Starting phenix.real_space_refine on Wed Jul 24 04:25:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t49_41024/07_2024/8t49_41024.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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 144 5.16 5 C 15642 2.51 5 N 4140 2.21 5 O 5013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24939 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "E" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "O" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "Q" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "F" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3445 Classifications: {'peptide': 434} Link IDs: {'PTRANS': 21, 'TRANS': 412} Chain breaks: 4 Chain: "P" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 967 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 798 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} 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: "S" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "T" 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: "U" 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: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "a" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "b" 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: "c" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "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: 14.79, per 1000 atoms: 0.59 Number of scatterers: 24939 At special positions: 0 Unit cell: (146.05, 149.5, 172.5, 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 144 16.00 O 5013 8.00 N 4140 7.00 C 15642 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=2.05 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=2.04 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 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 E 54 " - pdb=" SG CYS E 74 " distance=2.05 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=2.04 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 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 F 54 " - pdb=" SG CYS F 74 " distance=2.05 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=2.04 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=2.03 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.04 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 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 ALPHA1-2 " MAN S 4 " - " MAN S 5 " " MAN W 4 " - " MAN W 5 " " MAN a 4 " - " MAN a 5 " ALPHA1-3 " BMA S 3 " - " MAN S 4 " " BMA U 3 " - " MAN U 4 " " BMA W 3 " - " MAN W 4 " " BMA Y 3 " - " MAN Y 4 " " BMA a 3 " - " MAN a 4 " " BMA c 3 " - " MAN c 4 " ALPHA1-6 " BMA S 3 " - " MAN S 6 " " BMA W 3 " - " MAN W 6 " " BMA a 3 " - " MAN a 6 " BETA1-4 " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " 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 a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A 601 " - " ASN A 301 " " NAG A 602 " - " ASN A 88 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 234 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 386 " " 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 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 234 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 339 " " NAG E 609 " - " ASN E 386 " " 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 160 " " NAG F 604 " - " ASN F 197 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 295 " " NAG F 608 " - " ASN F 339 " " NAG F 609 " - " ASN F 386 " " 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 156 " " NAG U 1 " - " ASN A 262 " " NAG V 1 " - " ASN H 60 " " NAG W 1 " - " ASN E 332 " " NAG X 1 " - " ASN E 156 " " NAG Y 1 " - " ASN E 262 " " NAG Z 1 " - " ASN O 60 " " NAG a 1 " - " ASN F 332 " " NAG b 1 " - " ASN F 156 " " NAG c 1 " - " ASN F 262 " " NAG d 1 " - " ASN P 60 " Time building additional restraints: 10.78 Conformation dependent library (CDL) restraints added in 4.7 seconds 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5562 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 45 sheets defined 20.7% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100B through 100F Processing helix chain 'L' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU L 29 " --> pdb=" O ASP L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 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: 4.085A pdb=" N GLU D 83 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.667A 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 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 195 through 198 Processing helix chain 'E' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'E' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN E 428 " --> pdb=" O ASN E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 65 No H-bonds generated for 'chain 'O' and resid 63 through 65' Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'O' and resid 100B through 100F Processing helix chain 'Q' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU Q 29 " --> pdb=" O ASP Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 83 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: 4.084A pdb=" N GLU M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY G 527 " --> pdb=" O GLY G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 529 through 534 Processing helix chain 'G' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN G 540 " --> pdb=" O THR G 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN G 543 " --> pdb=" O VAL G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 596 Processing helix chain 'G' and resid 618 through 626 removed outlier: 3.668A 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 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 195 through 198 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.030A 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 387 through 391 Processing helix chain 'F' and resid 425 through 429 removed outlier: 4.247A pdb=" N GLN F 428 " --> pdb=" O ASN F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 