Starting phenix.real_space_refine on Tue Oct 15 01:39:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t75_25734/10_2024/7t75_25734.cif" } resolution = 2.7 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= 0.049 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 120 5.16 5 C 12024 2.51 5 N 3207 2.21 5 O 3876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19227 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "B" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "C" 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: "D" 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: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "K" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "M" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "N" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "K" 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: 3305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3305 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 20, 'TRANS': 398} Chain breaks: 3 Chain: "V" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 958 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "W" Number of atoms: 943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 943 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "X" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 811 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "Y" 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: "Z" 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: "0" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "1" 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: "2" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: "3" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 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: "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 Time building chain proxies: 12.26, per 1000 atoms: 0.64 Number of scatterers: 19227 At special positions: 0 Unit cell: (124.63, 128.75, 149.35, 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 120 16.00 O 3876 8.00 N 3207 7.00 C 12024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.05 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS J 119 " - pdb=" SG CYS J 205 " distance=2.06 Simple disulfide: pdb=" SG CYS J 126 " - pdb=" SG CYS J 196 " distance=2.05 Simple disulfide: pdb=" SG CYS J 131 " - pdb=" SG CYS J 157 " distance=2.04 Simple disulfide: pdb=" SG CYS J 218 " - pdb=" SG CYS J 247 " distance=2.05 Simple disulfide: pdb=" SG CYS J 228 " - pdb=" SG CYS J 239 " distance=2.03 Simple disulfide: pdb=" SG CYS J 296 " - pdb=" SG CYS J 331 " distance=2.03 Simple disulfide: pdb=" SG CYS J 378 " - pdb=" SG CYS J 445 " distance=2.04 Simple disulfide: pdb=" SG CYS J 385 " - pdb=" SG CYS J 418 " distance=2.02 Simple disulfide: pdb=" SG CYS J 501 " - pdb=" SG CYS K 605 " distance=2.02 Simple disulfide: pdb=" SG CYS K 598 " - pdb=" SG CYS K 604 " distance=2.02 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.02 Simple disulfide: pdb=" SG CYS U 119 " - pdb=" SG CYS U 205 " distance=2.06 Simple disulfide: pdb=" SG CYS U 126 " - pdb=" SG CYS U 196 " distance=2.05 Simple disulfide: pdb=" SG CYS U 131 " - pdb=" SG CYS U 157 " distance=2.04 Simple disulfide: pdb=" SG CYS U 218 " - pdb=" SG CYS U 247 " distance=2.05 Simple disulfide: pdb=" SG CYS U 228 " - pdb=" SG CYS U 239 " distance=2.03 Simple disulfide: pdb=" SG CYS U 296 " - pdb=" SG CYS U 331 " distance=2.03 Simple disulfide: pdb=" SG CYS U 378 " - pdb=" SG CYS U 445 " distance=2.04 Simple disulfide: pdb=" SG CYS U 385 " - pdb=" SG CYS U 418 " distance=2.02 Simple disulfide: pdb=" SG CYS U 501 " - pdb=" SG CYS V 605 " distance=2.02 Simple disulfide: pdb=" SG CYS V 598 " - pdb=" SG CYS V 604 " distance=2.02 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.02 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 0 3 " - " MAN 0 4 " " BMA E 3 " - " MAN E 4 " " BMA Q 3 " - " MAN Q 4 " BETA1-4 " NAG 0 1 " - " NAG 0 2 " " NAG 0 2 " - " BMA 0 3 " " NAG 1 1 " - " NAG 1 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG 2 1 " - " FUC 2 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG 3 1 " - " FUC 3 2 " " NAG G 1 " - " FUC G 2 " " NAG I 1 " - " FUC I 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " NAG-ASN " NAG 0 1 " - " ASN U 262 " " NAG 1 1 " - " ASN U 156 " " NAG 2 1 " - " ASN V 618 " " NAG 3 1 " - " ASN V 611 " " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 