Starting phenix.real_space_refine on Fri Sep 27 12:22:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/09_2024/7l8f_23232.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/09_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_23232/09_2024/7l8f_23232.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/09_2024/7l8f_23232.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/09_2024/7l8f_23232.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8f_23232/09_2024/7l8f_23232.cif" } 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. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 10.29, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 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: 4.97 Conformation dependent library (CDL) restraints added in 1.8 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... Secondary structure from input PDB file: 48 helices and 28 sheets defined 29.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.572A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) 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 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.190A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 549 removed outlier: 3.505A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.982A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.620A pdb=" N ASN E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.089A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.519A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.871A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 634 through 636 No H-bonds generated for 'chain 'F' and resid 634 through 636' Processing helix chain 'F' and resid 638 through 654 Processing helix chain 'F' and resid 654 through 661 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 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.113A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.996A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.811A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.500A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.912A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 65 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 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.426A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.197A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.316A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.829A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.180A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.452A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.673A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.371A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.610A pdb=" N VAL A 75 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.514A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 312 removed outlier: 6.609A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 11 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 52 current: chain 'H' and resid 116 through 117 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 102 through 104 Processing sheet with id=AC9, 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=AD1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.210A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1452 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: 5.18 Time building geometry restraints manager: 5.55 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: 0.00 - 2.16: 18217 2.16 - 4.32: 3122 4.32 - 6.48: 502 6.48 - 8.63: 68 8.63 - 10.79: 5 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: 14641 3.23 - 3.79: 23344 3.79 - 4.34: 31977 4.34 - 4.90: 50384 Nonbonded interactions: 120846 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 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.413 3.120 nonbonded pdb=" NZ LYS E 232 " pdb=" OE2 GLU E 269 " model vdw 2.418 3.120 nonbonded pdb=" CG2 ILE C 294 " pdb=" OG SER C 447 " model vdw 2.428 3.460 ... (remaining 120841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.170 Process input model: 38.160 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.560 ------------------------------------------------------------------------------- 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= 1.381 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 : 1.677 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: 0.2789 time to fit residues: 183.5608 Evaluate side-chains 223 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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: 0.9980 chunk 144 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 172 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 D 630 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 302 ASN E 352 HIS F 540 GLN F 607 ASN A 188 ASN A 425 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16111 Z= 0.240 Angle : 0.745 10.239 21914 Z= 0.373 Chirality : 0.051 0.619 2775 Planarity : 0.005 0.050 2696 Dihedral : 8.844 82.063 3824 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.22 % Allowed : 9.46 % Favored : 87.32 % 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: 0.93 (0.20), residues: 1669 helix: 1.42 (0.25), residues: 414 sheet: 0.66 (0.21), residues: 485 loop : 0.27 (0.22), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 479 HIS 0.010 0.001 HIS D 585 PHE 0.023 0.002 PHE E 391 TYR 0.020 0.002 TYR A 435 ARG 0.007 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 355 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 306 time to evaluate : 1.