474 through 484 removed outlier: 4.227A pdb=" N ASN F 478 " --> pdb=" O ASP F 474 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 65 No H-bonds generated for 'chain 'P' and resid 63 through 65' Processing helix chain 'P' and resid 73 through 75 No H-bonds generated for 'chain 'P' and resid 73 through 75' Processing helix chain 'P' and resid 83 through 87 Processing helix chain 'P' and resid 100B through 100F Processing helix chain 'R' and resid 26 through 30 removed outlier: 3.652A pdb=" N GLU R 29 " --> pdb=" O ASP R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 83 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: 4.085A pdb=" N GLU N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.441A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 543 removed outlier: 3.585A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN I 543 " --> pdb=" O VAL I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 573 through 596 Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.667A 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 sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.061A 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 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN A 301 " --> pdb=" O VAL A 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323 current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 469 Processing sheet with id=AA8, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'H' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP H 35 " --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=AB1, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 97 through 98 No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY C 16 " --> pdb=" O SER C 82B" (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 34 through 39 removed outlier: 5.805A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 57 through 59 current: chain 'C' and resid 100H through 103 Processing sheet with id=AB5, first strand: chain 'D' and resid 19 through 24 Processing sheet with id=AB6, first strand: chain 'D' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP D 35 " --> pdb=" O MET D 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 45 through 48 current: chain 'D' and resid 95A through 98 Processing sheet with id=AB7, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.361A pdb=" N VAL G 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL E 38 " --> pdb=" O THR G 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR G 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR E 40 " --> pdb=" O CYS G 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS G 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'E' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'E' and resid 172 through 177 Processing sheet with id=AC3, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN E 301 " --> pdb=" O VAL E 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 469 Processing sheet with id=AC5, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'O' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP O 35 " --> pdb=" O ASN O 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN O 50 " --> pdb=" O TRP O 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP O 36 " --> pdb=" O ILE O 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 57 through 59 current: chain 'O' and resid 100H through 103 Processing sheet with id=AC7, first strand: chain 'Q' and resid 5 through 6 Processing sheet with id=AC8, first strand: chain 'Q' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 9 through 12 current: chain 'Q' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 45 through 48 current: chain 'Q' and resid 97 through 98 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.807A pdb=" N GLY J 16 " --> pdb=" O SER J 82B" (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 57 through 59 current: chain 'J' and resid 100H through 103 Processing sheet with id=AD2, first strand: chain 'M' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'M' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP M 35 " --> pdb=" O MET M 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 45 through 48 current: chain 'M' and resid 95A through 98 Processing sheet with id=AD4, first strand: chain 'F' and resid 494 through 499 removed outlier: 5.360A pdb=" N VAL I 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL F 38 " --> pdb=" O THR I 606 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N THR I 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N TYR F 40 " --> pdb=" O CYS I 604 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N CYS I 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AD6, first strand: chain 'F' and resid 75 through 76 Processing sheet with id=AD7, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AD8, first strand: chain 'F' and resid 172 through 177 Processing sheet with id=AD9, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.446A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 312 removed outlier: 7.059A pdb=" N ASN F 301 " --> pdb=" O VAL F 323 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N VAL F 323 " --> pdb=" O ASN F 301 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N THR F 303 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 315 through 323 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 465 through 469 Processing sheet with id=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'P' and resid 34 through 39 removed outlier: 6.762A pdb=" N TRP P 35 " --> pdb=" O ASN P 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASN P 50 " --> pdb=" O TRP P 35 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N TRP P 36 " --> pdb=" O ILE P 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 57 through 59 current: chain 'P' and resid 100H through 103 Processing sheet with id=AE4, first strand: chain 'R' and resid 5 through 6 Processing sheet with id=AE5, first strand: chain 'R' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 9 through 12 current: chain 'R' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 45 through 48 current: chain 'R' and resid 97 through 98 No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 3 through 7 removed outlier: 3.808A pdb=" N GLY K 16 " --> pdb=" O SER K 82B" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 34 through 39 removed outlier: 5.804A pdb=" N ARG K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'K' and resid 57 through 59 current: chain 'K' and resid 100H through 103 Processing sheet with id=AE8, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AE9, first strand: chain 'N' and resid 33 through 38 removed outlier: 6.268A pdb=" N TRP N 35 " --> pdb=" O MET N 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 95A through 98 720 hydrogen bonds defined for protein. 