Starting phenix.real_space_refine on Sat Mar 16 22:20:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/03_2024/7l8f_23232_updated.pdb" } resolution = 3.66 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= 0.004 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 102 5.16 5 C 9855 2.51 5 N 2684 2.21 5 O 3199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 381": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15840 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3523 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3508 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3515 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 635 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'TRANS': 126} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 127 Planarities with less than four sites: {'UNK:plan-1': 127} Unresolved non-hydrogen planarities: 127 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" 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: "J" 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: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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: "N" 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: "O" 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: "P" 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: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" 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: "S" 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 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: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" 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: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 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 Time building chain proxies: 8.45, per 1000 atoms: 0.53 Number of scatterers: 15840 At special positions: 0 Unit cell: (143.17, 126.69, 134.93, 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 102 16.00 O 3199 8.00 N 2684 7.00 C 9855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.10 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 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 ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA Q 3 " - " MAN Q 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " NAG-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 386 " " NAG C 706 " - " ASN C 363 " " NAG C 707 " - " ASN C 234 " " NAG C 708 " - " ASN C 197 " " NAG C 709 " - " ASN C 133 " " NAG C 710 " - " ASN C 301 " " NAG C 711 " - " ASN C 88 " " NAG C 712 " - " ASN C 241 " " NAG C 713 " - " ASN C 289 " " NAG C 714 " - " ASN C 339 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 701 " - " ASN E 448 " " NAG E 702 " - " ASN E 160 " " NAG E 703 " - " ASN E 276 " " NAG E 704 " - " ASN E 386 " " NAG E 705 " - " ASN E 363 " " NAG E 706 " - " ASN E 234 " " NAG E 707 " - " ASN E 133 " " NAG E 708 " - " ASN E 301 " " NAG E 709 " - " ASN E 88 " " NAG E 710 " - " ASN E 241 " " NAG E 711 " - " ASN E 289 " " NAG E 712 " - " ASN E 355 " " NAG E 713 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 197 " " NAG O 1 " - " ASN E 156 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " Time building additional restraints: 7.00 Conformation dependent library (CDL) restraints added in 2.6 seconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 34 sheets defined 27.0% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 99 through 117 removed outlier: 4.445A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 140 through 150 No H-bonds generated for 'chain 'C' and resid 140 through 150' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 352 removed outlier: 4.356A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 475 through 485 removed outlier: 3.714A pdb=" N SER C 481 " --> pdb=" O ASN C 478 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N TYR C 484 " --> pdb=" O SER C 481 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 548 removed outlier: 3.996A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D 540 " --> pdb=" O LEU D 537 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA D 541 " --> pdb=" O THR D 538 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG D 542 " --> pdb=" O VAL D 539 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU D 544 " --> pdb=" O ALA D 541 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER D 546 " --> pdb=" O ASN D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 622 No H-bonds generated for 'chain 'D' and resid 619 through 622' Processing helix chain 'D' and resid 628 through 634 Processing helix chain 'D' and resid 636 through 660 removed outlier: 4.346A pdb=" N GLN D 640 " --> pdb=" O ASN D 637 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 115 Processing helix chain 'E' and resid 122 through 125 Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 391 No H-bonds generated for 'chain 'E' and resid 388 through 391' Processing helix chain 'E' and resid 475 through 483 Processing helix chain 'F' and resid 532 through 546 removed outlier: 3.519A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU F 537 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN F 540 " --> pdb=" O LEU F 537 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 541 " --> pdb=" O THR F 538 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 542 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN F 543 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N LEU F 544 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 635 removed outlier: 3.789A pdb=" N GLU F 634 " --> pdb=" O GLN F 630 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 639 through 660 removed outlier: 4.415A pdb=" N LYS F 655 " --> pdb=" O ASN F 651 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN F 656 " --> pdb=" O GLN F 652 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 140 through 150 No H-bonds generated for 'chain 'A' and resid 140 through 150' Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.996A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.577A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER A 481 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 549 removed outlier: 3.500A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL B 539 " --> pdb=" O MET B 535 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU B 545 " --> pdb=" O ALA B 541 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 547 " --> pdb=" O ASN B 543 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 548 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 628 through 659 removed outlier: 5.616A pdb=" N ASN B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N TYR B 638 " --> pdb=" O GLU B 634 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N THR B 639 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN B 640 " --> pdb=" O SER B 636 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N ILE B 641 " --> pdb=" O ASN B 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 91 through 94 Processing sheet with id= E, first strand: chain 'C' and resid 169 through 177 Processing sheet with id= F, first strand: chain 'C' and resid 200 through 203 Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.410A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 443 through 448 removed outlier: 7.278A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 301 through 308 removed outlier: 4.379A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= K, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'E' and resid 169 through 177 Processing sheet with id= N, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.791A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 284 through 287 removed outlier: 6.510A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N ALA E 362 " --> pdb=" O PRO E 470 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 393 " --> pdb=" O PHE E 361 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.701A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 301 through 303 Processing sheet with id= R, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.698A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= T, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= U, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= V, first strand: chain 'A' and resid 91 through 94 Processing sheet with id= W, first strand: chain 'A' and resid 169 through 177 Processing sheet with id= X, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.743A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'A' and resid 271 through 273 removed outlier: 4.856A pdb=" N THR A 467 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N ALA A 362 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 413 through 417 removed outlier: 4.203A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'A' and resid 374 through 378 Processing sheet with id= AB, first strand: chain 'A' and resid 301 through 308 removed outlier: 5.964A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 9 through 11 removed outlier: 6.782A pdb=" N UNK H 124 " --> pdb=" O UNK H 10 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 18 through 23 Processing sheet with id= AE, first strand: chain 'H' and resid 102 through 104 Processing sheet with id= AF, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.077A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 11 through 13 Processing sheet with id= AH, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.728A pdb=" N UNK L 37 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N UNK L 46 " --> pdb=" O UNK L 37 " (cutoff:3.500A) 552 hydrogen bonds defined for protein. 1377 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: 5.17 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3704 1.32 - 1.46: 5025 1.46 - 1.60: 7219 1.60 - 1.74: 35 1.74 - 1.88: 128 Bond restraints: 16111 Sorted by residual: bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.18e+01 bond pdb=" CG GLN E 348 " pdb=" CD GLN E 348 " ideal model delta sigma weight residual 1.516 1.385 0.131 2.50e-02 1.60e+03 2.76e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 16106 not shown) Histogram of bond angle deviations from ideal: 98.88 - 106.03: 403 106.03 - 113.18: 8891 113.18 - 120.33: 6616 120.33 - 127.48: 5803 127.48 - 134.63: 201 Bond angle restraints: 21914 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.15 -8.59 1.02e+00 9.61e-01 7.09e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.85 -8.29 1.01e+00 9.80e-01 6.74e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" N