Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 15:48:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/10_2023/7r7t_24304_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/10_2023/7r7t_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_24304/10_2023/7r7t_24304.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/10_2023/7r7t_24304.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/10_2023/7r7t_24304_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7t_24304/10_2023/7r7t_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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 16.80, per 1000 atoms: 0.48 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: 14.39 Conformation dependent library (CDL) restraints added in 5.5 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: 6.44 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: 11.14 Time building geometry restraints manager: 15.48 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.970 Check model and map are aligned: 0.510 Set scattering table: 0.310 Process input model: 84.850 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.720 ------------------------------------------------------------------------------- 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 *********************** 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 : 4.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 932 average time/residue: 0.5456 time to fit residues: 786.2681 Evaluate side-chains 538 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 3.975 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7587 ------------------------------------------------------------------------------- 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: 2.9990 chunk 226 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 347 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 211 optimal weight: 20.0000 chunk 258 optimal weight: 0.8980 chunk 402 optimal weight: 20.0000 overall best weight: 2.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN F 199 ASN F 384 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 558 ASN E 568 GLN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 384 HIS D 473 GLN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 35947 Z= 0.231 Angle : 0.726 10.543 48593 Z= 0.359 Chirality : 0.046 0.191 5470 Planarity : 0.006 0.072 6370 Dihedral : 10.267 175.990 4987 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.11 % Allowed : 4.96 % Favored : 94.93 % 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: -2.14 (0.12), residues: 4424 helix: -0.85 (0.12), residues: 1689 sheet: -0.61 (0.22), residues: 555 loop : -2.12 (0.12), residues: 2180 *********************** 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 666 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 662 time to evaluate : 4.023 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 outliers start: 4 outliers final: 1 residues processed: 666 average time/residue: 0.4945 time to fit residues: 525.7531 Evaluate side-chains 477 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 4.042 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3099 time to fit residues: 6.1520 ------------------------------------------------------------------------------- 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: 50.0000 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 110 optimal weight: 5.9990 chunk 403 optimal weight: 1.9990 chunk 435 optimal weight: 40.0000 chunk 358 optimal weight: 8.9990 chunk 399 optimal weight: 10.0000 chunk 137 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 533 ASN E 538 ASN E 558 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 760 GLN D 270 ASN D 317 HIS ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 404 HIS ** D 490 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** D 735 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN ** B 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 35947 Z= 0.378 Angle : 0.852 10.413 48593 Z= 0.433 Chirality : 0.048 0.170 5470 Planarity : 0.007 0.135 6370 Dihedral : 10.500 176.918 4987 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 26.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 0.16 % Allowed : 6.76 % Favored : 93.08 % 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: -2.19 (0.12), residues: 4424 helix: -0.85 (0.12), residues: 1674 sheet: -1.03 (0.21), residues: 591 loop : -2.06 (0.13), residues: 2159 *********************** 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 588 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 582 time to evaluate : 3.950 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 outliers start: 6 outliers final: 3 residues processed: 587 average time/residue: 0.4900 time to fit residues: 460.3466 Evaluate side-chains 447 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 444 time to evaluate : 3.898 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3263 time to fit residues: 7.5172 ------------------------------------------------------------------------------- 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: 10.0000 chunk 303 optimal weight: 0.3980 chunk 209 optimal weight: 20.0000 chunk 44 optimal weight: 8.9990 chunk 192 optimal weight: 0.9980 chunk 270 optimal weight: 10.0000 chunk 404 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 chunk 211 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- 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 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 533 ASN E 538 ASN D 260 ASN D 401 ASN ** 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 533 ASN ** B 296 ASN ** 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: 0.7613 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 35947 Z= 0.210 Angle : 0.727 10.964 48593 