1782 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: 8.28 Time building geometry restraints manager: 11.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7833 1.35 - 1.47: 6705 1.47 - 1.60: 10716 1.60 - 1.72: 0 1.72 - 1.85: 198 Bond restraints: 25452 Sorted by residual: bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.59e+00 bond pdb=" C5 MAN S 5 " pdb=" O5 MAN S 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C5 MAN W 5 " pdb=" O5 MAN W 5 " ideal model delta sigma weight residual 1.418 1.465 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C1 NAG d 2 " pdb=" O5 NAG d 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.49e+00 ... (remaining 25447 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.24: 333 104.24 - 111.71: 11690 111.71 - 119.18: 9831 119.18 - 126.65: 12222 126.65 - 134.12: 478 Bond angle restraints: 34554 Sorted by residual: angle pdb=" N LEU Q 97 " pdb=" CA LEU Q 97 " pdb=" C LEU Q 97 " ideal model delta sigma weight residual 107.93 96.77 11.16 1.65e+00 3.67e-01 4.58e+01 angle pdb=" N LEU L 97 " pdb=" CA LEU L 97 " pdb=" C LEU L 97 " ideal model delta sigma weight residual 107.93 96.78 11.15 1.65e+00 3.67e-01 4.57e+01 angle pdb=" N LEU R 97 " pdb=" CA LEU R 97 " pdb=" C LEU R 97 " ideal model delta sigma weight residual 107.93 96.79 11.14 1.65e+00 3.67e-01 4.56e+01 angle pdb=" CA TRP H 47 " pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 angle pdb=" CA TRP O 47 " pdb=" CB TRP O 47 " pdb=" CG TRP O 47 " ideal model delta sigma weight residual 113.60 122.87 -9.27 1.90e+00 2.77e-01 2.38e+01 ... (remaining 34549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15536 21.50 - 42.99: 541 42.99 - 64.49: 141 64.49 - 85.99: 81 85.99 - 107.49: 39 Dihedral angle restraints: 16338 sinusoidal: 7644 harmonic: 8694 Sorted by residual: dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.38 50.38 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.37 50.37 1 1.00e+01 1.00e-02 3.48e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -136.36 50.36 1 1.00e+01 1.00e-02 3.48e+01 ... (remaining 16335 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3889 0.122 - 0.245: 231 0.245 - 0.367: 14 0.367 - 0.489: 0 0.489 - 0.611: 3 Chirality restraints: 4137 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN O 60 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.35e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN H 60 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.29e+00 chirality pdb=" C1 NAG d 1 " pdb=" ND2 ASN P 60 " pdb=" C2 NAG d 1 " pdb=" O5 NAG d 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.28e+00 ... (remaining 4134 not shown) Planarity restraints: 4323 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 476 " 0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG A 476 " -0.069 2.00e-02 2.50e+03 pdb=" O ARG A 476 " 0.026 2.00e-02 2.50e+03 pdb=" N ASP A 477 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 476 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.58e+01 pdb=" C ARG E 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG E 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP E 477 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG F 476 " -0.020 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C ARG F 476 " 0.069 2.00e-02 2.50e+03 pdb=" O ARG F 476 " -0.025 2.00e-02 2.50e+03 pdb=" N ASP F 477 " -0.023 2.00e-02 2.50e+03 ... (remaining 4320 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1542 2.73 - 3.27: 23524 3.27 - 3.81: 40256 3.81 - 4.36: 50950 4.36 - 4.90: 84671 Nonbonded interactions: 200943 Sorted by model distance: nonbonded pdb=" OD1 ASP F 477 " pdb=" NH1 ARG F 480 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASP E 477 " pdb=" NH1 ARG E 480 " model vdw 2.187 2.520 nonbonded pdb=" OD1 ASP A 477 " pdb=" NH1 ARG A 480 " model vdw 2.187 2.520 nonbonded pdb=" O SER C 99 " pdb=" OG SER C 99 " model vdw 2.267 2.440 nonbonded pdb=" O SER J 99 " pdb=" OG SER J 99 " model vdw 2.267 2.440 ... (remaining 200938 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 'W' selection = chain 'a' } ncs_group { reference = chain 'T' selection = chain 'X' selection = chain 'b' } ncs_group { reference = chain 'U' selection = chain 'Y' selection = chain 'c' } ncs_group { reference = chain 'V' selection = chain 'Z' selection = chain 'd' } 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: 4.