PRO C 437 " pdb=" CA PRO C 437 " pdb=" C PRO C 437 " ideal model delta sigma weight residual 110.47 103.13 7.34 9.60e-01 1.09e+00 5.84e+01 ... (remaining 21909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 10471 21.28 - 42.56: 208 42.56 - 63.85: 72 63.85 - 85.13: 33 85.13 - 106.41: 15 Dihedral angle restraints: 10799 sinusoidal: 5179 harmonic: 5620 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.06 -53.06 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 10796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2031 0.127 - 0.255: 463 0.255 - 0.382: 197 0.382 - 0.509: 78 0.509 - 0.636: 6 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 ... (remaining 2772 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 706 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 706 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 706 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG E 706 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG E 706 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.343 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 701 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 710 " 0.340 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 710 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 710 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG E 710 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 710 " 0.103 2.00e-02 2.50e+03 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 500 2.67 - 3.23: 14654 3.23 - 3.79: 23293 3.79 - 4.34: 31969 4.34 - 4.90: 50386 Nonbonded interactions: 120802 Sorted by model distance: nonbonded pdb=" O ASP F 624 " pdb=" OD1 ASP F 624 " model vdw 2.118 3.040 nonbonded pdb=" O3 NAG B 703 " pdb=" O7 NAG B 703 " model vdw 2.244 2.440 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.413 2.520 nonbonded pdb=" NZ LYS E 232 " pdb=" OE2 GLU E 269 " model vdw 2.418 2.520 nonbonded pdb=" CG2 ILE C 294 " pdb=" OG SER C 447 " model vdw 2.428 3.460 ... (remaining 120797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 505 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 64 or resid 66 through 397 or resid 411 through \ 505 or resid 702 through 714)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 521 through 548 or resid 568 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'D' and (resid 521 through 548 or resid 568 through 661 or resid 701 thro \ ugh 702)) selection = (chain 'F' and (resid 521 through 661 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 7.830 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 44.360 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 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 : 0.022 0.138 16111 Z= 1.377 Angle : 1.692 10.793 21914 Z= 1.094 Chirality : 0.144 0.636 2775 Planarity : 0.017 0.294 2696 Dihedral : 11.247 106.409 7044 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1669 helix: 0.21 (0.23), residues: 440 sheet: 0.91 (0.23), residues: 415 loop : 0.88 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.009 TRP A 479 HIS 0.014 0.002 HIS A 249 PHE 0.026 0.006 PHE A 383 TYR 0.042 0.007 TYR F 638 ARG 0.007 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 455 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 ASN cc_start: 0.8016 (t0) cc_final: 0.7577 (t0) REVERT: D 523 LEU cc_start: 0.8502 (mt) cc_final: 0.8183 (mt) REVERT: D 588 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8210 (mtm-85) REVERT: D 591 GLN cc_start: 0.8907 (tt0) cc_final: 0.8541 (tp-100) REVERT: D 639 THR cc_start: 0.8233 (m) cc_final: 0.7518 (p) REVERT: A 125 LEU cc_start: 0.8607 (mt) cc_final: 0.8253 (mt) REVERT: A 153 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7224 (tp30) REVERT: A 207 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8402 (mmtm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.2839 time to fit residues: 186.4425 Evaluate side-chains 223 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.7980 chunk 144 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 137 ASN C 352 HIS C 432 GLN D 630 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN E 352 HIS F 540 GLN F 591 GLN F 607 ASN A 188 ASN A 425 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16111 Z= 0.219 Angle : 0.727 10.413 21914 Z= 0.368 Chirality : 0.050 0.548 2775 Planarity : 0.005 0.050 2696 Dihedral : 8.972 82.746 3824 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 3.15 % Allowed : 9.40 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.20), residues: 1669 helix: 1.26 (0.25), residues: 397 sheet: 0.77 (0.22), residues: 472 loop : 0.30 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 479 HIS 0.011 0.001 HIS D 585 PHE 0.022 0.002 PHE A 53 TYR 0.019 0.002 TYR A 435 ARG 0.005 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 305 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8530 (tpt) cc_final: 0.8064 (tpt) REVERT: C 377 ASN cc_start: 0.8176 (t0) cc_final: 0.7821 (t0) REVERT: D 588 ARG cc_start: 0.8597 (ttp80) cc_final: 0.8060 (ttm-80) REVERT: D 617 ARG cc_start: 0.5238 (OUTLIER) cc_final: 0.5024 (ttt90) REVERT: D 639 THR cc_start: 0.8161 (m) cc_final: 0.7578 (p) REVERT: E 233 PHE cc_start: 0.7743 (t80) cc_final: 0.6894 (t80) REVERT: F 631 TRP cc_start: 0.8222 (t-100) cc_final: 