Z= 0.354 Chirality : 0.047 0.209 5470 Planarity : 0.005 0.073 6370 Dihedral : 10.251 167.522 4987 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % 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: -1.95 (0.12), residues: 4424 helix: -0.57 (0.12), residues: 1668 sheet: -0.87 (0.22), residues: 571 loop : -2.00 (0.13), residues: 2185 *********************** 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 590 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 587 time to evaluate : 4.100 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 outliers start: 3 outliers final: 1 residues processed: 589 average time/residue: 0.5033 time to fit residues: 483.8146 Evaluate side-chains 456 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 455 time to evaluate : 4.260 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3670 time to fit residues: 6.4451 ------------------------------------------------------------------------------- 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: 7.9990 chunk 318 optimal weight: 0.9980 chunk 176 optimal weight: 0.9980 chunk 365 optimal weight: 20.0000 chunk 295 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 218 optimal weight: 9.9990 chunk 384 optimal weight: 0.0170 chunk 108 optimal weight: 7.9990 overall best weight: 3.6022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN D 260 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35947 Z= 0.244 Angle : 0.739 11.344 48593 Z= 0.364 Chirality : 0.047 0.178 5470 Planarity : 0.005 0.077 6370 Dihedral : 10.192 169.846 4987 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.22 % 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: -1.87 (0.12), residues: 4424 helix: -0.46 (0.12), residues: 1671 sheet: -0.85 (0.22), residues: 558 loop : -1.98 (0.13), residues: 2195 *********************** 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 561 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 559 time to evaluate : 4.055 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 outliers start: 2 outliers final: 1 residues processed: 561 average time/residue: 0.4716 time to fit residues: 433.0827 Evaluate side-chains 431 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 3.977 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3636 time to fit residues: 6.3248 ------------------------------------------------------------------------------- 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: 7.9990 chunk 385 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 251 optimal weight: 0.8980 chunk 105 optimal weight: 0.0970 chunk 428 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 chunk 225 optimal weight: 20.0000 overall best weight: 1.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 533 ASN E 538 ASN D 260 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 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 602 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35947 Z= 0.188 Angle : 0.716 10.568 48593 Z= 0.345 Chirality : 0.046 0.208 5470 Planarity : 0.005 0.078 6370 Dihedral : 10.045 172.474 4987 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % 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: -1.62 (0.12), residues: 4424 helix: -0.17 (0.13), residues: 1654 sheet: -0.65 (0.22), residues: 544 loop : -1.91 (0.13), residues: 2226 *********************** 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 573 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 571 time to evaluate : 3.915 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 outliers start: 2 outliers final: 2 residues processed: 573 average time/residue: 0.4787 time to fit residues: 446.5551 Evaluate side-chains 439 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 437 time to evaluate : 4.443 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4152 time to fit residues: 7.5958 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 313 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 360 optimal weight: 7.9990 chunk 239 optimal weight: 2.9990 chunk 426 optimal weight: 10.0000 chunk 267 optimal weight: 9.9990 chunk 260 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN D 260 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 692 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 602 ASN I 297 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 35947 Z= 0.275 Angle : 0.773 14.913 48593 Z= 0.382 Chirality : 0.047 0.229 5470 Planarity : 0.006 0.078 6370 Dihedral : 10.142 170.219 4987 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 0.03 % Allowed : 2.51 % Favored : 97.47 % 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: -1.80 (0.12), residues: 4424 helix: -0.35 (0.12), residues: 1657 sheet: -0.88 (0.22), residues: 550 loop : -1.96 (0.13), residues: 2217 *********************** 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 555 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 554 time to evaluate : 4.221 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 outliers start: 1 outliers final: 0 residues processed: 555 average time/residue: 0.4904 time to fit residues: 442.7461 Evaluate side-chains 413 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 4.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 8.9990 chunk 170 optimal weight: 5.9990 chunk 255 optimal weight: 4.9990 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 30.0000 chunk 82 optimal weight: 9.9990 chunk 271 optimal weight: 5.9990 chunk 290 optimal weight: 0.0670 chunk 211 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 335 optimal weight: 8.9990 overall best weight: 5.