Starting phenix.real_space_refine on Wed Jul 24 04:51:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4a_41025/07_2024/8t4a_41025.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.032 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: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 15660 2.51 5 N 4152 2.21 5 O 4962 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24924 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3459 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 21, 'TRANS': 414} Chain breaks: 4 Chain: "C" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "B" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3459 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 21, 'TRANS': 414} Chain breaks: 4 Chain: "J" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "G" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "O" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "Q" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "F" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3459 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 21, 'TRANS': 414} Chain breaks: 4 Chain: "K" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 937 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 789 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 950 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "P" Number of atoms: 1019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 788 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "S" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "T" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "W" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "I" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 14.21, per 1000 atoms: 0.57 Number of scatterers: 24924 At special positions: 0 Unit cell: (156.4, 147.2, 173.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4962 8.00 N 4152 7.00 C 15660 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.00 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.00 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.00 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.04 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.00 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS G 605 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 598 " - pdb=" SG CYS G 604 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 23 " - pdb=" SG CYS Q 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 74 " distance=2.00 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.00 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 501 " - pdb=" SG CYS I 605 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 92 " distance=2.04 Simple disulfide: pdb=" SG CYS R 23 " - pdb=" SG CYS R 88 " distance=2.04 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 Links applied ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 4 " " BMA V 3 " - " MAN V 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA Z 3 " - " MAN Z 4 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 156 " " NAG A 604 " - " ASN A 160 " " NAG A 605 " - " ASN A 197 " " NAG A 606 " - " ASN A 234 " " NAG A 607 " - " ASN A 276 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 339 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 289 " " NAG A 612 " - " ASN A 241 " " NAG A 613 " - " ASN A 355 " " NAG A 614 " - " ASN A 392 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG E 601 " - " ASN E 301 " " NAG E 602 " - " ASN E 88 " " NAG E 603 " - " ASN E 156 " " NAG E 604 " - " ASN E 160 " " NAG E 605 " - " ASN E 197 " " NAG E 606 " - " ASN E 234 " " NAG E 607 " - " ASN E 276 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 289 " " NAG E 612 " - " ASN E 241 " " NAG E 613 " - " ASN E 355 " " NAG E 614 " - " ASN E 392 " " NAG F 601 " - " ASN F 301 " " NAG F 602 " - " ASN F 88 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 197 " " NAG F 606 " - " ASN F 234 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 339 " " NAG F 610 " - " ASN F 448 " " NAG F 611 " - " ASN F 289 " " NAG F 612 " - " ASN F 241 " " NAG F 613 " - " ASN F 355 " " NAG F 614 " - " ASN F 392 " " NAG G 701 " - " ASN G 611 " " NAG G 702 " - " ASN G 618 " " NAG G 703 " - " ASN G 637 " " NAG I 701 " - " ASN I 611 " " NAG I 702 " - " ASN I 618 " " NAG I 703 " - " ASN I 637 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 262 " " NAG U 1 " - " ASN A 386 " " NAG V 1 " - " ASN E 332 " " NAG W 1 " - " ASN E 262 " " NAG X 1 " - " ASN E 386 " " NAG Y 1 " - " ASN F 332 " " NAG Z 1 " - " ASN F 262 " " NAG a 1 " - " ASN F 386 " Time building additional restraints: 10.78 Conformation dependent library (CDL) restraints added in 4.7 seconds 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5622 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 63 sheets defined 18.4% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS A 126 " --> pdb=" O THR A 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 126' Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 Processing helix chain 'C' and resid 61 through 64 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 removed outlier: 3.795A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 27 through 31 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.379A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.794A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU G 545 " --> pdb=" O ALA G 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER G 546 " --> pdb=" O ARG G 542 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET G 626 " --> pdb=" O ILE G 622 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 635 Processing helix chain 