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8546 (tpt) cc_final: 0.8091 (tpt) REVERT: C 377 ASN cc_start: 0.8255 (t0) cc_final: 0.7886 (t0) REVERT: D 588 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8107 (ttm-80) REVERT: D 617 ARG cc_start: 0.5205 (OUTLIER) cc_final: 0.4936 (tpt170) REVERT: D 632 ASP cc_start: 0.8179 (t0) cc_final: 0.7882 (t0) REVERT: E 233 PHE cc_start: 0.7731 (t80) cc_final: 0.6859 (t80) REVERT: F 647 GLU cc_start: 0.7556 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 634 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6980 (mt-10) outliers start: 49 outliers final: 29 residues processed: 343 average time/residue: 0.2630 time to fit residues: 134.3129 Evaluate side-chains 242 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 212 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 443 ILE 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 467 THR 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 84 ILE 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 172 optimal weight: 10.0000 chunk 186 optimal weight: 8.9990 chunk 153 optimal weight: 0.9980 chunk 171 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN C 432 GLN D 630 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 302 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN A 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16111 Z= 0.225 Angle : 0.673 15.404 21914 Z= 0.341 Chirality : 0.048 0.415 2775 Planarity : 0.004 0.063 2696 Dihedral : 8.134 75.565 3824 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.15 % Allowed : 11.50 % Favored : 85.35 % 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: 0.79 (0.20), residues: 1669 helix: 1.42 (0.25), residues: 415 sheet: 0.78 (0.22), residues: 461 loop : -0.03 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 610 HIS 0.006 0.001 HIS D 585 PHE 0.023 0.002 PHE A 53 TYR 0.022 0.001 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 276 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 228 time to evaluate : 1.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8558 (tpt) cc_final: 0.8356 (tpt) REVERT: C 377 ASN cc_start: 0.8390 (t0) cc_final: 0.8095 (t0) REVERT: D 588 ARG cc_start: 0.8631 (ttp80) cc_final: 0.8083 (ttm-80) REVERT: E 233 PHE cc_start: 0.7973 (t80) cc_final: 0.7060 (t80) REVERT: F 631 TRP cc_start: 0.8267 (t-100) cc_final: 0.7941 (t-100) REVERT: A 125 LEU cc_start: 0.8968 (mt) cc_final: 0.8627 (mm) REVERT: B 530 MET cc_start: 0.6824 (mtt) cc_final: 0.5470 (mtt) REVERT: B 634 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6805 (tt0) REVERT: B 636 SER cc_start: 0.7498 (OUTLIER) cc_final: 0.7129 (m) outliers start: 48 outliers final: 27 residues processed: 265 average time/residue: 0.2599 time to fit residues: 103.6503 Evaluate side-chains 231 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 1.715 ------------------------------------------------------------------------------- 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 419 ARG 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 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 127 VAL 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 636 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 164 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 114 GLN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 203 GLN ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 625 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 16111 Z= 0.411 Angle : 0.756 12.948 21914 Z= 0.378 Chirality : 0.051 0.418 2775 Planarity : 0.005 0.073 2696 Dihedral : 8.109 70.192 3824 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.01 % Allowed : 12.61 % Favored : 83.38 % 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: 0.30 (0.20), residues: 1669 helix: 1.16 (0.26), residues: 415 sheet: 0.39 (0.23), residues: 448 loop : -0.34 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP B 631 HIS 0.005 0.001 HIS E 330 PHE 0.020 0.003 PHE A 53 TYR 0.021 0.002 TYR C 217 ARG 0.009 0.001 ARG A 480 *********************** 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 279 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 218 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 64 LYS cc_start: 0.6760 (mttt) cc_final: 0.6550 (mmtt) REVERT: D 588 ARG cc_start: 0.8613 (ttp80) cc_final: 0.8125 (ttm-80) REVERT: E 233 PHE cc_start: 0.8301 (t80) cc_final: 0.7291 (t80) REVERT: A 303 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8646 (p) REVERT: B 548 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.6944 (mt) REVERT: B 616 ASN cc_start: 0.7170 (OUTLIER) cc_final: 0.6783 (m-40) outliers start: 61 outliers final: 39 residues processed: 258 average time/residue: 0.2842 time to fit residues: 107.0683 Evaluate side-chains 232 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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 172 VAL Chi-restraints excluded: chain C residue 184 ILE 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 D residue 530 MET 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 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 602 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP 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 166 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 205 CYS 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 A residue 434 MET 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 Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 164 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 195 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 425 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16111 Z= 0.253 Angle : 0.638 11.309 21914 Z= 0.318 Chirality : 0.047 0.411 2775 Planarity : 0.004 0.062 2696 Dihedral : 7.605 66.079 3824 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.81 % Allowed : 13.01 % Favored : 83.18 % 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: 0.38 (0.20), residues: 1669 helix: 1.46 (0.26), residues: 408 sheet: 0.36 (0.23), residues: 454 loop : -0.38 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP F 610 HIS 0.003 0.001 HIS C 105 PHE 0.017 0.002 PHE A 53 TYR 0.014 0.002 TYR A 435 ARG 0.006 0.001 ARG E 166 *********************** 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 270 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 212 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 588 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8072 (ttm-80) REVERT: E 125 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8621 (tt) REVERT: E 178 ARG cc_start: 0.8696 (ttp-170) cc_final: 0.8269 (ttp80) REVERT: B 548 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6908 (mt) REVERT: B 616 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6793 (m-40) outliers start: 58 outliers final: 38 residues processed: 253 average time/residue: 0.2638 time to fit residues: 99.0346 Evaluate side-chains 223 