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 70.040 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.190 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 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 0.073 25452 Z= 0.456 Angle : 1.164 11.163 34554 Z= 0.649 Chirality : 0.066 0.611 4137 Planarity : 0.007 0.074 4260 Dihedral : 14.060 107.487 10641 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.57 % Allowed : 5.25 % Favored : 94.18 % 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: 2979 helix: 0.71 (0.24), residues: 420 sheet: 1.18 (0.17), residues: 861 loop : 0.53 (0.14), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP P 47 HIS 0.006 0.002 HIS E 374 PHE 0.023 0.003 PHE E 383 TYR 0.018 0.003 TYR D 36 ARG 0.020 0.002 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 461 time to evaluate : 3.001 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 426 MET cc_start: 0.8906 (mtp) cc_final: 0.8621 (mtp) REVERT: L 21 MET cc_start: 0.5719 (mtm) cc_final: 0.5418 (mtm) REVERT: L 24 GLN cc_start: 0.7620 (tt0) cc_final: 0.7208 (tm-30) REVERT: L 58 ILE cc_start: 0.7348 (mm) cc_final: 0.6973 (pt) REVERT: L 75 ILE cc_start: 0.5727 (mt) cc_final: 0.5479 (tt) REVERT: L 85 ASP cc_start: 0.7101 (m-30) cc_final: 0.6445 (m-30) REVERT: L 86 TYR cc_start: 0.8223 (m-80) cc_final: 0.7929 (m-80) REVERT: C 86 ASP cc_start: 0.7786 (m-30) cc_final: 0.7484 (m-30) REVERT: C 94 THR cc_start: 0.8824 (m) cc_final: 0.8466 (p) REVERT: D 69 ASN cc_start: 0.8116 (m-40) cc_final: 0.7690 (m-40) REVERT: E 104 MET cc_start: 0.9467 (ttt) cc_final: 0.9246 (ttt) REVERT: E 426 MET cc_start: 0.8808 (mtp) cc_final: 0.8510 (mmm) REVERT: E 475 MET cc_start: 0.8550 (tpp) cc_final: 0.8342 (mmp) REVERT: O 101 ASP cc_start: 0.7412 (t70) cc_final: 0.7180 (t70) REVERT: Q 21 MET cc_start: 0.5762 (mtm) cc_final: 0.5493 (mtm) REVERT: Q 24 GLN cc_start: 0.7726 (tt0) cc_final: 0.7397 (tm-30) REVERT: Q 75 ILE cc_start: 0.5618 (mt) cc_final: 0.5170 (tt) REVERT: Q 85 ASP cc_start: 0.7311 (m-30) cc_final: 0.6397 (m-30) REVERT: Q 103 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7488 (tpt170) REVERT: J 75 LYS cc_start: 0.9148 (mtpp) cc_final: 0.8942 (mtpt) REVERT: M 6 GLN cc_start: 0.7692 (mt0) cc_final: 0.7341 (mt0) REVERT: M 85 ASP cc_start: 0.8274 (m-30) cc_final: 0.7603 (m-30) REVERT: G 535 MET cc_start: 0.8778 (mtt) cc_final: 0.8404 (mtm) REVERT: G 632 ASP cc_start: 0.8589 (t0) cc_final: 0.8292 (t0) REVERT: F 150 MET cc_start: 0.9018 (mmm) cc_final: 0.8719 (mmt) REVERT: F 426 MET cc_start: 0.8916 (mtp) cc_final: 0.8680 (mtp) REVERT: F 475 MET cc_start: 0.8702 (tpp) cc_final: 0.8241 (mmt) REVERT: R 21 MET cc_start: 0.6214 (mtm) cc_final: 0.5993 (mtt) REVERT: R 24 GLN cc_start: 0.7621 (tt0) cc_final: 0.7332 (tm-30) REVERT: N 74 THR cc_start: 0.7821 (m) cc_final: 0.7429 (p) REVERT: N 85 ASP cc_start: 0.8264 (m-30) cc_final: 0.7835 (m-30) REVERT: I 535 MET cc_start: 0.8654 (mtt) cc_final: 0.8408 (mtp) REVERT: I 657 GLU cc_start: 0.8242 (tt0) cc_final: 0.8007 (tt0) outliers start: 15 outliers final: 3 residues processed: 470 average time/residue: 0.4235 time to fit residues: 294.1122 Evaluate side-chains 336 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 333 time to evaluate : 2.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN 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: 9.9990 chunk 225 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 232 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS L 17 HIS L 51 ASN L 52 ASN C 52 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 374 HIS O 77 GLN Q 17 HIS Q 52 ASN J 13 GLN J 52 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 374 HIS R 17 HIS N 6 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25452 Z= 0.381 Angle : 0.679 7.144 34554 Z= 0.355 Chirality : 0.050 0.298 4137 Planarity : 0.005 0.043 4260 Dihedral : 10.005 81.272 5238 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.21 % Allowed : 6.74 % Favored : 91.06 % 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: 0.73 (0.15), residues: 2979 helix: 1.54 (0.26), residues: 429 sheet: 0.93 (0.17), residues: 876 loop : 0.02 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP O 47 HIS 0.012 0.002 HIS L 95B PHE 0.019 0.002 PHE G 522 TYR 0.019 0.002 TYR J 100G ARG 0.005 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 353 time to evaluate : 3.034 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 150 MET cc_start: 0.9329 (mmm) cc_final: 0.9093 (mmm) REVERT: A 241 ASN cc_start: 0.7590 (OUTLIER) cc_final: 0.7370 (m-40) REVERT: L 86 TYR cc_start: 0.8127 (m-80) cc_final: 0.7522 (m-80) REVERT: D 79 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7369 (mp10) REVERT: B 621 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7967 (mt-10) REVERT: O 3 GLN cc_start: 0.5686 (mp10) cc_final: 0.5468 (mp10) REVERT: Q 24 GLN cc_start: 0.7543 (tt0) cc_final: 0.7161 (tm-30) REVERT: Q 86 TYR cc_start: 0.8166 (m-80) cc_final: 0.7338 (m-80) REVERT: M 79 GLN cc_start: 0.7829 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: G 632 ASP cc_start: 0.8795 (t0) cc_final: 0.8421 (t0) REVERT: F 241 ASN cc_start: 0.7153 (OUTLIER) cc_final: 0.6924 (m-40) REVERT: P 5 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7917 (mm-40) REVERT: P 100 ASP cc_start: 0.7626 (t0) cc_final: 0.7395 (t0) REVERT: R 24 GLN cc_start: 0.7541 (tt0) cc_final: 0.7181 (tm-30) REVERT: R 61 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.8396 (ttm110) REVERT: K 13 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7463 (mm110) REVERT: N 79 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: N 85 ASP cc_start: 0.8330 (m-30) cc_final: 0.8124 (m-30) outliers start: 58 outliers final: 35 residues processed: 387 average time/residue: 0.4329 time to fit residues: 256.2228 Evaluate side-chains 342 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 302 time to evaluate : 2.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 241 ASN Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 241 ASN Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 149 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 224 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 270 optimal weight: 3.9990 chunk 291 optimal weight: 0.7980 chunk 240 optimal weight: 0.3980 chunk 267 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 216 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN M 17 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 103 GLN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25452 Z= 0.204 Angle : 0.563 7.959 34554 Z= 0.296 Chirality : 0.045 0.283 4137 Planarity : 0.004 0.034 4260 Dihedral : 8.401 76.636 5232 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.05 % Allowed : 7.76 % Favored : 90.18 % 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: 2979 helix: 1.81 (0.27), residues: 423 sheet: 1.03 (0.18), residues: 849 loop : -0.05 