024 0.001 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 641 time to evaluate : 4.067 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: 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 135 LEU cc_start: 0.8391 (mp) cc_final: 0.8169 (mm) REVERT: A 200 GLU cc_start: 0.8881 (pm20) cc_final: 0.8606 (mp0) REVERT: A 218 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8152 (tt0) REVERT: A 291 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8974 (mt-10) REVERT: A 305 GLU cc_start: 0.8114 (tp30) cc_final: 0.7433 (tp30) REVERT: A 321 GLU cc_start: 0.9090 (mp0) cc_final: 0.8865 (mp0) REVERT: A 344 MET cc_start: 0.9108 (mmt) cc_final: 0.8829 (mmp) REVERT: A 388 MET cc_start: 0.8068 (ppp) cc_final: 0.7415 (ppp) REVERT: A 449 MET cc_start: 0.8982 (tmm) cc_final: 0.8714 (tmm) REVERT: A 560 ARG cc_start: 0.9061 (mmm160) cc_final: 0.8664 (mmm160) REVERT: A 567 ARG cc_start: 0.9151 (mmm160) cc_final: 0.8667 (ttp-170) REVERT: A 603 GLN cc_start: 0.9685 (mm-40) cc_final: 0.8911 (mm-40) REVERT: A 607 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8386 (mm-30) REVERT: A 757 MET cc_start: 0.8723 (mtp) cc_final: 0.8421 (mmp) REVERT: F 55 ASP cc_start: 0.8773 (m-30) cc_final: 0.8500 (t0) REVERT: F 220 VAL cc_start: 0.9192 (t) cc_final: 0.8853 (p) REVERT: F 449 MET cc_start: 0.8692 (pmm) cc_final: 0.8260 (ppp) REVERT: F 478 ASP cc_start: 0.8766 (p0) cc_final: 0.7969 (t70) REVERT: F 498 GLU cc_start: 0.9225 (tt0) cc_final: 0.8979 (mt-10) REVERT: F 541 SER cc_start: 0.9052 (p) cc_final: 0.8844 (t) REVERT: F 551 TRP cc_start: 0.7728 (t60) cc_final: 0.7437 (t60) REVERT: F 639 LEU cc_start: 0.8598 (mp) cc_final: 0.8383 (tt) REVERT: F 642 LEU cc_start: 0.8167 (mt) cc_final: 0.7955 (mt) REVERT: F 757 MET cc_start: 0.8734 (tmm) cc_final: 0.8513 (tmm) REVERT: F 765 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7641 (tmm160) REVERT: E 253 LEU cc_start: 0.9279 (mp) cc_final: 0.8995 (mp) REVERT: E 273 GLU cc_start: 0.8991 (mp0) cc_final: 0.8365 (tm-30) REVERT: E 291 GLU cc_start: 0.8962 (mp0) cc_final: 0.8463 (mp0) REVERT: E 305 GLU cc_start: 0.9251 (tp30) cc_final: 0.8445 (tp30) REVERT: E 313 ARG cc_start: 0.9319 (tpp-160) cc_final: 0.8919 (tpt90) REVERT: E 342 ILE cc_start: 0.9331 (pt) cc_final: 0.8787 (mp) REVERT: E 410 ASP cc_start: 0.8694 (m-30) cc_final: 0.8486 (t0) REVERT: E 414 LEU cc_start: 0.9738 (mt) cc_final: 0.9327 (mt) REVERT: E 546 GLU cc_start: 0.9568 (tp30) cc_final: 0.9366 (tp30) REVERT: E 563 PHE cc_start: 0.9436 (m-80) cc_final: 0.9234 (m-80) REVERT: E 584 LYS cc_start: 0.8274 (tmtt) cc_final: 0.7999 (mttm) REVERT: E 608 MET cc_start: 0.7810 (tmm) cc_final: 0.7598 (tmm) REVERT: E 614 LYS cc_start: 0.9101 (mppt) cc_final: 0.8706 (tptt) REVERT: E 615 LYS cc_start: 0.9279 (mmtt) cc_final: 0.9020 (mmtp) REVERT: E 678 MET cc_start: 0.9160 (mpp) cc_final: 0.8653 (mpp) REVERT: E 757 MET cc_start: 0.9373 (ptt) cc_final: 0.9086 (tmm) REVERT: D 219 MET cc_start: 0.8722 (mmp) cc_final: 0.8456 (mmm) REVERT: D 244 TYR cc_start: 0.8409 (p90) cc_final: 0.7697 (p90) REVERT: D 292 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 344 MET cc_start: 0.8876 (tpt) cc_final: 0.8434 (tpp) REVERT: D 417 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8755 (tm-30) REVERT: D 427 MET cc_start: 0.8313 (tpt) cc_final: 0.8057 (tpp) REVERT: D 560 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8198 (mmm-85) REVERT: D 574 LEU cc_start: 0.9423 (mm) cc_final: 0.9152 (mm) REVERT: D 608 MET cc_start: 0.9480 (ttp) cc_final: 0.8915 (ttp) REVERT: D 609 ASP cc_start: 0.8635 (m-30) cc_final: 0.8397 (m-30) REVERT: C 84 MET cc_start: 0.6539 (ptp) cc_final: 0.5764 (ppp) REVERT: C 305 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8909 (mm-30) REVERT: C 449 MET cc_start: 0.8745 (ttm) cc_final: 0.8480 (mtp) REVERT: C 465 ARG cc_start: 0.8017 (mmt-90) cc_final: 0.7632 (mmt180) REVERT: C 607 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8131 (mt-10) REVERT: C 618 PHE cc_start: 0.8072 (t80) cc_final: 0.7831 (t80) REVERT: C 689 GLU cc_start: 0.9218 (tt0) cc_final: 0.8881 (mt-10) REVERT: C 736 PHE cc_start: 0.8490 (m-80) cc_final: 0.8226 (m-80) REVERT: C 740 MET cc_start: 0.8814 (ptt) cc_final: 0.8612 (ptt) REVERT: B 138 TYR cc_start: 0.3647 (t80) cc_final: 0.3042 (t80) REVERT: B 246 PRO cc_start: 0.9338 (Cg_exo) cc_final: 0.8997 (Cg_endo) REVERT: B 275 MET cc_start: 0.9146 (mtp) cc_final: 0.8635 (mtp) REVERT: B 301 ILE cc_start: 0.9144 (tp) cc_final: 0.8928 (tt) REVERT: B 305 GLU cc_start: 0.9121 (tp30) cc_final: 0.8919 (tp30) REVERT: B 379 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9232 (mm-30) REVERT: B 388 MET cc_start: 0.8779 (ppp) cc_final: 0.8565 (ppp) REVERT: B 407 VAL cc_start: 0.9306 (t) cc_final: 0.8767 (p) REVERT: B 417 GLU cc_start: 0.9518 (tp30) cc_final: 0.9141 (tm-30) REVERT: B 452 PHE cc_start: 0.9104 (m-80) cc_final: 0.8677 (m-80) REVERT: B 540 ILE cc_start: 0.9193 (mt) cc_final: 0.8903 (mt) REVERT: B 565 LYS cc_start: 0.9287 (ttmm) cc_final: 0.8553 (tppt) REVERT: B 568 GLN cc_start: 0.9326 (tp-100) cc_final: 0.9122 (tp-100) REVERT: B 678 MET cc_start: 0.7829 (mtt) cc_final: 0.7209 (mtt) REVERT: B 753 ARG cc_start: 0.9384 (ppt170) cc_final: 0.9013 (ttp80) REVERT: B 757 MET cc_start: 0.9268 (tmm) cc_final: 0.8980 (tmm) outliers start: 6 outliers final: 3 residues processed: 646 average time/residue: 0.4992 time to fit residues: 510.5685 Evaluate side-chains 487 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 484 time to evaluate : 4.