0.7978 (t-100) REVERT: F 635 ILE cc_start: 0.8415 (pt) cc_final: 0.8166 (pt) REVERT: F 647 GLU cc_start: 0.7449 (tm-30) cc_final: 0.7145 (tm-30) REVERT: B 636 SER cc_start: 0.7201 (p) cc_final: 0.6924 (m) outliers start: 48 outliers final: 32 residues processed: 341 average time/residue: 0.2628 time to fit residues: 133.5599 Evaluate side-chains 253 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 220 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 454 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 528 SER Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0040 chunk 53 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 172 optimal weight: 9.9990 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN D 543 ASN D 630 GLN E 302 ASN F 653 GLN A 188 ASN B 591 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16111 Z= 0.245 Angle : 0.697 16.097 21914 Z= 0.348 Chirality : 0.048 0.409 2775 Planarity : 0.005 0.063 2696 Dihedral : 8.568 75.873 3824 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.68 % Allowed : 11.56 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.06 % 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: 0.51 (0.19), residues: 1669 helix: 1.03 (0.26), residues: 398 sheet: 0.63 (0.22), residues: 460 loop : -0.09 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 610 HIS 0.006 0.001 HIS D 585 PHE 0.022 0.002 PHE A 53 TYR 0.022 0.002 TYR E 217 ARG 0.008 0.001 ARG E 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 221 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8829 (m-80) cc_final: 0.8523 (m-10) REVERT: C 377 ASN cc_start: 0.8420 (t0) cc_final: 0.8096 (t0) REVERT: D 588 ARG cc_start: 0.8574 (ttp80) cc_final: 0.8069 (ttm-80) REVERT: E 233 PHE cc_start: 0.8020 (t80) cc_final: 0.7130 (t80) REVERT: F 610 TRP cc_start: 0.7048 (t-100) cc_final: 0.6809 (t-100) REVERT: F 647 GLU cc_start: 0.7661 (tm-30) cc_final: 0.7442 (tm-30) REVERT: A 125 LEU cc_start: 0.8944 (mt) cc_final: 0.8618 (mm) REVERT: B 530 MET cc_start: 0.6678 (mtt) cc_final: 0.5722 (mtt) REVERT: B 636 SER cc_start: 0.7357 (p) cc_final: 0.7037 (m) outliers start: 56 outliers final: 32 residues processed: 267 average time/residue: 0.2704 time to fit residues: 108.1231 Evaluate side-chains 227 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 300 ASN Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 611 ASN Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 10.0000 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN F 591 GLN A 188 ASN A 203 GLN A 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 16111 Z= 0.348 Angle : 0.726 11.880 21914 Z= 0.362 Chirality : 0.050 0.442 2775 Planarity : 0.005 0.065 2696 Dihedral : 8.458 74.543 3824 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.88 % Allowed : 13.21 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.10 (0.19), residues: 1669 helix: 0.73 (0.26), residues: 403 sheet: 0.42 (0.23), residues: 426 loop : -0.38 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 631 HIS 0.004 0.001 HIS E 330 PHE 0.022 0.002 PHE A 53 TYR 0.023 0.002 TYR A 435 ARG 0.007 0.001 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 213 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7887 (tm-30) cc_final: 0.7637 (mm110) REVERT: D 588 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8055 (ttm-80) REVERT: D 655 LYS cc_start: 0.8334 (mttm) cc_final: 0.8083 (ptpt) REVERT: F 538 THR cc_start: 0.8516 (p) cc_final: 0.8296 (m) REVERT: F 591 GLN cc_start: 0.8885 (tt0) cc_final: 0.8580 (tt0) REVERT: B 548 ILE cc_start: 0.7524 (OUTLIER) cc_final: 0.6884 (mt) REVERT: B 615 SER cc_start: 0.7497 (t) cc_final: 0.7242 (m) REVERT: B 636 SER cc_start: 0.7454 (p) cc_final: 0.7133 (m) outliers start: 59 outliers final: 45 residues processed: 256 average time/residue: 0.2939 time to fit residues: 110.1545 Evaluate side-chains 224 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 178 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.0060 chunk 104 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 0.4980 chunk 156 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 0.2980 chunk 164 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN F 653 GLN A 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16111 Z= 0.168 Angle : 0.596 11.063 21914 Z= 0.297 Chirality : 0.045 0.369 2775 Planarity : 0.004 0.052 2696 Dihedral : 7.723 65.528 3824 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.88 % Allowed : 13.47 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: 0.10 (0.20), residues: 1669 helix: 0.70 (0.26), residues: 416 sheet: 0.46 (0.23), residues: 427 loop : -0.40 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 631 HIS 0.002 0.001 HIS C 105 PHE 0.017 0.001 PHE A 53 TYR 0.015 0.001 TYR A 435 ARG 0.009 0.000 ARG E 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 197 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 426 MET cc_start: 0.7616 (OUTLIER) cc_final: 0.7379 (mtm) REVERT: D 584 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7911 (mp0) REVERT: D 588 ARG cc_start: 0.8499 (ttp80) cc_final: 0.8009 (ttm-80) REVERT: E 125 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8125 (tt) REVERT: E 233 PHE cc_start: 0.8384 (t80) cc_final: 0.7568 (t80) REVERT: F 591 GLN cc_start: 0.8873 (tt0) cc_final: 