'G' and resid 638 through 662 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 27 through 31 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.399A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 126 removed outlier: 3.513A pdb=" N CYS F 126 " --> pdb=" O THR F 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 123 through 126' Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 3.855A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.378A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 484 removed outlier: 3.500A pdb=" N TRP F 479 " --> pdb=" O MET F 475 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.795A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 546 removed outlier: 3.639A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU I 545 " --> pdb=" O ALA I 541 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER I 546 " --> pdb=" O ARG I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.709A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 27 through 31 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.272A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU A 91 " --> pdb=" O CYS A 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL A 120 " --> pdb=" O GLN A 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.218A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.213A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB5, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE D 95B" --> pdb=" O ALA D 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB8, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS H 96 " --> pdb=" O TYR H 100K" (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AC4, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC6, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AC7, first strand: chain 'E' and resid 91 through 94 removed outlier: 3.633A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL E 120 " --> pdb=" O GLN E 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AD1, first strand: chain 'E' and resid 259 through 261 removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 271 through 274 removed outlier: 6.747A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN E 448 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 10.346A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.910A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 301 through 312 removed outlier: 6.888A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 3 through 8 Processing sheet with id=AD5, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD8, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE M 95B" --> pdb=" O ALA M 92 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS O 96 " --> pdb=" O TYR O 100K" (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP O 36 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG O 50 " --> pdb=" O VAL O 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL O 35A" --> pdb=" O ARG O 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP Q 35 " --> pdb=" O VAL Q 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL Q 11 " --> pdb=" O THR Q 105 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 19 through 24 Processing sheet with id=AE7, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.273A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AE9, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AF1, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.634A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 120 through 121 removed outlier: 3.518A pdb=" N VAL F 120 " --> pdb=" O GLN F 203 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AF4, first strand: chain 'F' and resid 259 through 261 removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 271 through 274 removed outlier: 6.746A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N THR F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.362A pdb=" N ASN F 448 " --> pdb=" O THR F 290 " (cutoff:3.500A) removed outlier: 10.347A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.498A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.214A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.909A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 301 through 312 removed outlier: 6.887A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'K' and resid 3 through 8 Processing sheet with id=AF8, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 57 through 59 removed outlier: 5.330A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AG2, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE N 95B" --> pdb=" O ALA N 92 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.303A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AG5, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS P 96 " --> pdb=" O TYR P 100K" (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 57 through 59 removed outlier: 6.689A pdb=" N TRP P 36 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ARG P 50 " --> pdb=" O VAL P 35A" (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL P 35A" --> pdb=" O ARG P 50 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP R 35 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'R' and resid 9 through 12 removed outlier: 6.561A pdb=" N VAL R 11 " --> pdb=" O THR R 105 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'R' and resid 19 through 24 1080 hydrogen bonds defined for protein. 