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 0.4980 chunk 124 optimal weight: 20.0000 chunk 334 optimal weight: 10.0000 chunk 273 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 403 optimal weight: 0.1980 chunk 435 optimal weight: 50.0000 chunk 358 optimal weight: 5.9990 chunk 399 optimal weight: 0.0770 chunk 137 optimal weight: 9.9990 chunk 323 optimal weight: 4.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 199 ASN F 384 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 533 ASN E 538 ASN E 558 ASN E 568 GLN D 260 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 404 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 35947 Z= 0.181 Angle : 0.697 11.322 48593 Z= 0.334 Chirality : 0.046 0.173 5470 Planarity : 0.005 0.076 6370 Dihedral : 10.190 175.001 4987 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.12), residues: 4424 helix: -0.34 (0.12), residues: 1672 sheet: -0.58 (0.22), residues: 541 loop : -2.02 (0.13), residues: 2211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 454 HIS 0.006 0.001 HIS F 735 PHE 0.031 0.001 PHE F 563 TYR 0.023 0.001 TYR D 495 ARG 0.011 0.000 ARG D 599 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 650 time to evaluate : 3.570 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: 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 200 GLU cc_start: 0.8807 (pm20) cc_final: 0.8569 (mp0) REVERT: A 218 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7799 (tt0) REVERT: A 274 ILE cc_start: 0.9797 (mt) cc_final: 0.9379 (tp) REVERT: A 305 GLU cc_start: 0.8219 (tp30) cc_final: 0.7555 (tp30) REVERT: A 312 LYS cc_start: 0.9455 (tptp) cc_final: 0.9081 (tptp) REVERT: A 321 GLU cc_start: 0.9155 (mp0) cc_final: 0.8910 (mp0) REVERT: A 344 MET cc_start: 0.9032 (mmt) cc_final: 0.8774 (mmp) REVERT: A 388 MET cc_start: 0.8016 (ppp) cc_final: 0.7328 (ppp) REVERT: A 516 PHE cc_start: 0.9188 (m-80) cc_final: 0.8773 (m-10) REVERT: A 560 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8648 (mmm160) REVERT: A 567 ARG cc_start: 0.9096 (mmm160) cc_final: 0.8703 (ttp-170) REVERT: A 607 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8262 (mm-30) REVERT: A 611 MET cc_start: 0.9197 (tpt) cc_final: 0.8686 (tpt) REVERT: A 757 MET cc_start: 0.8657 (mtp) cc_final: 0.8344 (mmp) REVERT: F 55 ASP cc_start: 0.8763 (m-30) cc_final: 0.8511 (t0) REVERT: F 220 VAL cc_start: 0.8930 (t) cc_final: 0.8585 (m) REVERT: F 319 GLU cc_start: 0.9120 (pp20) cc_final: 0.8711 (pp20) REVERT: F 348 ASN cc_start: 0.9096 (p0) cc_final: 0.8891 (p0) REVERT: F 381 LEU cc_start: 0.9721 (mt) cc_final: 0.9474 (pp) REVERT: F 449 MET cc_start: 0.8661 (pmm) cc_final: 0.8232 (ppp) REVERT: F 450 ASP cc_start: 0.8429 (t70) cc_final: 0.7787 (t0) REVERT: F 478 ASP cc_start: 0.8559 (p0) cc_final: 0.8077 (t70) REVERT: F 498 GLU cc_start: 0.9125 (tt0) cc_final: 0.8773 (mt-10) REVERT: F 508 MET cc_start: 0.4109 (ttm) cc_final: 0.3828 (ttm) REVERT: F 556 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8503 (mt-10) REVERT: F 562 ILE cc_start: 0.9375 (mm) cc_final: 0.9092 (mm) REVERT: F 642 LEU cc_start: 0.8115 (mt) cc_final: 0.7884 (mt) REVERT: F 757 MET cc_start: 0.8598 (tmm) cc_final: 0.8368 (tmm) REVERT: F 765 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7599 (tmm160) REVERT: E 243 LEU cc_start: 0.8785 (mp) cc_final: 0.8552 (mp) REVERT: E 253 LEU cc_start: 0.9259 (mp) cc_final: 0.9000 (mp) REVERT: E 273 GLU cc_start: 0.9005 (mp0) cc_final: 0.8515 (tm-30) REVERT: E 291 GLU cc_start: 0.8934 (mp0) cc_final: 0.8394 (mp0) REVERT: E 305 GLU cc_start: 0.9150 (tp30) cc_final: 0.8372 (tp30) REVERT: E 410 ASP cc_start: 0.8690 (m-30) cc_final: 0.8482 (t0) REVERT: E 414 LEU cc_start: 0.9680 (mt) cc_final: 0.9257 (mt) REVERT: E 462 SER cc_start: 0.9276 (t) cc_final: 0.8629 (t) REVERT: E 546 GLU cc_start: 0.9629 (tp30) cc_final: 0.9372 (tp30) REVERT: E 614 LYS cc_start: 0.9032 (mppt) cc_final: 0.8648 (tttt) REVERT: E 630 ASP cc_start: 0.8429 (t0) cc_final: 0.8203 (t0) REVERT: E 635 ARG cc_start: 0.8758 (ttp-110) cc_final: 0.8543 (ttp-110) REVERT: E 678 MET cc_start: 0.9161 (mpp) cc_final: 0.8321 (mpp) REVERT: D 244 TYR cc_start: 0.8590 (p90) cc_final: 0.7645 (p90) REVERT: D 292 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8287 (tm-30) REVERT: D 344 MET cc_start: 0.8817 (tpt) cc_final: 0.8575 (tpp) REVERT: D 415 CYS cc_start: 0.9412 (m) cc_final: 0.9122 (p) REVERT: D 417 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8721 (tm-30) REVERT: D 515 LEU cc_start: 0.9445 (tp) cc_final: 0.9186 (tp) REVERT: D 560 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8124 (mmm-85) REVERT: D 598 ASP cc_start: 0.8114 (m-30) cc_final: 0.7784 (m-30) REVERT: D 608 MET cc_start: 0.9482 (ttp) cc_final: 0.8925 (ttp) REVERT: D 609 ASP cc_start: 0.8440 (m-30) cc_final: 0.8199 (m-30) REVERT: C 46 MET cc_start: 0.1580 (mtt) cc_final: 0.1091 (mpp) REVERT: C 84 MET cc_start: 0.6559 (ptp) cc_final: 0.5749 (ppp) REVERT: C 305 GLU cc_start: 0.9291 (mm-30) cc_final: 0.8914 (mm-30) REVERT: C 449 MET cc_start: 0.8531 (ttm) cc_final: 0.8276 (mtp) REVERT: C 465 ARG cc_start: 0.8089 (mmt-90) cc_final: 0.7486 (mmt180) REVERT: C 560 ARG cc_start: 0.9401 (mtp180) cc_final: 0.9045 (mtp-110) REVERT: C 568 GLN cc_start: 0.9268 (tm-30) cc_final: 0.9057 (tm-30) REVERT: C 607 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8340 (mt-10) REVERT: C 640 ASP cc_start: 0.8133 (p0) cc_final: 0.7785 (p0) REVERT: C 689 GLU cc_start: 0.9225 (tt0) cc_final: 0.8854 (mt-10) REVERT: C 736 PHE cc_start: 0.8428 (m-80) cc_final: 0.8193 (m-10) REVERT: C 740 MET cc_start: 0.8826 (ptt) cc_final: 0.8561 (ptt) REVERT: B 246 PRO cc_start: 0.9335 (Cg_exo) cc_final: 0.9103 (Cg_endo) REVERT: B 266 PHE cc_start: 0.8958 (p90) cc_final: 0.8473 (p90) REVERT: B 274 ILE cc_start: 0.9569 (tp) cc_final: 0.9210 (tp) REVERT: B 301 ILE cc_start: 0.9163 (tp) cc_final: 0.8938 (tt) REVERT: B 407 VAL cc_start: 0.9246 (t) cc_final: 0.8699 (p) REVERT: B 410 ASP cc_start: 0.9294 (m-30) cc_final: 0.8829 (m-30) REVERT: B 417 GLU cc_start: 0.9478 (tp30) cc_final: 0.9080 (tm-30) REVERT: B 452 PHE cc_start: 0.9050 (m-80) cc_final: 0.8639 (m-80) REVERT: B 540 ILE cc_start: 0.9126 (mt) cc_final: 0.8786 (mt) REVERT: B 565 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8413 (tppt) REVERT: B 678 MET cc_start: 0.7668 (mtt) cc_final: 0.7143 (mtt) REVERT: B 753 ARG cc_start: 0.9341 (ppt170) cc_final: 0.8937 (ttp80) REVERT: B 757 MET cc_start: 0.9225 (tmm) cc_final: 0.8906 (tmm) REVERT: B 768 PHE cc_start: 0.8966 (p90) cc_final: 0.8757 (p90) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.4884 time to fit residues: 506.2214 Evaluate side-chains 514 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 4.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 0.0030 chunk 303 optimal weight: 30.0000 chunk 209 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 192 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 428 optimal weight: 5.9990 chunk 211 optimal weight: 3.9990 chunk 383 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35947 Z= 0.187 Angle : 0.691 10.115 48593 Z= 0.333 Chirality : 0.046 0.209 5470 Planarity : 0.005 0.072 6370 Dihedral : 10.002 170.729 4987 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.03 % Allowed : 3.67 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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: -1.60 (0.12), residues: 4424 helix: -0.15 (0.13), residues: 1679 sheet: -0.61 (0.22), residues: 549 loop : -1.93 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 476 HIS 0.004 0.001 HIS A 115 PHE 0.025 0.001 PHE D 363 TYR 0.020 0.001 TYR C 495 ARG 0.010 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 628 time to evaluate : 4.169 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: 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 200 GLU cc_start: 0.8800 (pm20) cc_final: 0.8580 (mp0) REVERT: A 218 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7787 (tt0) REVERT: A 219 MET cc_start: 0.7683 (tpt) cc_final: 0.7324 (tpp) REVERT: A 274 ILE cc_start: 0.9805 (mt) cc_final: 0.9552 (mt) REVERT: A 305 GLU cc_start: 0.8217 (tp30) cc_final: 0.7479 (tp30) REVERT: A 307 ASP cc_start: 0.8956 (m-30) cc_final: 0.8750 (m-30) REVERT: A 321 GLU cc_start: 0.9213 (mp0) cc_final: 0.8893 (pm20) REVERT: A 344 MET cc_start: 0.9116 (mmt) cc_final: 0.8795 (mmp) REVERT: A 388 MET cc_start: 0.8034 (ppp) cc_final: 0.7311 (ppp) REVERT: A 476 TRP cc_start: 0.7821 (t-100) cc_final: 0.7054 (t-100) REVERT: A 516 PHE cc_start: 0.9226 (m-80) cc_final: 0.8795 (m-10) REVERT: A 560 ARG cc_start: 0.9086 (mmm160) cc_final: 0.8188 (mmm-85) REVERT: A 561 GLU cc_start: 0.9539 (mp0) cc_final: 0.9224 (pp20) REVERT: A 562 ILE cc_start: 0.9704 (mt) cc_final: 0.8906 (mt) REVERT: A 565 LYS cc_start: 0.8986 (pttt) cc_final: 0.8759 (pttp) REVERT: A 567 ARG cc_start: 0.9155 (mmm160) cc_final: 0.8746 (ttp-170) REVERT: A 603 GLN cc_start: 0.9621 (mm-40) cc_final: 0.8095 (mm-40) REVERT: A 607 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 757 MET cc_start: 0.8664 (mtp) cc_final: 0.8362 (mmp) REVERT: F 55 ASP cc_start: 0.8757 (m-30) cc_final: 0.8507 (t0) REVERT: F 220 VAL cc_start: 0.8965 (t) cc_final: 0.8546 (m) REVERT: F 306 LEU cc_start: 0.9584 (tp) cc_final: 0.9335 (mm) REVERT: F 314 GLU cc_start: 0.9134 (pp20) cc_final: 0.8877 (pm20) REVERT: F 319 GLU cc_start: 0.9068 (pp20) cc_final: 0.8588 (pp20) REVERT: F 348 ASN cc_start: 0.9139 (p0) cc_final: 0.8916 (p0) REVERT: F 449 MET cc_start: 0.8718 (pmm) cc_final: 0.8290 (ppp) REVERT: F 478 ASP cc_start: 0.8475 (p0) cc_final: 0.8017 (t70) REVERT: F 498 GLU cc_start: 0.9125 (tt0) cc_final: 0.8868 (mt-10) REVERT: F 508 MET cc_start: 0.4116 (ttm) cc_final: 0.3762 (ttm) REVERT: F 757 MET cc_start: 0.8565 (tmm) cc_final: 0.8343 (tmm) REVERT: F 765 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7512 (tmm160) REVERT: E 206 ILE cc_start: 0.9476 (mm) cc_final: 0.9225 (mm) REVERT: E 253 LEU cc_start: 0.9247 (mp) cc_final: 0.8965 (mp) REVERT: E 273 GLU cc_start: 0.8987 (mp0) cc_final: 0.8533 (tm-30) REVERT: E 291 GLU cc_start: 0.8994 (mp0) cc_final: 0.8483 (mp0) REVERT: E 313 ARG cc_start: 0.9236 (tpp-160) cc_final: 0.8945 (tpt90) REVERT: E 410 ASP cc_start: 0.8652 (m-30) cc_final: 0.8443 (t70) REVERT: E 414 LEU cc_start: 0.9708 (mt) cc_final: 0.9318 (mt) REVERT: E 462 SER cc_start: 0.9139 (t) cc_final: 0.8262 (t) REVERT: E 563 PHE cc_start: 0.9412 (m-80) cc_final: 0.9190 (m-80) REVERT: E 614 LYS cc_start: 0.9034 (mppt) cc_final: 0.8669 (tttp) REVERT: E 615 LYS cc_start: 0.9244 (mmtt) cc_final: 0.8970 (mmtt) REVERT: E 635 ARG cc_start: 0.9062 (ttp-110) cc_final: 0.8816 (ttp-110) REVERT: D 219 MET cc_start: 0.8565 (mmp) cc_final: 0.8354 (mmm) REVERT: D 244 TYR cc_start: 0.8384 (p90) cc_final: 0.7634 (p90) REVERT: D 329 LEU cc_start: 0.9398 (mt) cc_final: 0.8915 (mt) REVERT: D 357 LEU cc_start: 0.9274 (mm) cc_final: 0.8922 (mm) REVERT: D 417 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8689 (tm-30) REVERT: D 445 LEU cc_start: 0.8975 (tp) cc_final: 0.8689 (mm) REVERT: D 515 LEU cc_start: 0.9375 (tp) cc_final: 0.9101 (tp) REVERT: D 560 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8232 (mmm-85) REVERT: D 608 MET cc_start: 0.9532 (ttp) cc_final: 0.9002 (ppp) REVERT: D 609 ASP cc_start: 0.8510 (m-30) cc_final: 0.7876 (m-30) REVERT: C 46 MET cc_start: 0.1585 (mtt) cc_final: 0.1146 (mpp) REVERT: C 84 MET cc_start: 0.6543 (ptp) cc_final: 0.5767 (ppp) REVERT: C 244 TYR cc_start: 0.7976 (p90) cc_final: 0.7733 (p90) REVERT: C 332 MET cc_start: 0.8533 (tmm) cc_final: 0.8271 (tmm) REVERT: C 369 ILE cc_start: 0.9533 (mp) cc_final: 0.9200 (tt) REVERT: C 465 ARG cc_start: 0.7916 (mmt-90) cc_final: 0.7692 (mmt180) REVERT: C 560 ARG cc_start: 0.9409 (mtp180) cc_final: 0.9190 (mtp-110) REVERT: C 568 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9083 (tm-30) REVERT: C 607 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8381 (mt-10) REVERT: C 689 GLU cc_start: 0.9225 (tt0) cc_final: 0.8886 (mt-10) REVERT: C 736 PHE cc_start: 0.8435 (m-80) cc_final: 0.8186 (m-80) REVERT: C 740 MET cc_start: 0.8622 (ptt) cc_final: 0.8405 (ptt) REVERT: B 236 LYS cc_start: 0.8611 (pttp) cc_final: 0.8389 (pttt) REVERT: B 246 PRO cc_start: 0.9346 (Cg_exo) cc_final: 0.9027 (Cg_endo) REVERT: B 266 PHE cc_start: 0.9042 (p90) cc_final: 0.8561 (p90) REVERT: B 275 MET cc_start: 0.9290 (mmp) cc_final: 0.9046 (mmm) REVERT: B 305 GLU cc_start: 0.9080 (tp30) cc_final: 0.8803 (tp30) REVERT: B 407 VAL cc_start: 0.9311 (t) cc_final: 0.8805 (p) REVERT: B 410 ASP cc_start: 0.9307 (m-30) cc_final: 0.8862 (m-30) REVERT: B 417 GLU cc_start: 0.9467 (tp30) cc_final: 0.9057 (tm-30) REVERT: B 452 PHE cc_start: 0.9047 (m-80) cc_final: 0.8697 (m-80) REVERT: B 538 ASN cc_start: 0.8551 (m-40) cc_final: 0.8277 (t0) REVERT: B 540 ILE cc_start: 0.9079 (mt) cc_final: 0.8740 (mt) REVERT: B 565 LYS cc_start: 0.9237 (ttmm) cc_final: 0.8407 (tppt) REVERT: B 609 ASP cc_start: 0.8319 (m-30) cc_final: 0.7779 (m-30) REVERT: B 678 MET cc_start: 0.7785 (mtt) cc_final: 0.7254 (mtt) REVERT: B 753 ARG cc_start: 0.9348 (ppt170) cc_final: 0.8980 (ttp80) REVERT: B 757 MET cc_start: 0.9240 (tmm) cc_final: 0.8928 (tmm) outliers start: 1 outliers final: 0 residues processed: 628 average time/residue: 0.4886 time to fit residues: 490.0042 Evaluate side-chains 513 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 20.0000 chunk 243 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 318 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 365 optimal weight: 20.0000 chunk 295 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 3.9990 chunk 384 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 327 GLN ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 313 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 35947 Z= 0.198 Angle : 0.695 11.301 48593 Z= 0.334 Chirality : 0.045 0.194 5470 Planarity : 0.005 0.072 6370 Dihedral : 9.922 170.273 4987 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 0.03 % Allowed : 2.85 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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: -1.50 (0.12), residues: 4424 helix: -0.02 (0.13), residues: 1683 sheet: -0.77 (0.21), residues: 566 loop : -1.86 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 454 HIS 0.005 0.001 HIS A 115 PHE 0.031 0.001 PHE F 516 TYR 0.020 0.001 TYR F 517 ARG 0.012 0.000 ARG A 338 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 617 time to evaluate : 4.157 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7786 (tt0) REVERT: A 219 MET cc_start: 0.7629 (tpt) cc_final: 0.7399 (tpt) REVERT: A 305 GLU cc_start: 0.8275 (tp30) cc_final: 