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 47 HIS 0.005 0.001 HIS F 105 PHE 0.009 0.001 PHE C 29 TYR 0.016 0.001 TYR K 100G ARG 0.006 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 322 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 79 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: E 150 MET cc_start: 0.9012 (mmt) cc_final: 0.8806 (mmt) REVERT: E 161 MET cc_start: 0.8895 (tpp) cc_final: 0.8656 (tpt) REVERT: Q 24 GLN cc_start: 0.7468 (tt0) cc_final: 0.7125 (tm-30) REVERT: Q 103 ARG cc_start: 0.7986 (mmm160) cc_final: 0.7676 (tpt170) REVERT: M 79 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7212 (mp10) REVERT: P 5 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7921 (mm-40) REVERT: P 100 ASP cc_start: 0.7481 (t0) cc_final: 0.7235 (t0) REVERT: P 105 ARG cc_start: 0.6138 (mmm160) cc_final: 0.5644 (mmp80) REVERT: R 24 GLN cc_start: 0.7572 (tt0) cc_final: 0.7220 (tm-30) REVERT: R 61 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8411 (ttm110) REVERT: K 13 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7398 (mm110) REVERT: K 97 MET cc_start: 0.8403 (ttp) cc_final: 0.8190 (ttp) REVERT: N 79 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7081 (mp10) REVERT: N 85 ASP cc_start: 0.8446 (m-30) cc_final: 0.8091 (m-30) outliers start: 54 outliers final: 31 residues processed: 351 average time/residue: 0.4105 time to fit residues: 217.3268 Evaluate side-chains 332 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 298 time to evaluate : 2.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 75 ILE Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 266 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 271 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 256 optimal weight: 0.9990 chunk 77 optimal weight: 0.0670 overall best weight: 1.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN H 39 GLN H 77 GLN L 38 GLN D 17 GLN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN ** F 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25452 Z= 0.305 Angle : 0.578 6.169 34554 Z= 0.300 Chirality : 0.046 0.301 4137 Planarity : 0.004 0.039 4260 Dihedral : 7.626 73.909 5232 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.85 % Allowed : 7.65 % Favored : 89.50 % 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: 0.53 (0.15), residues: 2979 helix: 1.68 (0.27), residues: 423 sheet: 0.82 (0.18), residues: 849 loop : -0.19 (0.14), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 479 HIS 0.006 0.001 HIS F 105 PHE 0.016 0.002 PHE K 29 TYR 0.022 0.002 TYR J 27 ARG 0.006 0.001 ARG R 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 308 time to evaluate : 2.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7440 (OUTLIER) cc_final: 0.7037 (t) REVERT: H 51 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.8084 (tt) REVERT: H 77 GLN cc_start: 0.8454 (tt0) cc_final: 0.7849 (mm-40) REVERT: D 79 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7078 (mp10) REVERT: E 161 MET cc_start: 0.8930 (tpp) cc_final: 0.8716 (tpt) REVERT: Q 24 GLN cc_start: 0.7510 (tt0) cc_final: 0.7156 (tm-30) REVERT: Q 79 GLN cc_start: 0.7965 (mm-40) cc_final: 0.6519 (pm20) REVERT: Q 103 ARG cc_start: 0.8050 (mmm160) cc_final: 0.7723 (tpt170) REVERT: M 79 GLN cc_start: 0.7935 (OUTLIER) cc_final: 0.7118 (mp10) REVERT: P 5 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7955 (mm-40) REVERT: P 105 ARG cc_start: 0.6114 (mmm160) cc_final: 0.5574 (mmp80) REVERT: R 24 GLN cc_start: 0.7537 (tt0) cc_final: 0.7182 (tm-30) REVERT: R 61 ARG cc_start: 0.8644 (mtm-85) cc_final: 0.8411 (ttm110) REVERT: R 98 PHE cc_start: 0.6015 (OUTLIER) cc_final: 0.3966 (t80) REVERT: K 13 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7266 (mm110) REVERT: K 23 ARG cc_start: 0.8389 (mmm-85) cc_final: 0.8123 (tpp-160) REVERT: N 79 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7108 (mp10) REVERT: I 624 ASP cc_start: 0.8971 (m-30) cc_final: 0.8524 (m-30) REVERT: I 657 GLU cc_start: 0.8293 (tt0) cc_final: 0.8078 (tt0) outliers start: 75 outliers final: 48 residues processed: 343 average time/residue: 0.3970 time to fit residues: 206.6426 Evaluate side-chains 346 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 292 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 77 GLN Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 28 LEU Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 239 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 198 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 chunk 257 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN A 195 ASN L 89 ASN D 79 GLN D 95 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Q 52 ASN Q 89 ASN M 79 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN P 3 GLN R 52 ASN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25452 Z= 0.317 Angle : 0.577 6.135 34554 Z= 0.299 Chirality : 0.046 0.291 4137 Planarity : 0.004 0.041 4260 Dihedral : 7.307 71.287 5232 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.04 % Allowed : 8.03 % Favored : 88.93 % 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: 0.35 (0.15), residues: 2979 helix: 1.59 (0.27), residues: 423 sheet: 0.63 (0.17), residues: 873 loop : -0.30 (0.14), residues: 1683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Q 91 HIS 0.006 0.001 HIS F 105 PHE 0.014 0.002 PHE K 29 TYR 0.015 0.002 TYR C 27 ARG 0.008 0.001 ARG K 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 311 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7405 (OUTLIER) cc_final: 0.6981 (t) REVERT: L 54 ARG cc_start: 0.7899 (mtp-110) cc_final: 0.7540 (mtp-110) REVERT: L 79 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7636 (mm110) REVERT: D 79 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.6962 (mp10) REVERT: Q 24 GLN cc_start: 0.7701 (tt0) cc_final: 0.7325 (tm-30) REVERT: Q 79 GLN cc_start: 0.8002 (mm-40) cc_final: 0.6801 (pm20) REVERT: J 72 ASP cc_start: 0.8055 (t0) cc_final: 0.7839 (t0) REVERT: M 79 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7694 (mp10) REVERT: P 5 