160 " " NAG A 603 " - " ASN A 234 " " NAG A 604 " - " ASN A 137 " " NAG A 605 " - " ASN A 355 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 392 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 295 " " NAG A 610 " - " ASN A 448 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 197 " " NAG A 613 " - " ASN A 133 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 637 " " NAG C 1 " - " ASN A 386 " " NAG D 1 " - " ASN A 332 " " NAG E 1 " - " ASN A 262 " " NAG F 1 " - " ASN A 156 " " NAG G 1 " - " ASN B 618 " " NAG I 1 " - " ASN B 611 " " NAG J 601 " - " ASN J 88 " " NAG J 602 " - " ASN J 160 " " NAG J 603 " - " ASN J 234 " " NAG J 604 " - " ASN J 137 " " NAG J 605 " - " ASN J 355 " " NAG J 606 " - " ASN J 276 " " NAG J 607 " - " ASN J 392 " " NAG J 608 " - " ASN J 339 " " NAG J 609 " - " ASN J 295 " " NAG J 610 " - " ASN J 448 " " NAG J 611 " - " ASN J 301 " " NAG J 612 " - " ASN J 197 " " NAG J 613 " - " ASN J 133 " " NAG K 701 " - " ASN K 625 " " NAG K 702 " - " ASN K 637 " " NAG O 1 " - " ASN J 386 " " NAG P 1 " - " ASN J 332 " " NAG Q 1 " - " ASN J 262 " " NAG R 1 " - " ASN J 156 " " NAG S 1 " - " ASN K 618 " " NAG T 1 " - " ASN K 611 " " NAG U 601 " - " ASN U 88 " " NAG U 602 " - " ASN U 160 " " NAG U 603 " - " ASN U 234 " " NAG U 604 " - " ASN U 137 " " NAG U 605 " - " ASN U 355 " " NAG U 606 " - " ASN U 276 " " NAG U 607 " - " ASN U 392 " " NAG U 608 " - " ASN U 339 " " NAG U 609 " - " ASN U 295 " " NAG U 610 " - " ASN U 448 " " NAG U 611 " - " ASN U 301 " " NAG U 612 " - " ASN U 197 " " NAG U 613 " - " ASN U 133 " " NAG V 701 " - " ASN V 625 " " NAG V 702 " - " ASN V 637 " " NAG Y 1 " - " ASN U 386 " " NAG Z 1 " - " ASN U 332 " Time building additional restraints: 5.63 Conformation dependent library (CDL) restraints added in 2.0 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4248 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 33 sheets defined 20.3% alpha, 22.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY B 525 " --> pdb=" O GLY B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 532 Processing helix chain 'B' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN B 538 " --> pdb=" O THR B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 624 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP B 659 " --> pdb=" O LYS B 655 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'J' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU J 102 " --> pdb=" O ASN J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 335 through 350 Processing helix chain 'J' and resid 368 through 373 removed outlier: 3.554A pdb=" N THR J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 484 removed outlier: 4.084A pdb=" N GLU J 482 " --> pdb=" O ASN J 478 " (cutoff:3.500A) Processing helix chain 'K' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY K 525 " --> pdb=" O GLY K 522 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 532 Processing helix chain 'K' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN K 538 " --> pdb=" O THR K 534 " (cutoff:3.500A) Processing helix chain 'K' and resid 572 through 596 Processing helix chain 'K' and resid 618 through 624 Processing helix chain 'K' and resid 627 through 636 Processing helix chain 'K' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS K 655 " --> pdb=" O ASN K 651 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP K 659 " --> pdb=" O LYS K 655 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 Processing helix chain 'U' and resid 98 through 115 removed outlier: 4.195A pdb=" N GLU U 102 " --> pdb=" O ASN U 98 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 335 through 350 Processing helix chain 'U' and resid 368 through 373 removed outlier: 3.555A pdb=" N THR U 373 " --> pdb=" O LEU U 369 " (cutoff:3.500A) Processing helix chain 'U' and resid 475 through 484 removed outlier: 4.085A pdb=" N GLU U 482 " --> pdb=" O ASN U 478 " (cutoff:3.500A) Processing helix chain 'V' and resid 521 through 526 removed outlier: 4.412A pdb=" N GLY V 525 " --> pdb=" O GLY V 522 " (cutoff:3.500A) Processing helix chain 'V' and resid 527 through 532 Processing helix chain 'V' and resid 534 through 540 removed outlier: 3.524A pdb=" N GLN V 538 " --> pdb=" O THR V 534 " (cutoff:3.500A) Processing helix chain 'V' and resid 572 through 596 Processing helix chain 'V' and resid 618 through 624 Processing helix chain 'V' and resid 627 through 636 Processing helix