0.7553 (tp30) REVERT: A 307 ASP cc_start: 0.9006 (m-30) cc_final: 0.8741 (m-30) REVERT: A 321 GLU cc_start: 0.9261 (mp0) cc_final: 0.8918 (pm20) REVERT: A 331 LEU cc_start: 0.9158 (mt) cc_final: 0.8953 (mt) REVERT: A 344 MET cc_start: 0.9092 (mmt) cc_final: 0.8719 (mmt) REVERT: A 388 MET cc_start: 0.8116 (ppp) cc_final: 0.7389 (ppp) REVERT: A 476 TRP cc_start: 0.7802 (t-100) cc_final: 0.7025 (t-100) REVERT: A 516 PHE cc_start: 0.9242 (m-80) cc_final: 0.8888 (m-80) REVERT: A 560 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8258 (mmm160) REVERT: A 562 ILE cc_start: 0.9758 (mt) cc_final: 0.9103 (mt) REVERT: A 567 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8753 (ttp-170) REVERT: A 603 GLN cc_start: 0.9583 (mm-40) cc_final: 0.8613 (mm-40) REVERT: A 606 THR cc_start: 0.8889 (p) cc_final: 0.8576 (p) REVERT: A 607 GLU cc_start: 0.8741 (mm-30) cc_final: 0.8371 (mm-30) REVERT: A 611 MET cc_start: 0.9069 (tpt) cc_final: 0.8623 (tpt) REVERT: A 757 MET cc_start: 0.8694 (mtp) cc_final: 0.8402 (mmp) REVERT: F 55 ASP cc_start: 0.8762 (m-30) cc_final: 0.8512 (t0) REVERT: F 203 TYR cc_start: 0.8651 (m-80) cc_final: 0.8228 (m-10) REVERT: F 220 VAL cc_start: 0.9166 (t) cc_final: 0.8776 (m) REVERT: F 306 LEU cc_start: 0.9578 (tp) cc_final: 0.9328 (mm) REVERT: F 319 GLU cc_start: 0.9052 (pp20) cc_final: 0.8533 (pp20) REVERT: F 348 ASN cc_start: 0.9175 (p0) cc_final: 0.8917 (p0) REVERT: F 449 MET cc_start: 0.8807 (pmm) cc_final: 0.8390 (ppp) REVERT: F 478 ASP cc_start: 0.8434 (p0) cc_final: 0.7973 (t70) REVERT: F 498 GLU cc_start: 0.9134 (tt0) cc_final: 0.8788 (mt-10) REVERT: F 556 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8175 (mm-30) REVERT: F 765 ARG cc_start: 0.8113 (tpp80) cc_final: 0.7445 (tmm160) REVERT: E 206 ILE cc_start: 0.9509 (mm) cc_final: 0.9236 (mm) REVERT: E 253 LEU cc_start: 0.9278 (mp) cc_final: 0.8995 (mp) REVERT: E 273 GLU cc_start: 0.8988 (mp0) cc_final: 0.8516 (tm-30) REVERT: E 291 GLU cc_start: 0.8958 (mp0) cc_final: 0.8504 (mp0) REVERT: E 313 ARG cc_start: 0.9207 (tpp-160) cc_final: 0.8875 (tpt90) REVERT: E 410 ASP cc_start: 0.8674 (m-30) cc_final: 0.8474 (t70) REVERT: E 414 LEU cc_start: 0.9719 (mt) cc_final: 0.9310 (mt) REVERT: E 462 SER cc_start: 0.9084 (t) cc_final: 0.8226 (t) REVERT: E 516 PHE cc_start: 0.8542 (m-10) cc_final: 0.8293 (m-80) REVERT: E 546 GLU cc_start: 0.9657 (tp30) cc_final: 0.9270 (tp30) REVERT: E 563 PHE cc_start: 0.9368 (m-80) cc_final: 0.9114 (m-80) REVERT: E 607 GLU cc_start: 0.9345 (mm-30) cc_final: 0.8832 (mm-30) REVERT: E 614 LYS cc_start: 0.9017 (mppt) cc_final: 0.8705 (tptt) REVERT: E 635 ARG cc_start: 0.9042 (ttp-110) cc_final: 0.8799 (ttp-110) REVERT: E 678 MET cc_start: 0.9066 (mpp) cc_final: 0.8466 (mpp) REVERT: D 209 CYS cc_start: 0.8121 (m) cc_final: 0.7894 (m) REVERT: D 244 TYR cc_start: 0.8550 (p90) cc_final: 0.8339 (p90) REVERT: D 266 PHE cc_start: 0.8166 (t80) cc_final: 0.7891 (t80) REVERT: D 307 ASP cc_start: 0.9105 (t70) cc_final: 0.8871 (t0) REVERT: D 344 MET cc_start: 0.8966 (tpt) cc_final: 0.8637 (tpp) REVERT: D 357 LEU cc_start: 0.9303 (mm) cc_final: 0.8860 (mt) REVERT: D 417 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8684 (tm-30) REVERT: D 608 MET cc_start: 0.9550 (ttp) cc_final: 0.9038 (ppp) REVERT: D 609 ASP cc_start: 0.8476 (m-30) cc_final: 0.7832 (m-30) REVERT: D 625 ARG cc_start: 0.8885 (mtt-85) cc_final: 0.8606 (mmt180) REVERT: C 46 MET cc_start: 0.1638 (mtt) cc_final: 0.0916 (mpp) REVERT: C 84 MET cc_start: 0.6559 (ptp) cc_final: 0.5770 (ppp) REVERT: C 244 TYR cc_start: 0.7991 (p90) cc_final: 0.7755 (p90) REVERT: C 369 ILE cc_start: 0.9550 (mp) cc_final: 0.9184 (tt) REVERT: C 449 MET cc_start: 0.8780 (ttm) cc_final: 0.8501 (mtp) REVERT: C 465 ARG cc_start: 0.8078 (mmt-90) cc_final: 0.7717 (mmt90) REVERT: C 560 ARG cc_start: 0.9393 (mtp180) cc_final: 0.9181 (mtp-110) REVERT: C 568 GLN cc_start: 0.9332 (tm-30) cc_final: 0.9109 (tm-30) REVERT: C 607 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8444 (mt-10) REVERT: C 689 GLU cc_start: 0.9226 (tt0) cc_final: 0.8903 (mt-10) REVERT: C 736 PHE cc_start: 0.8467 (m-80) cc_final: 0.8200 (m-80) REVERT: C 740 MET cc_start: 0.8511 (ptt) cc_final: 0.8290 (ptt) REVERT: B 209 CYS cc_start: 0.8936 (p) cc_final: 0.8713 (p) REVERT: B 236 LYS cc_start: 0.8685 (pttp) cc_final: 0.8419 (pttt) REVERT: B 246 PRO cc_start: 0.9350 (Cg_exo) cc_final: 0.9086 (Cg_endo) REVERT: B 302 PHE cc_start: 0.8492 (t80) cc_final: 0.8277 (t80) REVERT: B 305 GLU cc_start: 0.9091 (tp30) cc_final: 0.8816 (tp30) REVERT: B 407 VAL cc_start: 0.9366 (t) cc_final: 0.9020 (t) REVERT: B 410 ASP cc_start: 0.9305 (m-30) cc_final: 0.9043 (m-30) REVERT: B 417 GLU cc_start: 0.9473 (tp30) cc_final: 0.9038 (tm-30) REVERT: B 452 PHE cc_start: 0.9027 (m-80) cc_final: 0.8657 (m-80) REVERT: B 538 ASN cc_start: 0.8617 (m-40) cc_final: 0.8332 (t0) REVERT: B 540 ILE cc_start: 0.9220 (mt) cc_final: 0.8865 (mt) REVERT: B 565 LYS cc_start: 0.9199 (ttmm) cc_final: 0.8534 (tppt) REVERT: B 578 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7851 (mm-30) REVERT: B 608 MET cc_start: 0.9551 (ppp) cc_final: 0.9273 (ppp) REVERT: B 609 ASP cc_start: 0.8265 (m-30) cc_final: 0.7666 (m-30) REVERT: B 678 MET cc_start: 0.7847 (mtt) cc_final: 0.7336 (mtt) REVERT: B 753 ARG cc_start: 0.9353 (ppt170) cc_final: 0.8978 (ttp80) REVERT: B 757 MET cc_start: 0.9239 (tmm) cc_final: 0.8944 (tmm) outliers start: 1 outliers final: 0 residues processed: 618 average time/residue: 0.4782 time to fit residues: 473.8072 Evaluate side-chains 495 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 495 time to evaluate : 3.