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 182 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 530 MET 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 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 654 GLU 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 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 119 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 205 CYS Chi-restraints excluded: chain A residue 244 THR 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 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 Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 183 optimal weight: 10.0000 chunk 152 optimal weight: 0.0070 chunk 85 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 overall best weight: 0.9002 ------------------------------------------------------------------------------- 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** ** D 585 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.5225 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= 0.193 Angle : 0.609 9.643 21914 Z= 0.306 Chirality : 0.046 0.394 2775 Planarity : 0.004 0.056 2696 Dihedral : 7.232 61.285 3824 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.29 % Allowed : 14.59 % Favored : 82.13 % 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: 0.42 (0.20), residues: 1669 helix: 1.55 (0.26), residues: 409 sheet: 0.39 (0.23), residues: 453 loop : -0.40 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP F 610 HIS 0.004 0.001 HIS D 585 PHE 0.015 0.001 PHE A 53 TYR 0.013 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 249 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 199 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7387 (mm110) REVERT: C 99 ASN cc_start: 0.8484 (t0) cc_final: 0.8041 (t0) REVERT: C 504 ARG cc_start: 0.6867 (tpt90) cc_final: 0.6220 (mtt180) REVERT: D 588 ARG cc_start: 0.8570 (ttp80) cc_final: 0.8066 (ttm-80) REVERT: D 623 TRP cc_start: 0.7510 (m-10) cc_final: 0.7252 (m100) REVERT: E 233 PHE cc_start: 0.8377 (t80) cc_final: 0.7718 (t80) REVERT: A 325 ASP cc_start: 0.8215 (t0) cc_final: 0.7853 (t0) REVERT: B 548 ILE cc_start: 0.7410 (OUTLIER) cc_final: 0.6934 (mt) outliers start: 50 outliers final: 34 residues processed: 234 average time/residue: 0.3114 time to fit residues: 112.4375 Evaluate side-chains 219 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 184 time to evaluate : 1.721 ------------------------------------------------------------------------------- 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 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 443 ILE 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 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP 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 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 A residue 434 MET 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 606 THR Chi-restraints excluded: chain B residue 635 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 183 optimal weight: 9.9990 chunk 114 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16111 Z= 0.307 Angle : 0.678 14.667 21914 Z= 0.333 Chirality : 0.048 0.390 2775 Planarity : 0.004 0.048 2696 Dihedral : 7.202 59.456 3824 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % 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: 0.24 (0.20), residues: 1669 helix: 1.47 (0.26), residues: 409 sheet: 0.25 (0.23), residues: 448 loop : -0.53 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP F 610 HIS 0.004 0.001 HIS E 330 PHE 0.022 0.002 PHE D 522 TYR 0.017 0.002 TYR C 217 ARG 0.007 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 241 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 190 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8505 (t0) cc_final: 0.8053 (t0) REVERT: C 504 ARG cc_start: 0.7243 (tpt90) cc_final: 0.6794 (mtt180) REVERT: D 588 ARG cc_start: 0.8586 (ttp80) cc_final: 0.8076 (ttm-80) REVERT: D 623 TRP cc_start: 0.7759 (m-10) cc_final: 0.7547 (m100) REVERT: E 233 PHE cc_start: 0.8428 (t80) cc_final: 0.7869 (t80) REVERT: A 140 ASP cc_start: 0.8539 (t0) cc_final: 0.8312 (t0) REVERT: A 325 ASP cc_start: 0.8333 (t0) cc_final: 0.8073 (t0) REVERT: A 425 ASN cc_start: 0.8409 (m-40) cc_final: 0.8166 (m-40) REVERT: B 548 ILE cc_start: 0.7384 (OUTLIER) cc_final: 0.6916 (mt) REVERT: B 631 TRP cc_start: 0.7314 (t-100) cc_final: 0.6998 (t-100) outliers start: 51 outliers final: 36 residues processed: 225 average time/residue: 0.2530 time to fit residues: 86.7410 Evaluate side-chains 221 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 184 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 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 372 THR Chi-restraints excluded: chain C residue 443 ILE 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 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 265 LEU Chi-restraints excluded: chain E residue 320 THR 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 A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE 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 A residue 434 MET 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 606 THR Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** D 607 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16111 Z= 0.231 Angle : 0.629 12.798 21914 Z= 0.312 Chirality : 0.046 0.388 2775 Planarity : 0.004 0.061 2696 Dihedral : 6.752 56.920 3824 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.96 % Allowed : 15.64 % Favored : 81.41 % 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: 0.24 (0.20), residues: 1669 helix: 1.51 (0.26), residues: 414 sheet: 0.29 (0.23), residues: 450 loop : -0.59 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 610 HIS 0.003 0.001 HIS D 585 PHE 0.016 0.002 PHE D 522 TYR 0.012 0.001 TYR F 638 ARG 0.007 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 237 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 192 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8549 (t0) cc_final: 0.8078 (t0) REVERT: C 164 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8064 (pm20) REVERT: C 504 ARG cc_start: 0.7269 (tpt90) cc_final: 0.6836 (mtt180) REVERT: D 588 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8079 (ttm-80) REVERT: E 233 PHE