2727 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: 10.24 Time building geometry restraints manager: 11.79 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: 7654 1.34 - 1.46: 6465 1.46 - 1.59: 11120 1.59 - 1.71: 0 1.71 - 1.83: 210 Bond restraints: 25449 Sorted by residual: bond pdb=" CG LEU L 4 " pdb=" CD1 LEU L 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU Q 4 " pdb=" CD1 LEU Q 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.68e+00 bond pdb=" CG LEU R 4 " pdb=" CD1 LEU R 4 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.63e+00 bond pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " ideal model delta sigma weight residual 1.532 1.567 -0.035 1.43e-02 4.89e+03 5.91e+00 bond pdb=" CB VAL H 79 " pdb=" CG2 VAL H 79 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.89e+00 ... (remaining 25444 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.37: 780 106.37 - 113.34: 13954 113.34 - 120.31: 9446 120.31 - 127.28: 10013 127.28 - 134.25: 367 Bond angle restraints: 34560 Sorted by residual: angle pdb=" CA ASP O 55 " pdb=" CB ASP O 55 " pdb=" CG ASP O 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP H 55 " pdb=" CB ASP H 55 " pdb=" CG ASP H 55 " ideal model delta sigma weight residual 112.60 117.73 -5.13 1.00e+00 1.00e+00 2.63e+01 angle pdb=" CA ASP P 55 " pdb=" CB ASP P 55 " pdb=" CG ASP P 55 " ideal model delta sigma weight residual 112.60 117.72 -5.12 1.00e+00 1.00e+00 2.62e+01 angle pdb=" N THR P 31 " pdb=" CA THR P 31 " pdb=" C THR P 31 " ideal model delta sigma weight residual 112.12 105.63 6.49 1.34e+00 5.57e-01 2.34e+01 angle pdb=" N THR O 31 " pdb=" CA THR O 31 " pdb=" C THR O 31 " ideal model delta sigma weight residual 112.12 105.64 6.48 1.34e+00 5.57e-01 2.34e+01 ... (remaining 34555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 15405 22.19 - 44.38: 546 44.38 - 66.57: 153 66.57 - 88.75: 51 88.75 - 110.94: 24 Dihedral angle restraints: 16179 sinusoidal: 7407 harmonic: 8772 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 158.66 -65.66 1 1.00e+01 1.00e-02 5.64e+01 ... (remaining 16176 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3588 0.097 - 0.194: 471 0.194 - 0.291: 24 0.291 - 0.388: 6 0.388 - 0.485: 3 Chirality restraints: 4092 Sorted by residual: chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN A 386 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.88e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN F 386 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.86e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN E 386 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.83e+00 ... (remaining 4089 not shown) Planarity restraints: 4341 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG A 476 " -0.079 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.023 2.00e-02 2.50e+03 4.59e-02 2.11e+01 pdb=" C ARG F 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.030 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C ARG E 476 " 0.079 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.029 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.027 2.00e-02 2.50e+03 ... (remaining 4338 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4092 2.77 - 3.31: 22717 3.31 - 3.84: 40823 3.84 - 4.37: 48738 4.37 - 4.90: 82792 Nonbonded interactions: 199162 Sorted by model distance: nonbonded pdb=" NH2 ARG E 500 " pdb=" OG SER J 98 " model vdw 2.243 2.520 nonbonded pdb=" NH2 ARG F 500 " pdb=" OG SER K 98 " model vdw 2.243 2.520 nonbonded pdb=" NH2 ARG A 500 " pdb=" OG SER C 98 " model vdw 2.244 2.520 nonbonded pdb=" OD1 ASN L 27 " pdb=" OG SER L 30 " model vdw 2.244 2.440 nonbonded pdb=" OD1 ASN Q 27 " pdb=" OG SER Q 30 " model vdw 2.244 2.440 ... (remaining 199157 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' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'O' selection = chain 'P' } ncs_group { reference = chain 'L' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'U' selection = chain 'X' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 25.880 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 68.750 Find NCS groups from input model: 2.530 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.007 0.091 25449 Z= 0.463 Angle : 1.152 10.842 34560 Z= 0.644 Chirality : 0.064 0.485 4092 Planarity : 0.007 0.046 4281 Dihedral : 13.266 110.943 10422 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.23 % Allowed : 4.30 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.15), residues: 2991 helix: 1.09 (0.24), residues: 393 sheet: 1.39 (0.17), residues: 924 loop : 0.61 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.004 TRP O 100H HIS 0.015 0.002 HIS J 82A PHE 0.023 0.003 PHE R 62 TYR 0.024 0.003 TYR L 95B ARG 0.009 0.001 ARG E 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 435 time to evaluate : 2.844 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: C 82 MET cc_start: 0.8215 (mtm) cc_final: 0.7918 (mtm) REVERT: H 64 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7679 (mttm) REVERT: L 27 ASN cc_start: 0.7741 (t0) cc_final: 0.7422 (t0) REVERT: L 54 ARG cc_start: 0.7167 (ttm110) cc_final: 0.6496 (mtp85) REVERT: L 58 ILE cc_start: 0.6773 (mm) cc_final: 0.6350 (mm) REVERT: L 92 ASP cc_start: 0.7074 (t0) cc_final: 0.6859 (t70) REVERT: J 87 THR cc_start: 0.8978 (m) cc_final: 0.8692 (p) REVERT: M 70 THR cc_start: 0.9443 (m) cc_final: 0.9196 (t) REVERT: M 79 GLN cc_start: 0.7208 (mp10) cc_final: 0.6949 (mp10) REVERT: O 64 LYS cc_start: 0.7672 (mtpp) cc_final: 0.7443 (mttm) REVERT: Q 2 TYR cc_start: 0.3510 (t80) cc_final: 0.2708 (t80) REVERT: Q 58 ILE cc_start: 0.6535 (mm) cc_final: 0.6069 (mm) REVERT: Q 92 ASP cc_start: 0.6843 (t0) cc_final: 0.6625 (t70) REVERT: Q 95 LYS cc_start: 0.8328 (mmmm) cc_final: 0.8062 (mmmm) REVERT: N 70 THR cc_start: 0.9453 (m) cc_final: 0.9184 (p) REVERT: P 52 TYR cc_start: 0.7882 (m-80) cc_final: 0.7644 (m-80) REVERT: P 71 LYS cc_start: 0.7446 (ttpt) cc_final: 0.6729 (pttm) REVERT: P 72 ASP cc_start: 0.8296 (t0) cc_final: 0.8043 (t70) REVERT: R 27 ASN cc_start: 0.7768 (t0) cc_final: 0.7352 (t0) REVERT: R 58 ILE cc_start: 0.6501 (mm) cc_final: 0.5997 (mm) REVERT: R 92 ASP cc_start: 0.7052 (t0) cc_final: 0.6705 (t70) REVERT: R 95 LYS cc_start: 0.8249 (mmmm) cc_final: 0.7894 (mmmm) outliers start: 6 outliers final: 2 residues processed: 441 average time/residue: 0.4162 time to fit residues: 273.3306 Evaluate side-chains 293 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 291 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 4 LEU Chi-restraints excluded: chain R residue 4 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 250 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 124 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 120 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 269 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN H 82BASN L 37 GLN E 114 GLN J 3 GLN M 37 GLN F 114 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN P 82BASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25449 Z= 0.321 Angle : 0.659 8.287 34560 Z= 0.347 Chirality : 0.047 0.231 4092 Planarity : 0.004 0.042 4281 Dihedral : 8.783 69.442 4957 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.93 % Allowed : 6.98 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 1.17 (0.15), residues: 2991 helix: 2.32 (0.26), residues: 393 sheet: 1.22 (0.17), residues: 924 loop : 0.20 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 479 HIS 0.006 0.001 HIS J 82A PHE 0.016 0.002 PHE K 29 TYR 0.021 0.002 TYR K 27 ARG 0.005 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 326 time to evaluate : 2.928 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: C 97 MET cc_start: 0.8443 (ttt) cc_final: 0.7873 (ttm) REVERT: D 50 ASP cc_start: 0.7898 (m-30) cc_final: 0.7672 (m-30) REVERT: H 55 ASP cc_start: 0.7563 (t0) cc_final: 0.7341 (t0) REVERT: H 57 LYS cc_start: 0.8578 (mtpp) cc_final: 0.8344 (mtpp) REVERT: L 92 ASP cc_start: 0.6896 (t0) cc_final: 0.6686 (t70) REVERT: L 95 LYS cc_start: 0.8270 (mmmm) cc_final: 0.8055 (mmmm) REVERT: M 70 THR cc_start: 0.9427 (m) cc_final: 0.9215 (t) REVERT: M 79 GLN cc_start: 0.7326 (mp10) cc_final: 0.6816 (mp10) REVERT: O 57 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8308 (mtpp) REVERT: O 64 LYS cc_start: 0.7706 (mtpp) cc_final: 0.7417 (mttm) REVERT: O 100 TYR cc_start: 0.7211 (t80) cc_final: 0.7010 (t80) REVERT: K 72 ASP cc_start: 0.6990 (t0) cc_final: 0.6771 (t0) REVERT: K 75 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8702 (mtpt) REVERT: N 95 THR cc_start: 0.8262 (m) cc_final: 0.8025 (t) REVERT: P 56 ASP cc_start: 0.8484 (m-30) cc_final: 0.8274 (m-30) REVERT: P 57 LYS cc_start: 0.8574 (mtpp) cc_final: 0.8246 (mtpp) REVERT: P 96 LYS cc_start: 0.7341 (tttt) cc_final: 0.7051 (ttpt) REVERT: R 36 TYR cc_start: 0.7671 (m-80) cc_final: 0.7432 (m-10) REVERT: R 92 ASP cc_start: 0.6882 (t0) cc_final: 0.6675 (t70) REVERT: R 95 LYS cc_start: 0.8147 (mmmm) cc_final: 0.7907 (mmmm) outliers start: 51 outliers final: 33 residues processed: 354 average time/residue: 0.4224 time to fit residues: 222.3679 Evaluate side-chains 309 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 276 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 48 ILE Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 58 ILE Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 224 optimal weight: 0.7980 chunk 183 optimal weight: 0.1980 chunk 74 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 chunk 291 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 267 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN ** E 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN K 3 GLN R 17 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25449 Z= 0.245 Angle : 0.587 8.127 34560 Z= 0.308 Chirality : 0.046 0.400 4092 Planarity : 0.004 0.050 4281 Dihedral : 7.418 53.651 4953 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 7.25 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2991 helix: 2.46 (0.27), residues: 393 sheet: 1.33 (0.17), residues: 885 loop : -0.06 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 479 HIS 0.006 0.001 HIS J 82A PHE 0.016 0.002 PHE R 62 TYR 0.017 0.002 TYR O 100K ARG 0.008 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 300 time to evaluate : 2.673 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: A 111 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8727 (mp) REVERT: C 23 ARG cc_start: 0.8155 (tpp-160) cc_final: 0.7911 (ttm110) REVERT: C 75 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8722 (mtpt) REVERT: C 97 MET cc_start: 0.8367 (ttt) cc_final: 0.7814 (ttm) REVERT: H 55 ASP cc_start: 0.7491 (t0) cc_final: 0.7278 (t0) REVERT: H 57 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8267 (mtpp) REVERT: H 66 ARG cc_start: 0.7394 (mtp85) cc_final: 0.7145 (mtp-110) REVERT: H 82 ASN cc_start: 0.8499 (t0) cc_final: 0.8252 (t0) REVERT: L 95 LYS cc_start: 0.8247 (mmmm) cc_final: 0.8039 (mmmm) REVERT: E 161 MET cc_start: 0.8777 (tpp) cc_final: 0.8361 (tpt) REVERT: J 75 LYS cc_start: 0.9072 (mtpp) cc_final: 0.8820 (mtmt) REVERT: M 79 GLN cc_start: 0.7272 (mp10) cc_final: 0.6711 (mp10) REVERT: O 57 LYS cc_start: 0.8528 (mtpp) cc_final: 0.8194 (mtpp) REVERT: O 58 TYR cc_start: 0.8462 (m-80) cc_final: 0.8184 (m-80) REVERT: O 100 TYR cc_start: 0.7140 (t80) cc_final: 0.6940 (t80) REVERT: Q 95 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7942 (mmmm) REVERT: F 111 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8647 (mt) REVERT: K 72 ASP cc_start: 0.7030 (t0) cc_final: 0.6781 (t0) REVERT: K 75 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8735 (mtpt) REVERT: K 82 MET cc_start: 0.8580 (mtm) cc_final: 0.8378 (mtm) REVERT: P 5 LYS cc_start: 0.9237 (mttt) cc_final: 0.8753 (tptp) REVERT: P 57 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8095 (mtpp) REVERT: P 58 TYR cc_start: 0.8536 (m-80) cc_final: 0.7962 (m-80) REVERT: R 36 TYR cc_start: 0.7681 (m-80) cc_final: 0.7446 (m-10) REVERT: R 95 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7481 (mmmm) outliers start: 57 outliers final: 36 residues processed: 337 average time/residue: 0.4517 time to fit residues: 229.1989 Evaluate side-chains 305 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 267 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Chi-restraints excluded: chain R residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 1.9990 chunk 203 optimal weight: 3.9990 chunk 140 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 271 optimal weight: 3.9990 chunk 287 optimal weight: 0.0670 chunk 141 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 6 GLN K 3 GLN P 82BASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25449 Z= 0.224 Angle : 0.561 7.584 34560 Z= 0.292 Chirality : 0.045 0.257 4092 Planarity : 0.004 0.036 4281 Dihedral : 6.532 53.764 4953 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.00 % Allowed : 8.42 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.15), residues: 2991 helix: 2.52 (0.27), residues: 393 sheet: 1.34 (0.17), residues: 855 loop : -0.22 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 479 HIS 0.005 0.001 HIS K 82A PHE 0.013 0.001 PHE R 62 TYR 0.018 0.001 TYR K 27 ARG 0.006 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 304 time to evaluate : 2.597 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: A 151 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.8287 (ttt180) REVERT: C 97 MET cc_start: 0.8348 (ttt) cc_final: 0.7805 (ttm) REVERT: H 5 LYS cc_start: 0.9107 (mttt) cc_final: 0.8661 (tptp) REVERT: H 55 ASP cc_start: 0.7518 (t0) cc_final: 0.7289 (t0) REVERT: H 57 LYS cc_start: 0.8561 (mtpp) cc_final: 0.8136 (mtpp) REVERT: H 100 TYR cc_start: 0.7344 (t80) cc_final: 0.7020 (t80) REVERT: L 28 ILE cc_start: 0.8537 (mm) cc_final: 0.8222 (mm) REVERT: M 79 GLN cc_start: 0.7193 (mp10) cc_final: 0.6737 (mp10) REVERT: O 57 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8161 (mtpp) REVERT: Q 95 LYS cc_start: 0.8177 (mmmm) cc_final: 0.7959 (mmmm) REVERT: F 111 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8635 (mt) REVERT: P 5 LYS cc_start: 0.9208 (mttt) cc_final: 0.8766 (tptp) REVERT: P 38 ARG cc_start: 0.7087 (ttm170) cc_final: 0.6854 (ttm170) REVERT: P 57 LYS cc_start: 0.8402 (mtpp) cc_final: 0.8059 (mtpp) REVERT: P 58 TYR cc_start: 0.8661 (m-80) cc_final: 0.8016 (m-80) REVERT: P 71 LYS cc_start: 0.7221 (ttpt) cc_final: 0.6592 (pttm) REVERT: P 82 MET cc_start: 0.5912 (mtp) cc_final: 0.5696 (mtp) REVERT: R 27 ASN cc_start: 0.7639 (t0) cc_final: 0.7276 (t0) REVERT: R 36 TYR cc_start: 0.7748 (m-80) cc_final: 0.7470 (m-10) REVERT: R 95 LYS cc_start: 0.8309 (mmmm) cc_final: 0.7883 (mmmm) outliers start: 53 outliers final: 39 residues processed: 340 average time/residue: 0.4297 time to fit residues: 216.4763 Evaluate side-chains 307 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 266 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 38 ARG Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 198 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 0.6980 chunk 257 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 79 GLN H 82BASN L 37 GLN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN P 39 GLN P 82BASN R 38 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 25449 Z= 0.380 Angle : 0.633 13.985 34560 Z= 0.325 Chirality : 0.047 0.362 4092 Planarity : 0.004 0.042 4281 Dihedral : 6.499 55.244 4953 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.30 % Allowed : 9.17 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2991 helix: 2.19 (0.27), residues: 393 sheet: 1.26 (0.17), residues: 861 loop : -0.35 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 479 HIS 0.004 0.001 HIS K 82A PHE 0.017 0.002 PHE J 29 TYR 0.019 0.002 TYR R 95B ARG 0.010 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 267 time to evaluate : 2.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8347 (ttt180) REVERT: C 75 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8681 (mttp) REVERT: H 5 LYS cc_start: 0.9111 (mttt) cc_final: 0.8667 (tptp) REVERT: H 55 ASP cc_start: 0.7607 (t0) cc_final: 0.7378 (t0) REVERT: H 66 ARG cc_start: 0.7700 (mtp85) cc_final: 0.7377 (ttm110) REVERT: H 82 MET cc_start: 0.4436 (ppp) cc_final: 0.4121 (ppp) REVERT: H 82 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8076 (t0) REVERT: H 100 TYR cc_start: 0.7377 (t80) cc_final: 0.6889 (t80) REVERT: L 95 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7882 (mmmm) REVERT: M 47 MET cc_start: 0.8577 (mmm) cc_final: 0.8334 (mmm) REVERT: M 79 GLN cc_start: 0.7297 (mp10) cc_final: 0.6868 (mp10) REVERT: O 57 LYS cc_start: 0.8468 (mtpp) cc_final: 0.8049 (mtpp) REVERT: F 111 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8741 (mt) REVERT: K 75 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8671 (mtpt) REVERT: P 41 PRO cc_start: 0.7428 (Cg_exo) cc_final: 0.7127 (Cg_endo) REVERT: P 57 LYS cc_start: 0.8354 (mtpp) cc_final: 0.7973 (mtpp) REVERT: P 58 TYR cc_start: 0.8585 (m-80) cc_final: 0.8103 (m-80) REVERT: P 82 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7887 (t0) REVERT: R 27 ASN cc_start: 0.7698 (t0) cc_final: 0.7375 (t0) REVERT: R 36 TYR cc_start: 0.7788 (m-80) cc_final: 0.7454 (m-10) REVERT: R 86 TYR cc_start: 0.7368 (m-10) cc_final: 0.7035 (m-10) REVERT: R 95 LYS cc_start: 0.8263 (mmmm) cc_final: 0.7862 (mmmm) outliers start: 61 outliers final: 43 residues processed: 310 average time/residue: 0.4215 time to fit residues: 194.0042 Evaluate side-chains 297 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 250 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 82 ASN Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 70 THR Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain I residue 573 ILE Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 47 VAL Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain R residue 70 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 287 optimal weight: 0.1980 chunk 238 optimal weight: 0.0470 chunk 133 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 overall best weight: 0.7882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82BASN R 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25449 Z= 0.196 Angle : 0.563 11.764 34560 Z= 0.290 Chirality : 0.044 0.258 4092 Planarity : 0.004 0.046 4281 Dihedral : 6.129 54.315 4953 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.85 % Allowed : 9.70 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2991 helix: 2.48 (0.27), residues: 393 sheet: 1.34 (0.17), residues: 855 loop : -0.38 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 479 HIS 0.005 0.001 HIS K 82A PHE 0.009 0.001 PHE F 176 TYR 0.020 0.001 TYR K 27 ARG 0.007 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 269 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8320 (ttt180) REVERT: D 79 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.6750 (mp10) REVERT: B 648 GLU cc_start: 0.7900 (tp30) cc_final: 0.7698 (tp30) REVERT: H 5 LYS cc_start: 0.9109 (mttt) cc_final: 0.8685 (tptp) REVERT: H 55 ASP cc_start: 0.7513 (t0) cc_final: 0.7238 (t0) REVERT: H 57 LYS cc_start: 0.8537 (mtpp) cc_final: 0.8173 (mtpp) REVERT: H 82 MET cc_start: 0.4219 (ppp) cc_final: 0.3918 (ppp) REVERT: H 82 ASN cc_start: 0.8451 (t0) cc_final: 0.8154 (t0) REVERT: H 100 TYR cc_start: 0.7309 (t80) cc_final: 0.6961 (t80) REVERT: L 28 ILE cc_start: 0.8519 (mm) cc_final: 0.8147 (mm) REVERT: L 95 LYS cc_start: 0.8163 (mmmm) cc_final: 0.7945 (mmmt) REVERT: M 79 GLN cc_start: 0.7126 (mp10) cc_final: 0.6722 (mp10) REVERT: O 57 LYS cc_start: 0.8452 (mtpp) cc_final: 0.8028 (mtpp) REVERT: F 111 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8676 (mt) REVERT: F 161 MET cc_start: 0.8721 (tpp) cc_final: 0.8099 (tpt) REVERT: K 75 LYS cc_start: 0.8997 (mtmt) cc_final: 0.8784 (mtpt) REVERT: N 17 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7290 (pt0) REVERT: N 79 GLN cc_start: 0.6498 (mp10) cc_final: 0.6130 (mp10) REVERT: P 57 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7904 (mtpp) REVERT: P 58 TYR cc_start: 0.8513 (m-80) cc_final: 0.7958 (m-80) REVERT: P 66 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7011 (mtp-110) REVERT: P 82 ASN cc_start: 0.8625 (t0) cc_final: 0.8394 (t0) REVERT: R 17 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5378 (mp10) REVERT: R 27 ASN cc_start: 0.7728 (t0) cc_final: 0.7458 (t0) REVERT: R 39 LYS cc_start: 0.7230 (tptt) cc_final: 0.6929 (mptt) REVERT: R 95 LYS cc_start: 0.8243 (mmmm) cc_final: 0.7862 (mmmm) outliers start: 49 outliers final: 36 residues processed: 304 average time/residue: 0.4353 time to fit residues: 196.5681 Evaluate side-chains 296 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 256 time to evaluate : 2.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain M residue 58 VAL Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 34 MET Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 17 GLN Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 9.9990 chunk 32 optimal weight: 0.5980 chunk 163 optimal weight: 1.9990 chunk 209 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 286 optimal weight: 6.9990 chunk 179 optimal weight: 0.1980 chunk 174 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82BASN ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25449 Z= 0.247 Angle : 0.567 10.637 34560 Z= 0.292 Chirality : 0.044 0.244 4092 Planarity : 0.004 0.047 4281 Dihedral : 6.019 54.337 4953 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.89 % Allowed : 10.15 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2991 helix: 2.44 (0.27), residues: 393 sheet: 1.35 (0.17), residues: 840 loop : -0.42 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 479 HIS 0.004 0.001 HIS K 82A PHE 0.011 0.001 PHE J 29 TYR 0.018 0.001 TYR R 95B ARG 0.011 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 265 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8354 (ttt180) REVERT: C 66 ARG cc_start: 0.8352 (ptp90) cc_final: 0.8056 (mtm110) REVERT: D 79 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.6791 (mp10) REVERT: B 648 GLU cc_start: 0.7936 (tp30) cc_final: 0.7708 (tp30) REVERT: H 5 LYS cc_start: 0.9098 (mttt) cc_final: 0.8720 (tptp) REVERT: H 55 ASP cc_start: 0.7545 (t0) cc_final: 0.7237 (t0) REVERT: H 57 LYS cc_start: 0.8533 (mtpp) cc_final: 0.8147 (mtpp) REVERT: H 66 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7615 (mtp-110) REVERT: H 100 TYR cc_start: 0.7356 (t80) cc_final: 0.7043 (t80) REVERT: L 28 ILE cc_start: 0.8556 (mm) cc_final: 0.8213 (mm) REVERT: L 95 LYS cc_start: 0.8186 (mmmm) cc_final: 0.7942 (mmmt) REVERT: M 79 GLN cc_start: 0.7179 (mp10) cc_final: 0.6780 (mp10) REVERT: O 57 LYS cc_start: 0.8432 (mtpp) cc_final: 0.8011 (mtpp) REVERT: F 111 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8693 (mt) REVERT: F 161 MET cc_start: 0.8747 (tpp) cc_final: 0.8149 (tpt) REVERT: K 75 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8805 (mtpt) REVERT: N 79 GLN cc_start: 0.6615 (mp10) cc_final: 0.6229 (mp10) REVERT: I 648 GLU cc_start: 0.7852 (tp30) cc_final: 0.7488 (tp30) REVERT: P 57 LYS cc_start: 0.8337 (mtpp) cc_final: 0.7894 (mtpp) REVERT: P 58 TYR cc_start: 0.8540 (m-80) cc_final: 0.8023 (m-80) REVERT: P 66 ARG cc_start: 0.7366 (mtp-110) cc_final: 0.7145 (mtp-110) REVERT: P 82 ASN cc_start: 0.8575 (t0) cc_final: 0.8350 (t0) REVERT: R 17 GLN cc_start: 0.6193 (pt0) cc_final: 0.5426 (mp10) REVERT: R 27 ASN cc_start: 0.7715 (t0) cc_final: 0.7457 (t0) REVERT: R 39 LYS cc_start: 0.7275 (tptt) cc_final: 0.6987 (mptt) REVERT: R 95 LYS cc_start: 0.8329 (mmmm) cc_final: 0.7976 (mmmm) outliers start: 50 outliers final: 40 residues processed: 303 average time/residue: 0.4415 time to fit residues: 198.8879 Evaluate side-chains 294 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 573 ILE Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 27 ASP Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain I residue 544 LEU Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 177 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 55 optimal weight: 4.9990 chunk 181 optimal weight: 0.4980 chunk 195 optimal weight: 8.9990 chunk 141 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25449 Z= 0.212 Angle : 0.562 13.037 34560 Z= 0.289 Chirality : 0.044 0.251 4092 Planarity : 0.004 0.065 4281 Dihedral : 5.836 54.176 4953 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.93 % Allowed : 10.53 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.15), residues: 2991 helix: 2.52 (0.27), residues: 393 sheet: 1.35 (0.17), residues: 846 loop : -0.45 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS K 82A PHE 0.009 0.001 PHE J 29 TYR 0.022 0.001 TYR L 95B ARG 0.007 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 255 time to evaluate : 2.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8346 (ttt180) REVERT: D 42 LYS cc_start: 0.7808 (pttm) cc_final: 0.7438 (pttp) REVERT: D 79 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6829 (mp10) REVERT: B 648 GLU cc_start: 0.7911 (tp30) cc_final: 0.7701 (tp30) REVERT: H 55 ASP cc_start: 0.7568 (t0) cc_final: 0.7341 (t0) REVERT: H 57 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8105 (mtpp) REVERT: H 100 TYR cc_start: 0.7312 (t80) cc_final: 0.7001 (t80) REVERT: L 28 ILE cc_start: 0.8549 (mm) cc_final: 0.8190 (mm) REVERT: L 95 LYS cc_start: 0.8142 (mmmm) cc_final: 0.7898 (mmmt) REVERT: M 42 LYS cc_start: 0.7542 (pttm) cc_final: 0.7262 (pttp) REVERT: M 47 MET cc_start: 0.8440 (mmm) cc_final: 0.8007 (mmm) REVERT: M 79 GLN cc_start: 0.7277 (mp10) cc_final: 0.6884 (mp10) REVERT: O 57 LYS cc_start: 0.8429 (mtpp) cc_final: 0.8032 (mtpp) REVERT: F 95 MET cc_start: 0.9050 (ptm) cc_final: 0.8421 (ptm) REVERT: F 111 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8697 (mt) REVERT: K 75 LYS cc_start: 0.9028 (mtmt) cc_final: 0.8737 (mtpp) REVERT: N 79 GLN cc_start: 0.6796 (mp10) cc_final: 0.6419 (mp10) REVERT: I 648 GLU cc_start: 0.7843 (tp30) cc_final: 0.7463 (tp30) REVERT: P 57 LYS cc_start: 0.8317 (mtpp) cc_final: 0.7797 (mtpp) REVERT: P 82 ASN cc_start: 0.8579 (t0) cc_final: 0.8356 (t0) REVERT: R 17 GLN cc_start: 0.6500 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: R 27 ASN cc_start: 0.7682 (t0) cc_final: 0.7448 (t0) REVERT: R 39 LYS cc_start: 0.7464 (tptt) cc_final: 0.7215 (mptt) outliers start: 51 outliers final: 42 residues processed: 293 average time/residue: 0.4198 time to fit residues: 183.1476 Evaluate side-chains 283 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 237 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 17 GLN Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 10.0000 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 5.9990 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 241 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 54 ASN R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25449 Z= 0.228 Angle : 0.567 11.578 34560 Z= 0.293 Chirality : 0.044 0.353 4092 Planarity : 0.004 0.071 4281 Dihedral : 5.793 54.294 4953 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.00 % Allowed : 10.72 % Favored : 87.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.15), residues: 2991 helix: 2.51 (0.27), residues: 393 sheet: 1.40 (0.17), residues: 843 loop : -0.50 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 479 HIS 0.004 0.001 HIS K 82A PHE 0.012 0.001 PHE L 62 TYR 0.027 0.001 TYR O 90 ARG 0.008 0.001 ARG L 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 246 time to evaluate : 2.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8360 (ttt180) REVERT: D 79 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6856 (mp10) REVERT: H 55 ASP cc_start: 0.7476 (t0) cc_final: 0.7256 (t0) REVERT: H 57 LYS cc_start: 0.8501 (mtpp) cc_final: 0.8180 (mtpp) REVERT: H 100 TYR cc_start: 0.7308 (t80) cc_final: 0.6999 (t80) REVERT: L 95 LYS cc_start: 0.8137 (mmmm) cc_final: 0.7902 (mmmt) REVERT: M 47 MET cc_start: 0.8432 (mmm) cc_final: 0.8066 (mmp) REVERT: M 79 GLN cc_start: 0.7307 (mp10) cc_final: 0.6904 (mp10) REVERT: O 57 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8052 (mtpp) REVERT: F 95 MET cc_start: 0.9063 (ptm) cc_final: 0.8470 (ptm) REVERT: F 111 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8702 (mt) REVERT: K 75 LYS cc_start: 0.9044 (mtmt) cc_final: 0.8757 (mtpp) REVERT: N 79 GLN cc_start: 0.6908 (mp10) cc_final: 0.6539 (mp10) REVERT: I 648 GLU cc_start: 0.7875 (tp30) cc_final: 0.7481 (tp30) REVERT: P 57 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7791 (mtpp) REVERT: R 17 GLN cc_start: 0.6214 (OUTLIER) cc_final: 0.5387 (mp10) REVERT: R 27 ASN cc_start: 0.7700 (t0) cc_final: 0.7435 (t0) REVERT: R 39 LYS cc_start: 0.7518 (tptt) cc_final: 0.7176 (mptt) outliers start: 53 outliers final: 46 residues processed: 285 average time/residue: 0.4311 time to fit residues: 184.1138 Evaluate side-chains 289 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 46 LEU Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 17 GLN Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 175 optimal weight: 2.9990 chunk 282 optimal weight: 8.9990 chunk 172 optimal weight: 1.9990 chunk 133 optimal weight: 0.0040 chunk 196 optimal weight: 3.9990 chunk 295 optimal weight: 8.9990 chunk 272 optimal weight: 0.9980 chunk 235 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 chunk 144 optimal weight: 6.9990 overall best weight: 0.8014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82BASN R 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25449 Z= 0.195 Angle : 0.561 11.682 34560 Z= 0.289 Chirality : 0.044 0.266 4092 Planarity : 0.004 0.052 4281 Dihedral : 5.673 54.095 4953 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.00 % Allowed : 10.80 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2991 helix: 2.46 (0.27), residues: 399 sheet: 1.43 (0.17), residues: 843 loop : -0.50 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 69 HIS 0.004 0.001 HIS K 82A PHE 0.009 0.001 PHE L 62 TYR 0.020 0.001 TYR R 95B ARG 0.011 0.001 ARG P 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5982 Ramachandran restraints generated. 2991 Oldfield, 0 Emsley, 2991 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 252 time to evaluate : 2.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8343 (ttt180) REVERT: C 61 ASP cc_start: 0.8382 (p0) cc_final: 0.8172 (p0) REVERT: D 61 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7660 (mtm110) REVERT: D 79 GLN cc_start: 0.7169 (OUTLIER) cc_final: 0.6941 (mp10) REVERT: H 55 ASP cc_start: 0.7316 (t0) cc_final: 0.7079 (t0) REVERT: H 57 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8190 (mtpp) REVERT: H 100 TYR cc_start: 0.7278 (t80) cc_final: 0.7021 (t80) REVERT: L 95 LYS cc_start: 0.8145 (mmmm) cc_final: 0.7920 (mmmt) REVERT: M 47 MET cc_start: 0.8439 (mmm) cc_final: 0.8063 (mmp) REVERT: O 57 LYS cc_start: 0.8428 (mtpp) cc_final: 0.8051 (mtpp) REVERT: F 95 MET cc_start: 0.9067 (ptm) cc_final: 0.8471 (ptm) REVERT: F 111 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8695 (mt) REVERT: K 75 LYS cc_start: 0.9034 (mtmt) cc_final: 0.8743 (mtpp) REVERT: N 47 MET cc_start: 0.8502 (mmm) cc_final: 0.7986 (mmm) REVERT: N 79 GLN cc_start: 0.6888 (mp10) cc_final: 0.6562 (mp10) REVERT: I 648 GLU cc_start: 0.7878 (tp30) cc_final: 0.7444 (tp30) REVERT: P 5 LYS cc_start: 0.9136 (mttt) cc_final: 0.8745 (tptp) REVERT: P 57 LYS cc_start: 0.8347 (mtpp) cc_final: 0.7850 (mtpp) REVERT: R 27 ASN cc_start: 0.7724 (t0) cc_final: 0.7481 (t0) REVERT: R 39 LYS cc_start: 0.7492 (tptt) cc_final: 0.7187 (mptt) REVERT: R 61 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7889 (mtp-110) outliers start: 53 outliers final: 45 residues processed: 290 average time/residue: 0.4464 time to fit residues: 191.9600 Evaluate side-chains 292 residues out of total 2649 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 244 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 296 CYS Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 52 ASP Chi-restraints excluded: chain D residue 26 THR Chi-restraints excluded: chain D residue 33 VAL Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain H residue 24 PHE Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 91 TYR Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 94 THR Chi-restraints excluded: chain M residue 26 THR Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain G residue 544 LEU Chi-restraints excluded: chain O residue 24 PHE Chi-restraints excluded: chain O residue 91 TYR Chi-restraints excluded: chain O residue 95 VAL Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 51 ASP Chi-restraints excluded: chain Q residue 72 THR Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 296 CYS Chi-restraints excluded: chain K residue 52 ASP Chi-restraints excluded: chain K residue 101 ASP Chi-restraints excluded: chain N residue 26 THR Chi-restraints excluded: chain N residue 33 VAL Chi-restraints excluded: chain P residue 24 PHE Chi-restraints excluded: chain P residue 79 VAL Chi-restraints excluded: chain P residue 82 ASN Chi-restraints excluded: chain P residue 91 TYR Chi-restraints excluded: chain R residue 3 VAL Chi-restraints excluded: chain R residue 28 ILE Chi-restraints excluded: chain R residue 51 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 235 optimal weight: 0.6980 chunk 98 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 82BASN ** R 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.095615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067712 restraints weight = 62418.889| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.96 r_work: 0.3107 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 25449 Z= 0.262 Angle : 0.710 59.094 34560 Z= 0.399 Chirality : 0.044 0.269 4092 Planarity : 0.004 0.051 4281 Dihedral : 5.680 54.089 4953 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 10.76 % Favored : 87.28 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.15), residues: 2991 helix: 2.45 (0.27), residues: 399 sheet: 1.43 (0.17), residues: 843 loop : -0.50 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 69 HIS 0.004 0.001 HIS K 82A PHE 0.008 0.001 PHE L 62 TYR 0.017 0.001 TYR R 95B ARG 0.024 0.001 ARG R 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5663.60 seconds wall clock time: 102 minutes 23.82 seconds (6143.82 seconds total)