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 9.9990 chunk 385 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 251 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 428 optimal weight: 20.0000 chunk 355 optimal weight: 3.9990 chunk 198 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 225 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN D 317 HIS ** D 473 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 490 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 660 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 533 ASN C 692 GLN B 36 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 35947 Z= 0.329 Angle : 0.808 9.666 48593 Z= 0.404 Chirality : 0.048 0.308 5470 Planarity : 0.006 0.072 6370 Dihedral : 10.179 166.540 4987 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.65 % Favored : 90.35 % Rotamer: Outliers : 0.05 % Allowed : 3.78 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4424 helix: -0.42 (0.12), residues: 1663 sheet: -1.01 (0.21), residues: 559 loop : -2.00 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 476 HIS 0.008 0.001 HIS E 340 PHE 0.025 0.002 PHE B 302 TYR 0.021 0.002 TYR C 495 ARG 0.032 0.001 ARG F 635 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 569 time to evaluate : 4.564 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 84 MET cc_start: 0.9047 (ttp) cc_final: 0.8812 (tmm) REVERT: A 218 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8127 (mt-10) REVERT: A 305 GLU cc_start: 0.8196 (tp30) cc_final: 0.7665 (tp30) REVERT: A 321 GLU cc_start: 0.9340 (mp0) cc_final: 0.9114 (mp0) REVERT: A 344 MET cc_start: 0.9159 (mmt) cc_final: 0.8904 (mmp) REVERT: A 388 MET cc_start: 0.8281 (ppp) cc_final: 0.7586 (ppp) REVERT: A 516 PHE cc_start: 0.9281 (m-80) cc_final: 0.8803 (m-80) REVERT: A 567 ARG cc_start: 0.9185 (mmm160) cc_final: 0.8855 (ttp-170) REVERT: A 642 LEU cc_start: 0.9451 (mp) cc_final: 0.9132 (tp) REVERT: A 757 MET cc_start: 0.8746 (mtp) cc_final: 0.8502 (mmp) REVERT: F 220 VAL cc_start: 0.9293 (t) cc_final: 0.8846 (m) REVERT: F 348 ASN cc_start: 0.9284 (p0) cc_final: 0.8925 (p0) REVERT: F 425 LYS cc_start: 0.9393 (ttmt) cc_final: 0.9161 (pttm) REVERT: F 449 MET cc_start: 0.8849 (pmm) cc_final: 0.8457 (ppp) REVERT: F 478 ASP cc_start: 0.8628 (p0) cc_final: 0.8328 (p0) REVERT: F 498 GLU cc_start: 0.9277 (tt0) cc_final: 0.8993 (mt-10) REVERT: F 556 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8121 (mm-30) REVERT: F 563 PHE cc_start: 0.8863 (t80) cc_final: 0.8468 (t80) REVERT: F 572 CYS cc_start: 0.7647 (p) cc_final: 0.7123 (p) REVERT: E 84 MET cc_start: 0.0419 (tpt) cc_final: -0.0216 (tpt) REVERT: E 206 ILE cc_start: 0.9497 (mm) cc_final: 0.9287 (mm) REVERT: E 253 LEU cc_start: 0.9287 (mp) cc_final: 0.9017 (mp) REVERT: E 273 GLU cc_start: 0.9029 (mp0) cc_final: 0.8347 (tm-30) REVERT: E 291 GLU cc_start: 0.9142 (mp0) cc_final: 0.8576 (mp0) REVERT: E 313 ARG cc_start: 0.9239 (tpp-160) cc_final: 0.8970 (tpt90) REVERT: E 414 LEU cc_start: 0.9749 (mt) cc_final: 0.9292 (mt) REVERT: E 427 MET cc_start: 0.8361 (pmm) cc_final: 0.7969 (ppp) REVERT: E 462 SER cc_start: 0.9183 (t) cc_final: 0.8600 (t) REVERT: E 546 GLU cc_start: 0.9557 (tp30) cc_final: 0.9241 (tp30) REVERT: E 607 GLU cc_start: 0.9387 (mm-30) cc_final: 0.8952 (mm-30) REVERT: E 635 ARG cc_start: 0.9050 (ttp-110) cc_final: 0.8787 (ttp-110) REVERT: E 757 MET cc_start: 0.9055 (ppp) cc_final: 0.8845 (ppp) REVERT: D 219 MET cc_start: 0.8891 (mmp) cc_final: 0.8576 (mmm) REVERT: D 292 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8543 (tm-30) REVERT: D 305 GLU cc_start: 0.9257 (tp30) cc_final: 0.9027 (tp30) REVERT: D 332 MET cc_start: 0.8790 (tmm) cc_final: 0.8504 (tmm) REVERT: D 344 MET cc_start: 0.8997 (tpt) cc_final: 0.8586 (tpp) REVERT: D 417 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8717 (tm-30) REVERT: D 564 ASP cc_start: 0.9084 (m-30) cc_final: 0.8834 (m-30) REVERT: D 608 MET cc_start: 0.9610 (ttp) cc_final: 0.9072 (ppp) REVERT: D 609 ASP cc_start: 0.8350 (m-30) cc_final: 0.7661 (m-30) REVERT: D 652 SER cc_start: 0.8940 (t) cc_final: 0.8739 (p) REVERT: C 46 MET cc_start: 0.2198 (mtt) cc_final: 0.1470 (mpp) REVERT: C 84 MET cc_start: 0.6716 (ptp) cc_final: 0.6340 (ptm) REVERT: C 560 ARG cc_start: 0.9332 (mtp180) cc_final: 0.9072 (mtp-110) REVERT: C 568 GLN cc_start: 0.9359 (tm-30) cc_final: 0.9144 (tm-30) REVERT: C 607 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8519 (mt-10) REVERT: C 640 