0.8582 (tt0) REVERT: A 325 ASP cc_start: 0.7422 (t0) cc_final: 0.7125 (t0) REVERT: B 635 ILE cc_start: 0.6768 (pt) cc_final: 0.6509 (mt) REVERT: B 636 SER cc_start: 0.7572 (p) cc_final: 0.7246 (m) outliers start: 59 outliers final: 38 residues processed: 242 average time/residue: 0.2524 time to fit residues: 92.9806 Evaluate side-chains 219 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 179 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 530 MET Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 2.9990 chunk 165 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 152 optimal weight: 0.0270 chunk 85 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 60 optimal weight: 0.0050 chunk 96 optimal weight: 1.9990 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 GLN C 137 ASN D 585 HIS E 425 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16111 Z= 0.182 Angle : 0.597 9.969 21914 Z= 0.298 Chirality : 0.045 0.382 2775 Planarity : 0.004 0.063 2696 Dihedral : 7.411 62.655 3824 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.35 % Allowed : 14.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: 0.19 (0.20), residues: 1669 helix: 0.84 (0.26), residues: 402 sheet: 0.59 (0.24), residues: 422 loop : -0.40 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP B 631 HIS 0.004 0.001 HIS D 585 PHE 0.016 0.002 PHE A 53 TYR 0.014 0.001 TYR A 435 ARG 0.007 0.000 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 189 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 426 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7469 (mtm) REVERT: C 504 ARG cc_start: 0.7192 (tpt90) cc_final: 0.6741 (tpp80) REVERT: D 588 ARG cc_start: 0.8490 (ttp80) cc_final: 0.8006 (ttm-80) REVERT: E 233 PHE cc_start: 0.8388 (t80) cc_final: 0.7507 (t80) REVERT: F 591 GLN cc_start: 0.8900 (tt0) cc_final: 0.8564 (tt0) REVERT: A 325 ASP cc_start: 0.7400 (t0) cc_final: 0.7099 (t0) REVERT: B 548 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.6950 (mt) REVERT: B 636 SER cc_start: 0.7580 (p) cc_final: 0.7297 (m) outliers start: 51 outliers final: 40 residues processed: 226 average time/residue: 0.2651 time to fit residues: 90.3911 Evaluate side-chains 217 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 175 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain A residue 65 LYS Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 2.9990 chunk 134 optimal weight: 0.0980 chunk 154 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 111 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 113 optimal weight: 4.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN D 585 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16111 Z= 0.407 Angle : 0.755 15.059 21914 Z= 0.371 Chirality : 0.050 0.387 2775 Planarity : 0.005 0.057 2696 Dihedral : 7.927 60.835 3824 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.81 % Allowed : 14.98 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.27 (0.20), residues: 1669 helix: 0.58 (0.26), residues: 409 sheet: 0.21 (0.23), residues: 444 loop : -0.73 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP B 631 HIS 0.004 0.001 HIS C 330 PHE 0.017 0.003 PHE E 361 TYR 0.025 0.002 TYR C 217 ARG 0.008 0.001 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 504 ARG cc_start: 0.7367 (tpt90) cc_final: 0.7165 (tpp80) REVERT: D 588 ARG cc_start: 0.8553 (ttp80) cc_final: 0.8046 (ttm-80) REVERT: E 125 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8440 (tt) REVERT: E 199 SER cc_start: 0.9501 (p) cc_final: 0.9001 (m) REVERT: F 591 GLN cc_start: 0.8997 (tt0) cc_final: 0.8624 (tt0) REVERT: A 166 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7457 (mmp80) REVERT: B 548 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7010 (mt) REVERT: B 615 SER cc_start: 0.7546 (t) cc_final: 0.7259 (m) REVERT: B 631 TRP cc_start: 0.6363 (t-100) cc_final: 0.6034 (t-100) REVERT: B 636 SER cc_start: 0.7426 (p) cc_final: 0.7185 (m) outliers start: 58 outliers final: 39 residues processed: 232 average time/residue: 0.2602 time to fit residues: 91.3851 Evaluate side-chains 214 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 172 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 630 GLN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 175 optimal weight: 7.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16111 Z= 0.191 Angle : 0.619 13.063 21914 Z= 0.306 Chirality : 0.045 0.386 2775 Planarity : 0.004 0.052 2696 Dihedral : 7.178 59.930 3824 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.22 % Allowed : 16.56 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.10 (0.20), residues: 1669 helix: 0.79 (0.26), residues: 409 sheet: 0.42 (0.24), residues: 427 loop : -0.73 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 631 HIS 0.003 0.001 HIS D 585 PHE 0.015 0.002 PHE A 53 TYR 0.018 0.001 TYR F 638 ARG 0.008 0.000 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 186 time to evaluate : 1.