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN E 183 HIS E 533 ASN E 538 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 641 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 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 602 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 316 HIS I 345 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 35947 Z= 0.311 Angle : 0.816 15.156 48593 Z= 0.407 Chirality : 0.048 0.242 5470 Planarity : 0.006 0.077 6370 Dihedral : 10.290 169.008 4987 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 27.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.58 % Favored : 90.42 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % 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: -2.02 (0.12), residues: 4424 helix: -0.57 (0.12), residues: 1644 sheet: -0.99 (0.21), residues: 568 loop : -2.05 (0.13), residues: 2212 *********************** REFINEMENT MACRO_CYCLE 8 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 532 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 532 time to evaluate : 4.239 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 outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.4827 time to fit residues: 419.7892 Evaluate side-chains 400 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 6.9990 chunk 409 optimal weight: 10.0000 chunk 373 optimal weight: 0.0670 chunk 397 optimal weight: 7.9990 chunk 408 optimal weight: 7.9990 chunk 239 optimal weight: 1.9990 chunk 173 optimal weight: 0.0000 chunk 312 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 chunk 359 optimal weight: 8.9990 chunk 376 optimal weight: 1.9990 overall best weight: 1.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN E 183 HIS ** E 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN D 260 ASN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 641 GLN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 533 ASN ** C 692 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 602 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: 0.7637 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 35947 Z= 0.196 Angle : 0.760 13.014 48593 Z= 0.368 Chirality : 0.048 0.235 5470 Planarity : 0.005 0.077 6370 Dihedral : 10.049 174.410 4987 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -1.70 (0.12), residues: 4424 helix: -0.29 (0.13), residues: 1657 sheet: -0.73 (0.22), residues: 548 loop : -1.91 (0.13), residues: 2219 *********************** REFINEMENT MACRO_CYCLE 9 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 548 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 4.061 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 outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.4874 time to fit residues: 436.7509 Evaluate side-chains 419 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 419 time to evaluate : 4.158 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 3.9990 chunk 261 optimal weight: 10.0000 chunk 420 optimal weight: 0.9980 chunk 256 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 292 optimal weight: 8.9990 chunk 441 optimal weight: 2.9990 chunk 406 optimal weight: 9.9990 chunk 351 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN D 406 HIS ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 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 602 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35947 Z= 0.252 Angle : 0.775 11.569 48593 Z= 0.383 Chirality : 0.048 0.235 5470 Planarity : 0.005 0.078 6370 Dihedral : 10.027 173.692 4987 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.41 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4424 helix: -0.42 (0.12), residues: 1665 sheet: -0.78 (0.22), residues: 543 loop : -1.94 (0.13), residues: 2216 ********************** REFINEMENT MACRO_CYCLE 10 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 521 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 521 time to evaluate : 3.881 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 outliers start: 0 outliers final: 0 residues processed: 521 average time/residue: 0.4809 time to fit residues: 412.3228 Evaluate side-chains 399 residues out of total 3820 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 4.026 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 9.9990 chunk 279 optimal weight: 0.8980 chunk 374 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 324 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 352 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 361 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN ** A 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 603 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 HIS ** F 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 602 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 533 ASN E 538 ASN ** E 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 ASN ** D 406 HIS ** 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 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 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 602 ASN ** I 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.106388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.073627 restraints weight = 148136.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.075671 restraints weight = 101843.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077081 restraints weight = 77657.207| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 35947 Z= 0.245 Angle : 0.767 11.806 48593 Z= 0.378 Chirality : 0.048 0.209 5470 Planarity : 0.005 0.090 6370 Dihedral : 9.995 171.974 4987 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 24.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.41 % 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: -1.85 (0.12), residues: 4424 helix: -0.44 (0.12), residues: 1676 sheet: -0.83 (0.22), residues: 551 loop : -1.98 (0.13), residues: 2197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8358.51 seconds wall clock time: 152 minutes 1.99 seconds (9121.99 seconds total)