ASP cc_start: 0.8295 (p0) cc_final: 0.7836 (p0) REVERT: C 689 GLU cc_start: 0.9120 (tt0) cc_final: 0.8854 (mt-10) REVERT: B 236 LYS cc_start: 0.8736 (pttp) cc_final: 0.8497 (pttt) REVERT: B 275 MET cc_start: 0.9362 (mmp) cc_final: 0.9161 (mmm) REVERT: B 305 GLU cc_start: 0.9196 (tp30) cc_final: 0.8834 (tp30) REVERT: B 379 GLU cc_start: 0.9321 (mp0) cc_final: 0.9065 (mp0) REVERT: B 417 GLU cc_start: 0.9503 (tp30) cc_final: 0.9035 (tm-30) REVERT: B 452 PHE cc_start: 0.9074 (m-80) cc_final: 0.8684 (m-10) REVERT: B 538 ASN cc_start: 0.8773 (m-40) cc_final: 0.8460 (t0) REVERT: B 540 ILE cc_start: 0.9385 (mt) cc_final: 0.8820 (mm) REVERT: B 565 LYS cc_start: 0.9314 (ttmm) cc_final: 0.8730 (tppt) REVERT: B 609 ASP cc_start: 0.8246 (m-30) cc_final: 0.7592 (m-30) REVERT: B 678 MET cc_start: 0.8269 (mtt) cc_final: 0.7624 (mtt) REVERT: B 753 ARG cc_start: 0.9428 (ppt170) cc_final: 0.8917 (ttp80) REVERT: B 757 MET cc_start: 0.9261 (tmm) cc_final: 0.8975 (tmm) outliers start: 2 outliers final: 0 residues processed: 571 average time/residue: 0.4785 time to fit residues: 442.0243 Evaluate side-chains 446 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 4.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 244 optimal weight: 0.7980 chunk 313 optimal weight: 5.9990 chunk 242 optimal weight: 0.7980 chunk 360 optimal weight: 0.0970 chunk 239 optimal weight: 0.9990 chunk 426 optimal weight: 1.9990 chunk 267 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 260 ASN ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN E 183 HIS E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 297 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 35947 Z= 0.183 Angle : 0.725 12.161 48593 Z= 0.347 Chirality : 0.047 0.221 5470 Planarity : 0.005 0.071 6370 Dihedral : 9.909 172.209 4987 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.12), residues: 4424 helix: -0.05 (0.13), residues: 1672 sheet: -0.79 (0.22), residues: 546 loop : -1.87 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 454 HIS 0.013 0.001 HIS A 499 PHE 0.026 0.002 PHE E 736 TYR 0.023 0.001 TYR C 517 ARG 0.019 0.001 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 590 time to evaluate : 3.884 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: symmetry clash REVERT: A 84 MET cc_start: 0.9038 (ttp) cc_final: 0.8756 (tmm) REVERT: A 218 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7831 (pt0) REVERT: A 305 GLU cc_start: 0.8437 (tp30) cc_final: 0.7776 (tp30) REVERT: A 306 LEU cc_start: 0.9228 (pt) cc_final: 0.9026 (pt) REVERT: A 321 GLU cc_start: 0.9344 (mp0) cc_final: 0.8941 (pm20) REVERT: A 331 LEU cc_start: 0.9094 (mt) cc_final: 0.8853 (mt) REVERT: A 388 MET cc_start: 0.8310 (ppp) cc_final: 0.7623 (ppp) REVERT: A 516 PHE cc_start: 0.9202 (m-80) cc_final: 0.8671 (m-80) REVERT: A 567 ARG cc_start: 0.9181 (mmm160) cc_final: 0.8507 (ttp-170) REVERT: A 603 GLN cc_start: 0.9526 (mm-40) cc_final: 0.8897 (mm-40) REVERT: A 606 THR cc_start: 0.8807 (p) cc_final: 0.8466 (p) REVERT: A 607 GLU cc_start: 0.8698 (mm-30) cc_final: 0.8483 (mm-30) REVERT: A 757 MET cc_start: 0.8664 (mtp) cc_final: 0.8393 (mmp) REVERT: F 203 TYR cc_start: 0.8599 (m-80) cc_final: 0.8231 (m-10) REVERT: F 220 VAL cc_start: 0.9166 (t) cc_final: 0.8726 (p) REVERT: F 319 GLU cc_start: 0.9067 (pp20) cc_final: 0.8511 (pp20) REVERT: F 348 ASN cc_start: 0.9254 (p0) cc_final: 0.9012 (p0) REVERT: F 425 LYS cc_start: 0.9275 (ttmt) cc_final: 0.9053 (pttm) REVERT: F 449 MET cc_start: 0.8794 (pmm) cc_final: 0.8353 (ppp) REVERT: F 478 ASP cc_start: 0.8474 (p0) cc_final: 0.8057 (t70) REVERT: F 498 GLU cc_start: 0.9211 (tt0) cc_final: 0.8946 (mt-10) REVERT: F 556 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8088 (mm-30) REVERT: F 572 CYS cc_start: 0.7653 (p) cc_final: 0.7117 (p) REVERT: F 757 MET cc_start: 0.8571 (tmm) cc_final: 0.8350 (tmm) REVERT: E 84 MET cc_start: -0.0385 (tpt) cc_final: -0.0828 (tpt) REVERT: E 183 HIS cc_start: 0.8443 (m-70) cc_final: 0.8216 (m-70) REVERT: E 219 MET cc_start: 0.9287 (mpp) cc_final: 0.9084 (mpp) REVERT: E 243 LEU cc_start: 0.8939 (mp) cc_final: 0.8733 (mp) REVERT: E 253 LEU cc_start: 0.9276 (mp) cc_final: 0.9007 (mp) REVERT: E 273 GLU cc_start: 0.8794 (mp0) cc_final: 0.8291 (tm-30) REVERT: E 291 GLU cc_start: 0.9002 (mp0) cc_final: 0.8448 (mp0) REVERT: E 305 GLU cc_start: 0.9215 (tp30) cc_final: 0.8418 (tp30) REVERT: E 313 ARG cc_start: 0.9208 (tpp-160) cc_final: 0.8938 (tpt90) REVERT: E 410 ASP cc_start: 0.8980 (t0) cc_final: 0.8627 (t0) REVERT: E 414 LEU cc_start: 0.9691 (mt) cc_final: 0.9299 (mt) REVERT: E 427 MET cc_start: 0.8350 (pmm) cc_final: 0.8059 (ppp) REVERT: E 462 SER cc_start: 0.8947 (t) cc_final: 0.8469 (t) REVERT: E 516 PHE cc_start: 0.8627 (m-10) cc_final: 0.8306 (m-80) REVERT: E 546 GLU cc_start: 0.9565 (tp30) cc_final: 0.9228 (tp30) REVERT: E 607 GLU cc_start: 0.9349 (mm-30) cc_final: 0.8904 (mm-30) REVERT: E 614 LYS cc_start: 0.8948 (mmpt) cc_final: 0.8657 (tppt) REVERT: E 615 LYS cc_start: 0.9234 (mmtm) cc_final: 0.9014 (mmtt) REVERT: E 635 