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8019 (mm-40) REVERT: P 105 ARG cc_start: 0.6284 (mmm160) cc_final: 0.5717 (mmp80) REVERT: R 24 GLN cc_start: 0.7604 (tt0) cc_final: 0.7073 (tm-30) REVERT: R 61 ARG cc_start: 0.8683 (mtm-85) cc_final: 0.8442 (ttm110) REVERT: R 98 PHE cc_start: 0.6200 (OUTLIER) cc_final: 0.3893 (t80) REVERT: K 13 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7367 (mm110) REVERT: K 23 ARG cc_start: 0.8402 (mmm-85) cc_final: 0.8142 (tpp-160) REVERT: N 79 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.7194 (mp10) REVERT: I 624 ASP cc_start: 0.8961 (m-30) cc_final: 0.8505 (m-30) REVERT: I 657 GLU cc_start: 0.8304 (tt0) cc_final: 0.8081 (tt0) outliers start: 80 outliers final: 59 residues processed: 354 average time/residue: 0.4079 time to fit residues: 221.4833 Evaluate side-chains 362 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 298 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 79 GLN Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 7 THR Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 11 VAL Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 27 ILE Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 27 ILE Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 96 optimal weight: 0.3980 chunk 258 optimal weight: 0.0000 chunk 56 optimal weight: 8.9990 chunk 168 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 287 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN H 77 GLN D 79 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN O 39 GLN Q 38 GLN Q 52 ASN M 79 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN F 195 ASN R 89 ASN K 105 GLN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25452 Z= 0.177 Angle : 0.523 6.139 34554 Z= 0.272 Chirality : 0.044 0.276 4137 Planarity : 0.004 0.050 4260 Dihedral : 6.929 68.029 5232 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.17 % Allowed : 9.40 % Favored : 88.43 % 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: 0.45 (0.15), residues: 2979 helix: 1.60 (0.27), residues: 441 sheet: 0.66 (0.17), residues: 894 loop : -0.22 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP Q 91 HIS 0.004 0.001 HIS F 105 PHE 0.022 0.001 PHE O 78 TYR 0.015 0.001 TYR K 100G ARG 0.010 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 316 time to evaluate : 2.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7412 (OUTLIER) cc_final: 0.7055 (t) REVERT: L 79 GLN cc_start: 0.7975 (mm-40) cc_final: 0.6691 (pm20) REVERT: Q 24 GLN cc_start: 0.7634 (tt0) cc_final: 0.7231 (tm-30) REVERT: Q 79 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7750 (mm110) REVERT: J 72 ASP cc_start: 0.8023 (t0) cc_final: 0.7782 (t0) REVERT: M 78 LEU cc_start: 0.7847 (mp) cc_final: 0.7638 (mp) REVERT: M 79 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7698 (mp10) REVERT: P 105 ARG cc_start: 0.6317 (mmm160) cc_final: 0.5747 (mmp80) REVERT: R 24 GLN cc_start: 0.7571 (tt0) cc_final: 0.7108 (tm-30) REVERT: R 61 ARG cc_start: 0.8712 (mtm-85) cc_final: 0.8485 (ttm110) REVERT: R 98 PHE cc_start: 0.6392 (OUTLIER) cc_final: 0.4071 (t80) REVERT: K 13 GLN cc_start: 0.7590 (mm-40) cc_final: 0.7314 (mm110) REVERT: K 23 ARG cc_start: 0.8423 (mmm-85) cc_final: 0.8135 (tpp-160) REVERT: N 79 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6948 (mp-120) REVERT: I 624 ASP cc_start: 0.8957 (m-30) cc_final: 0.8501 (m-30) outliers start: 57 outliers final: 43 residues processed: 341 average time/residue: 0.4086 time to fit residues: 211.5865 Evaluate side-chains 348 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 301 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 33 ASN Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 195 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 277 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 209 optimal weight: 0.5980 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 179 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN L 89 ASN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN O 77 GLN Q 52 ASN ** M 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25452 Z= 0.282 Angle : 0.550 6.363 34554 Z= 0.285 Chirality : 0.045 0.270 4137 Planarity : 0.004 0.055 4260 Dihedral : 6.877 67.064 5232 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.51 % Allowed : 9.47 % Favored : 88.01 % 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: 0.36 (0.15), residues: 2979 helix: 1.51 (0.26), residues: 441 sheet: 0.60 (0.17), residues: 885 loop : -0.26 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 479 HIS 0.005 0.001 HIS F 105 PHE 0.018 0.002 PHE H 78 TYR 0.014 0.001 TYR C 27 ARG 0.013 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 311 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7518 (OUTLIER) cc_final: 0.7179 (t) REVERT: H 27 ASP cc_start: 0.6416 (OUTLIER) cc_final: 0.6106 (m-30) REVERT: L 24 GLN cc_start: 0.7834 (tt0) cc_final: 0.7561 (tm-30) REVERT: L 61 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8231 (ttp-110) REVERT: L 79 GLN cc_start: 0.8031 (mm-40) cc_final: 0.7627 (mm110) REVERT: O 27 ASP cc_start: 0.6495 (OUTLIER) cc_final: 0.6175 (m-30) REVERT: Q 24 GLN cc_start: 0.7721 (tt0) cc_final: 0.7300 (tm-30) REVERT: Q 79 GLN cc_start: 0.8078 (mm-40) cc_final: 0.6975 (pm20) REVERT: J 72 ASP cc_start: 0.8041 (t0) cc_final: 0.7796 (t0) REVERT: M 79 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7680 (mp-120) REVERT: P 5 GLN cc_start: 0.8235 (mm-40) cc_final: 0.8030 (mm-40) REVERT: P 24 VAL cc_start: 0.7429 (OUTLIER) cc_final: 0.7179 (t) REVERT: P 27 ASP cc_start: 0.6655 (OUTLIER) cc_final: 0.6422 (m-30) REVERT: P 105 ARG cc_start: 0.6328 (mmm160) cc_final: 0.5731 (mmp80) REVERT: R 24 GLN cc_start: 0.7544 (tt0) cc_final: 0.7062 (tm-30) REVERT: R 61 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8480 (ttm110) REVERT: K 13 GLN cc_start: 0.7598 (mm-40) cc_final: 0.7331 (mm110) REVERT: K 23 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8132 (tpp-160) REVERT: N 79 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7865 (mp10) REVERT: I 624 ASP cc_start: 0.8978 (m-30) cc_final: 0.8508 (m-30) outliers start: 66 outliers final: 51 residues processed: 339 average time/residue: 0.4099 time to fit residues: 211.7510 Evaluate side-chains 360 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 302 time to evaluate : 2.