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 164 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8230 (pm20) REVERT: D 588 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8047 (ttm-80) REVERT: E 125 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8083 (tt) REVERT: E 199 SER cc_start: 0.9531 (p) cc_final: 0.8945 (m) REVERT: F 591 GLN cc_start: 0.8995 (tt0) cc_final: 0.8605 (tt0) REVERT: A 325 ASP cc_start: 0.7976 (t0) cc_final: 0.7697 (t0) REVERT: B 548 ILE cc_start: 0.7599 (OUTLIER) cc_final: 0.7027 (mt) REVERT: B 636 SER cc_start: 0.7472 (p) cc_final: 0.7259 (m) outliers start: 49 outliers final: 37 residues processed: 221 average time/residue: 0.2679 time to fit residues: 89.3797 Evaluate side-chains 218 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 178 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 358 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 154 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 HIS E 425 ASN A 195 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 16111 Z= 0.399 Angle : 0.739 13.821 21914 Z= 0.363 Chirality : 0.050 0.389 2775 Planarity : 0.004 0.051 2696 Dihedral : 7.639 58.072 3824 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.15 % Allowed : 16.95 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.25 % 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: -0.28 (0.20), residues: 1669 helix: 0.81 (0.26), residues: 402 sheet: 0.15 (0.24), residues: 430 loop : -0.82 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP B 631 HIS 0.004 0.001 HIS A 105 PHE 0.015 0.002 PHE A 53 TYR 0.023 0.002 TYR C 217 ARG 0.008 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 588 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8154 (ttp-170) REVERT: E 125 LEU cc_start: 0.8577 (OUTLIER) cc_final: 0.8253 (tt) REVERT: E 199 SER cc_start: 0.9509 (p) cc_final: 0.8971 (m) REVERT: F 591 GLN cc_start: 0.9032 (tt0) cc_final: 0.8663 (tt0) REVERT: F 599 SER cc_start: 0.8531 (p) cc_final: 0.8239 (t) REVERT: F 640 GLN cc_start: 0.7911 (pm20) cc_final: 0.7603 (pm20) REVERT: A 140 ASP cc_start: 0.8522 (t0) cc_final: 0.8237 (t0) REVERT: B 535 MET cc_start: 0.8181 (mmm) cc_final: 0.7882 (mmt) REVERT: B 548 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7105 (mt) REVERT: B 631 TRP cc_start: 0.6212 (t-100) cc_final: 0.5985 (t-100) REVERT: B 636 SER cc_start: 0.7450 (p) cc_final: 0.7213 (m) outliers start: 48 outliers final: 37 residues processed: 215 average time/residue: 0.2596 time to fit residues: 84.7892 Evaluate side-chains 208 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 87 GLU Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 654 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 chunk 15 optimal weight: 0.0670 chunk 116 optimal weight: 0.7980 chunk 92 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 160 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN D 585 HIS E 425 ASN F 585 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16111 Z= 0.176 Angle : 0.616 12.869 21914 Z= 0.305 Chirality : 0.045 0.380 2775 Planarity : 0.004 0.050 2696 Dihedral : 6.816 55.853 3824 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.43 % Allowed : 17.81 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.09 (0.20), residues: 1669 helix: 1.00 (0.26), residues: 402 sheet: 0.39 (0.24), residues: 416 loop : -0.78 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP B 631 HIS 0.003 0.001 HIS D 585 PHE 0.016 0.001 PHE C 53 TYR 0.017 0.001 TYR F 638 ARG 0.009 0.001 ARG E 166 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 187 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 588 ARG cc_start: 0.8506 (ttp80) cc_final: 0.8008 (ttm-80) REVERT: E 199 SER cc_start: 0.9564 (p) cc_final: 0.8940 (m) REVERT: F 591 GLN cc_start: 0.9003 (tt0) cc_final: 0.8598 (tt0) REVERT: A 140 ASP cc_start: 0.8483 (t0) cc_final: 0.8207 (t0) REVERT: B 535 MET cc_start: 0.8191 (mmm) cc_final: 0.7838 (mmt) REVERT: B 548 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6985 (mt) REVERT: B 636 SER cc_start: 0.7408 (p) cc_final: 0.7198 (m) outliers start: 37 outliers final: 30 residues processed: 215 average time/residue: 0.2596 time to fit residues: 84.5488 Evaluate side-chains 205 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 196 CYS Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain D residue 530 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 592 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 150 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 132 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 585 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.115900 restraints weight = 26281.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.118461 restraints weight = 19469.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120338 restraints weight = 13718.648| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.6309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16111 Z= 0.196 Angle : 0.606 12.042 21914 Z= 0.300 Chirality : 0.045 0.377 2775 Planarity : 0.004 0.092 2696 Dihedral : 6.608 55.489 3824 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.56 % Allowed : 17.74 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.01 (0.20), residues: 1669 helix: 1.05 (0.26), residues: 403 sheet: 0.47 (0.24), residues: 417 loop : -0.75 (0.21), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 631 HIS 0.003 0.001 HIS A 330 PHE 0.018 0.002 PHE B 522 TYR 0.018 0.001 TYR F 638 ARG 0.011 0.000 ARG E 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3074.29 seconds wall clock time: 56 minutes 29.18 seconds (3389.18 seconds total)