ARG cc_start: 0.8981 (ttp-110) cc_final: 0.8770 (ttp-110) REVERT: E 738 GLU cc_start: 0.7462 (tp30) cc_final: 0.6931 (pt0) REVERT: E 757 MET cc_start: 0.9020 (ppp) cc_final: 0.8806 (ppp) REVERT: D 344 MET cc_start: 0.8957 (tpt) cc_final: 0.8443 (tpp) REVERT: D 357 LEU cc_start: 0.9514 (mm) cc_final: 0.8932 (mt) REVERT: D 417 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8662 (tm-30) REVERT: D 564 ASP cc_start: 0.9093 (m-30) cc_final: 0.8789 (m-30) REVERT: D 608 MET cc_start: 0.9592 (ttp) cc_final: 0.9083 (ppp) REVERT: D 609 ASP cc_start: 0.8201 (m-30) cc_final: 0.7622 (m-30) REVERT: C 46 MET cc_start: 0.1796 (mtt) cc_final: 0.1062 (mpp) REVERT: C 84 MET cc_start: 0.6437 (ptp) cc_final: 0.5649 (ppp) REVERT: C 369 ILE cc_start: 0.9527 (mp) cc_final: 0.9212 (tt) REVERT: C 442 MET cc_start: 0.7399 (mmt) cc_final: 0.6884 (tmm) REVERT: C 560 ARG cc_start: 0.9365 (mtp180) cc_final: 0.8917 (mtp-110) REVERT: C 568 GLN cc_start: 0.9342 (tm-30) cc_final: 0.9096 (tm-30) REVERT: C 607 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8743 (mt-10) REVERT: C 614 LYS cc_start: 0.9196 (mptt) cc_final: 0.8882 (mmtt) REVERT: C 689 GLU cc_start: 0.9081 (tt0) cc_final: 0.8803 (mt-10) REVERT: C 736 PHE cc_start: 0.8555 (m-80) cc_final: 0.8325 (m-80) REVERT: B 267 PHE cc_start: 0.9073 (t80) cc_final: 0.8548 (t80) REVERT: B 305 GLU cc_start: 0.9124 (tp30) cc_final: 0.8839 (tp30) REVERT: B 330 THR cc_start: 0.8956 (t) cc_final: 0.8741 (p) REVERT: B 417 GLU cc_start: 0.9475 (tp30) cc_final: 0.8968 (tm-30) REVERT: B 452 PHE cc_start: 0.9051 (m-80) cc_final: 0.8601 (m-80) REVERT: B 464 LEU cc_start: 0.9478 (pt) cc_final: 0.9241 (pt) REVERT: B 465 ARG cc_start: 0.9008 (ptt90) cc_final: 0.8673 (ptp-170) REVERT: B 538 ASN cc_start: 0.8710 (m-40) cc_final: 0.8382 (t0) REVERT: B 540 ILE cc_start: 0.9348 (mt) cc_final: 0.8822 (mm) REVERT: B 565 LYS cc_start: 0.9292 (ttmm) cc_final: 0.8621 (tppt) REVERT: B 678 MET cc_start: 0.8104 (mtt) cc_final: 0.7551 (mtt) REVERT: B 753 ARG cc_start: 0.9439 (ppt170) cc_final: 0.9043 (ttp80) REVERT: B 757 MET cc_start: 0.9274 (tmm) cc_final: 0.8957 (tmm) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.4779 time to fit residues: 453.0882 Evaluate side-chains 483 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 3.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8707 > 50: distance: 45 - 51: 30.485 distance: 51 - 52: 35.330 distance: 52 - 53: 40.354 distance: 52 - 55: 57.192 distance: 53 - 54: 35.054 distance: 53 - 59: 45.060 distance: 55 - 56: 57.114 distance: 56 - 57: 47.126 distance: 56 - 58: 51.476 distance: 59 - 60: 28.729 distance: 60 - 61: 17.615 distance: 60 - 63: 18.484 distance: 61 - 62: 8.010 distance: 61 - 70: 5.483 distance: 63 - 64: 6.114 distance: 64 - 65: 14.567 distance: 64 - 66: 15.637 distance: 65 - 67: 22.071 distance: 66 - 68: 3.306 distance: 67 - 69: 13.433 distance: 68 - 69: 11.733 distance: 70 - 71: 8.339 distance: 71 - 72: 9.135 distance: 71 - 74: 12.058 distance: 72 - 73: 13.908 distance: 72 - 79: 33.338 distance: 74 - 75: 12.161 distance: 75 - 76: 4.612 distance: 76 - 77: 9.571 distance: 76 - 78: 10.267 distance: 79 - 80: 13.148 distance: 80 - 81: 10.560 distance: 80 - 83: 21.867 distance: 81 - 82: 11.141 distance: 81 - 86: 20.358 distance: 83 - 84: 39.110 distance: 83 - 85: 42.307 distance: 86 - 87: 24.445 distance: 87 - 88: 24.591 distance: 87 - 90: 8.467 distance: 88 - 89: 18.044 distance: 88 - 98: 42.575 distance: 90 - 91: 12.698 distance: 91 - 92: 22.503 distance: 91 - 93: 21.532 distance: 92 - 94: 24.980 distance: 93 - 95: 16.537 distance: 94 - 96: 3.547 distance: 95 - 96: 21.535 distance: 96 - 97: 19.359 distance: 98 - 99: 24.877 distance: 99 - 100: 22.037 distance: 99 - 102: 22.559 distance: 100 - 101: 39.850 distance: 100 - 106: 13.607 distance: 102 - 103: 48.838 distance: 103 - 104: 29.231 distance: 103 - 105: 7.191 distance: 106 - 107: 38.725 distance: 107 - 108: 33.391 distance: 107 - 110: 63.802 distance: 108 - 109: 22.574 distance: 108 - 115: 24.830 distance: 110 - 111: 28.797 distance: 111 - 112: 27.871 distance: 112 - 113: 20.545 distance: 113 - 114: 19.189 distance: 115 - 116: 68.304 distance: 115 - 121: 35.346 distance: 116 - 117: 42.671 distance: 116 - 119: 49.977 distance: 117 - 118: 56.031 distance: 117 - 122: 10.677 distance: 119 - 120: 43.815 distance: 120 - 121: 20.391 distance: 122 - 123: 34.115 distance: 123 - 124: 37.432 distance: 123 - 126: 14.302 distance: 124 - 125: 11.769 distance: 124 - 134: 21.308 distance: 126 - 127: 9.496 distance: 127 - 128: 8.776 distance: 127 - 129: 18.503 distance: 128 - 130: 8.217 distance: 129 - 131: 16.599 distance: 130 - 132: 10.839 distance: 131 - 132: 9.435 distance: 132 - 133: 13.879 distance: 134 - 135: 46.225 distance: 135 - 136: 36.892 distance: 135 - 138: 39.399 distance: 136 - 137: 63.832 distance: 136 - 145: 35.042 distance: 138 - 139: 26.616 distance: 139 - 140: 12.679 distance: 139 - 141: 20.903 distance: 140 - 142: 31.075 distance: 141 - 143: 18.410 distance: 142 - 144: 17.821 distance: 143 - 144: 23.097