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 78 PHE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 52 ASN Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 98 PHE Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE 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: 2.9990 chunk 170 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 181 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 225 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 GLN ** B 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN Q 52 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25452 Z= 0.277 Angle : 0.552 6.575 34554 Z= 0.285 Chirality : 0.045 0.265 4137 Planarity : 0.004 0.067 4260 Dihedral : 6.799 65.302 5232 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.63 % Allowed : 9.51 % Favored : 87.86 % 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: 0.34 (0.15), residues: 2979 helix: 1.52 (0.26), residues: 441 sheet: 0.58 (0.17), residues: 885 loop : -0.29 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 479 HIS 0.005 0.001 HIS F 105 PHE 0.018 0.002 PHE H 78 TYR 0.014 0.001 TYR K 100G ARG 0.012 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 304 time to evaluate : 3.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7320 (OUTLIER) cc_final: 0.7030 (t) REVERT: H 27 ASP cc_start: 0.6760 (OUTLIER) cc_final: 0.6343 (m-30) REVERT: H 77 GLN cc_start: 0.8332 (tt0) cc_final: 0.7791 (mm-40) REVERT: L 24 GLN cc_start: 0.7908 (tt0) cc_final: 0.7662 (tm-30) REVERT: L 54 ARG cc_start: 0.7739 (mtp-110) cc_final: 0.7423 (mtp-110) REVERT: L 61 ARG cc_start: 0.8524 (ttm110) cc_final: 0.8219 (ttp-110) REVERT: L 79 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7631 (mm110) REVERT: O 27 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6380 (m-30) REVERT: Q 24 GLN cc_start: 0.7802 (tt0) cc_final: 0.7356 (tm-30) REVERT: Q 61 ARG cc_start: 0.8579 (ttm110) cc_final: 0.8161 (ttp-110) REVERT: Q 79 GLN cc_start: 0.8098 (mm-40) cc_final: 0.7770 (mm110) REVERT: J 72 ASP cc_start: 0.8028 (t0) cc_final: 0.7768 (t0) REVERT: M 79 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7619 (mp10) REVERT: P 24 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.7205 (t) REVERT: P 27 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6529 (m-30) REVERT: P 105 ARG cc_start: 0.6386 (mmm160) cc_final: 0.5711 (mmp80) REVERT: R 24 GLN cc_start: 0.7580 (tt0) cc_final: 0.7079 (tm-30) REVERT: R 61 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8478 (ttm110) REVERT: K 13 GLN cc_start: 0.7559 (mm-40) cc_final: 0.7331 (mm110) REVERT: K 23 ARG cc_start: 0.8432 (mmm-85) cc_final: 0.8134 (tpp-160) REVERT: K 53 ARG cc_start: 0.9316 (OUTLIER) cc_final: 0.9067 (mtm-85) REVERT: I 624 ASP cc_start: 0.8979 (m-30) cc_final: 0.8527 (m-30) outliers start: 69 outliers final: 54 residues processed: 336 average time/residue: 0.3990 time to fit residues: 203.2660 Evaluate side-chains 359 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 298 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 43 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain M residue 79 GLN Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 20 SER Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 260 optimal weight: 20.0000 chunk 274 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 chunk 266 optimal weight: 1.9990 chunk 160 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 209 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 265 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 ASN B 607 ASN B 653 GLN E 33 ASN M 79 GLN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25452 Z= 0.357 Angle : 0.594 8.487 34554 Z= 0.304 Chirality : 0.046 0.263 4137 Planarity : 0.004 0.054 4260 Dihedral : 6.866 64.183 5232 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 2.59 % Allowed : 9.78 % Favored : 87.63 % 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: 0.21 (0.15), residues: 2979 helix: 1.41 (0.26), residues: 441 sheet: 0.48 (0.17), residues: 885 loop : -0.35 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 479 HIS 0.006 0.001 HIS F 105 PHE 0.025 0.002 PHE O 78 TYR 0.014 0.002 TYR C 27 ARG 0.011 0.001 ARG Q 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 298 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7406 (OUTLIER) cc_final: 0.7121 (t) REVERT: H 27 ASP cc_start: 0.6873 (OUTLIER) cc_final: 0.6440 (m-30) REVERT: H 77 GLN cc_start: 0.8377 (tt0) cc_final: 0.7971 (tm-30) REVERT: H 78 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: L 24 GLN cc_start: 0.7972 (tt0) cc_final: 0.7685 (tm-30) REVERT: L 61 ARG cc_start: 0.8544 (ttm110) cc_final: 0.8243 (ttp-110) REVERT: L 79 GLN cc_start: 0.8045 (mm-40) cc_final: 0.7659 (mm110) REVERT: L 97 LEU cc_start: 0.7070 (tt) cc_final: 0.6820 (tt) REVERT: O 24 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7300 (t) REVERT: O 27 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6496 (m-30) REVERT: O 105 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6824 (mmp80) REVERT: Q 79 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7853 (mm110) REVERT: J 72 ASP cc_start: 0.8065 (t0) cc_final: 0.7798 (t0) REVERT: P 27 ASP cc_start: 0.6999 (OUTLIER) cc_final: 0.6653 (m-30) REVERT: P 105 ARG cc_start: 0.6353 (mmm160) cc_final: 0.5738 (mmp80) REVERT: R 61 ARG cc_start: 0.8715 (mtm-85) cc_final: 0.8472 (ttm110) REVERT: K 13 GLN cc_start: 0.7574 (mm-40) cc_final: 0.7359 (mm110) REVERT: K 23 ARG cc_start: 0.8434 (mmm-85) cc_final: 0.8127 (tpp-160) REVERT: K 53 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9101 (mtm-85) REVERT: I 624 ASP cc_start: 0.8983 (m-30) cc_final: 0.8518 (m-30) outliers start: 68 outliers final: 55 residues processed: 333 average time/residue: 0.3977 time to fit residues: 201.8495 Evaluate side-chains 357 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 295 time to evaluate : 2.