cc_start: 0.8441 (t80) cc_final: 0.8000 (t80) REVERT: A 140 ASP cc_start: 0.8513 (t0) cc_final: 0.8269 (t0) REVERT: A 425 ASN cc_start: 0.8310 (m-40) cc_final: 0.8084 (m-40) REVERT: B 631 TRP cc_start: 0.7186 (t-100) cc_final: 0.6868 (t-100) outliers start: 45 outliers final: 34 residues processed: 225 average time/residue: 0.2660 time to fit residues: 90.4332 Evaluate side-chains 214 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 179 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain C residue 496 VAL 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 83 GLU Chi-restraints excluded: chain E residue 111 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 F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP 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 A residue 501 CYS 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 603 ILE Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 170 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 154 optimal weight: 5.9990 chunk 161 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 180 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 HIS ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 16111 Z= 0.487 Angle : 0.819 13.864 21914 Z= 0.401 Chirality : 0.052 0.396 2775 Planarity : 0.005 0.068 2696 Dihedral : 7.719 59.989 3824 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.89 % Allowed : 16.16 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.27 (0.20), residues: 1669 helix: 1.06 (0.26), residues: 417 sheet: -0.08 (0.23), residues: 450 loop : -0.85 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP F 610 HIS 0.004 0.001 HIS E 330 PHE 0.018 0.003 PHE D 522 TYR 0.027 0.003 TYR C 217 ARG 0.008 0.001 ARG A 480 *********************** 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 231 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 187 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8625 (t0) cc_final: 0.8221 (t0) REVERT: C 504 ARG cc_start: 0.7304 (tpt90) cc_final: 0.7062 (tpp80) REVERT: D 588 ARG cc_start: 0.8598 (ttp80) cc_final: 0.8127 (ttm-80) REVERT: D 648 GLU cc_start: 0.7971 (tp30) cc_final: 0.7707 (tp30) REVERT: E 161 MET cc_start: 0.8717 (tpp) cc_final: 0.7764 (ttt) REVERT: E 233 PHE cc_start: 0.8542 (t80) cc_final: 0.8065 (t80) REVERT: B 530 MET cc_start: 0.6879 (mmm) cc_final: 0.6337 (mtt) REVERT: B 589 ASP cc_start: 0.8980 (m-30) cc_final: 0.8722 (m-30) outliers start: 44 outliers final: 34 residues processed: 217 average time/residue: 0.2593 time to fit residues: 85.7704 Evaluate side-chains 209 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.660 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain D residue 530 MET 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 599 SER Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 83 GLU 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 F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 638 TYR 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 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 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 603 ILE Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 9.9990 chunk 150 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16111 Z= 0.226 Angle : 0.681 13.767 21914 Z= 0.339 Chirality : 0.048 0.530 2775 Planarity : 0.004 0.087 2696 Dihedral : 7.085 57.239 3824 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.17 % Allowed : 17.21 % Favored : 80.62 % 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: -0.02 (0.20), residues: 1669 helix: 1.44 (0.27), residues: 405 sheet: 0.09 (0.24), residues: 438 loop : -0.79 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.002 TRP F 610 HIS 0.003 0.001 HIS E 374 PHE 0.017 0.002 PHE D 522 TYR 0.039 0.002 TYR B 638 ARG 0.009 0.000 ARG E 504 ********************** 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 213 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 99 ASN cc_start: 0.8621 (t0) cc_final: 0.8187 (t0) REVERT: C 504 ARG cc_start: 0.7295 (tpt90) cc_final: 0.7068 (tpp80) REVERT: D 588 ARG cc_start: 0.8581 (ttp80) cc_final: 0.8089 (ttm-80) REVERT: D 648 GLU cc_start: 0.7967 (tp30) cc_final: 0.7716 (tp30) REVERT: E 233 PHE cc_start: 0.8516 (t80) cc_final: 0.8108 (t80) REVERT: B 530 MET cc_start: 0.6693 (mmm) cc_final: 0.6001 (mtt) REVERT: B 589 ASP cc_start: 0.8957 (m-30) cc_final: 0.8728 (m-30) outliers start: 33 outliers final: 31 residues processed: 204 average time/residue: 0.2657 time to fit residues: 81.4413 Evaluate side-chains 205 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 174 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 488 VAL Chi-restraints excluded: chain C residue 496 VAL 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 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 164 GLU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU 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 534 SER Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 636 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.0070 chunk 41 optimal weight: 0.0370 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** F 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN A 188 ASN ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.112624 restraints weight = 25932.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.115156 restraints weight = 19979.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115935 restraints weight = 14720.002| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.6239 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= 0.200 Angle : 0.633 13.875 21914 Z= 0.316 Chirality : 0.046 0.376 2775 Planarity : 0.004 0.078 2696 Dihedral : 6.518 56.587 3824 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.30 % Allowed : 17.35 % Favored : 80.35 % 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: 0.13 (0.20), residues: 1669 helix: 1.61 (0.27), residues: 409 sheet: 0.24 (0.24), residues: 435 loop : -0.76 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP F 610 HIS 0.003 0.001 HIS E 374 PHE 0.017 0.002 PHE D 522 TYR 0.014 0.001 TYR F 638 ARG 0.012 0.001 ARG E 166 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3063.35 seconds wall clock time: 55 minutes 46.29 seconds (3346.29 seconds total)