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 78 PHE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain B residue 612 SER Chi-restraints excluded: chain E residue 33 ASN Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 58 ILE Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 99 SER Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 27 ASP Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 95 MET Chi-restraints excluded: chain F residue 100 MET Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 60 VAL Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 99 SER Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE 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: 7.9990 chunk 172 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 295 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 235 optimal weight: 0.0040 chunk 24 optimal weight: 0.9990 chunk 181 optimal weight: 0.7980 chunk 144 optimal weight: 0.0980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25452 Z= 0.170 Angle : 0.528 6.323 34554 Z= 0.273 Chirality : 0.044 0.268 4137 Planarity : 0.004 0.037 4260 Dihedral : 6.510 60.272 5232 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.90 % Allowed : 10.50 % Favored : 87.60 % 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: 0.34 (0.15), residues: 2979 helix: 1.66 (0.27), residues: 441 sheet: 0.46 (0.17), residues: 921 loop : -0.26 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP O 35 HIS 0.004 0.001 HIS A 105 PHE 0.030 0.001 PHE O 78 TYR 0.015 0.001 TYR J 100G ARG 0.008 0.001 ARG Q 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5958 Ramachandran restraints generated. 2979 Oldfield, 0 Emsley, 2979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 297 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 24 VAL cc_start: 0.7368 (OUTLIER) cc_final: 0.7086 (t) REVERT: H 27 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6425 (m-30) REVERT: H 77 GLN cc_start: 0.8487 (tt0) cc_final: 0.8151 (tm-30) REVERT: L 24 GLN cc_start: 0.8128 (tt0) cc_final: 0.7885 (tm-30) REVERT: L 61 ARG cc_start: 0.8528 (ttm110) cc_final: 0.7998 (ttp-110) REVERT: L 79 GLN cc_start: 0.8024 (mm-40) cc_final: 0.6591 (pm20) REVERT: O 24 VAL cc_start: 0.7531 (OUTLIER) cc_final: 0.7288 (t) REVERT: O 27 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6512 (m-30) REVERT: O 105 ARG cc_start: 0.7060 (tpp80) cc_final: 0.6813 (mmp80) REVERT: Q 24 GLN cc_start: 0.7868 (tt0) cc_final: 0.7632 (tm-30) REVERT: Q 29 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7379 (mm-30) REVERT: Q 79 GLN cc_start: 0.8100 (mm-40) cc_final: 0.7031 (pm20) REVERT: J 72 ASP cc_start: 0.8005 (t0) cc_final: 0.7745 (t0) REVERT: F 504 ARG cc_start: 0.7088 (mpt180) cc_final: 0.6810 (mmt-90) REVERT: P 27 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: P 105 ARG cc_start: 0.6337 (mmm160) cc_final: 0.5718 (mmp80) REVERT: R 24 GLN cc_start: 0.7663 (tt0) cc_final: 0.7401 (tm-30) REVERT: R 61 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.8474 (ttm110) REVERT: K 23 ARG cc_start: 0.8473 (mmm-85) cc_final: 0.8163 (tpp-160) REVERT: N 79 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6702 (mm110) REVERT: I 624 ASP cc_start: 0.8971 (m-30) cc_final: 0.8505 (m-30) outliers start: 50 outliers final: 38 residues processed: 317 average time/residue: 0.4105 time to fit residues: 197.5898 Evaluate side-chains 337 residues out of total 2628 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 293 time to evaluate : 2.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 141 MET Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 27 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 92 ASP Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 241 ASN Chi-restraints excluded: chain E residue 426 MET Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain O residue 24 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 92 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 108 LEU Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain F residue 188 ASN Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain P residue 27 ASP Chi-restraints excluded: chain R residue 13 VAL Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 92 ASP Chi-restraints excluded: chain R residue 104 LEU Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 108 LEU Chi-restraints excluded: chain N residue 5 THR Chi-restraints excluded: chain N residue 79 GLN Chi-restraints excluded: chain N residue 97 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 187 optimal weight: 0.7980 chunk 250 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 217 optimal weight: 0.9980 chunk 34 optimal weight: 0.0670 chunk 65 optimal weight: 6.9990 chunk 235 optimal weight: 0.0000 chunk 98 optimal weight: 1.9990 chunk 242 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 ASN ** G 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 33 ASN K 13 GLN N 79 GLN ** I 607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.107068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075322 restraints weight = 47485.643| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.67 r_work: 0.2950 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25452 Z= 0.195 Angle : 0.530 8.140 34554 Z= 0.272 Chirality : 0.044 0.266 4137 Planarity : 0.004 0.062 4260 Dihedral : 6.339 57.739 5232 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.83 % Allowed : 10.62 % Favored : 87.56 % 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: 0.46 (0.15), residues: 2979 helix: 1.95 (0.27), residues: 423 sheet: 0.48 (0.17), residues: 945 loop : -0.20 (0.15), residues: 1611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP O 35 HIS 0.004 0.001 HIS A 105 PHE 0.027 0.001 PHE O 78 TYR 0.018 0.001 TYR C 27 ARG 0.016 0.001 ARG Q 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5833.40 seconds wall clock time: 104 minutes 43.78 seconds (6283.78 seconds total)