chain 'V' and resid 638 through 659 removed outlier: 3.740A pdb=" N LYS V 655 " --> pdb=" O ASN V 651 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP V 659 " --> pdb=" O LYS V 655 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 32 Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'X' and resid 79 through 83 Processing sheet with id=1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.405A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.614A 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 466 through 470 Processing sheet with id=8, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=9, first strand: chain 'H' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 11 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 100H through 103 Processing sheet with id=10, first strand: chain 'L' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 12 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=10 Processing sheet with id=11, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=12, first strand: chain 'J' and resid 494 through 499 removed outlier: 5.332A pdb=" N VAL K 608 " --> pdb=" O VAL J 36 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N VAL J 38 " --> pdb=" O THR K 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR K 606 " --> pdb=" O VAL J 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR J 40 " --> pdb=" O CYS K 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS K 604 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'J' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE J 225 " --> pdb=" O VAL J 245 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'J' and resid 53 through 55 Processing sheet with id=15, first strand: chain 'J' and resid 91 through 94 Processing sheet with id=16, first strand: chain 'J' and resid 169 through 177 Processing sheet with id=17, first strand: chain 'J' and resid 201 through 203 removed outlier: 6.404A pdb=" N THR J 202 " --> pdb=" O TYR J 435 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'J' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 259 through 261 current: chain 'J' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN J 301 " --> pdb=" O ILE J 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE J 323 " --> pdb=" O ASN J 301 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR J 303 " --> pdb=" O GLY J 321 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN J 315 " --> pdb=" O ILE J 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 315 through 323A current: chain 'J' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 381 through 385 current: chain 'J' and resid 466 through 470 Processing sheet with id=19, first strand: chain 'M' and resid 3 through 6 Processing sheet with id=20, first strand: chain 'M' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 11 through 12 current: chain 'M' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 57 through 59 current: chain 'M' and resid 100H through 103 Processing sheet with id=21, first strand: chain 'N' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 12 through 13 current: chain 'N' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 48 current: chain 'N' and resid 96 through 98 No H-bonds generated for sheet with id=21 Processing sheet with id=22, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=23, first strand: chain 'U' and resid 494 through 499 removed outlier: 5.333A pdb=" N VAL V 608 " --> pdb=" O VAL U 36 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N VAL U 38 " --> pdb=" O THR V 606 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N THR V 606 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N TYR U 40 " --> pdb=" O CYS V 604 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N CYS V 604 " --> pdb=" O TYR U 40 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'U' and resid 45 through 47 removed outlier: 3.678A pdb=" N ILE U 225 " --> pdb=" O VAL U 245 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'U' and resid 53 through 55 Processing sheet with id=26, first strand: chain 'U' and resid 91 through 94 Processing sheet with id=27, first strand: chain 'U' and resid 169 through 177 Processing sheet with id=28, first strand: chain 'U' and resid 201 through 203 removed outlier: 6.406A pdb=" N THR U 202 " --> pdb=" O TYR U 435 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'U' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 259 through 261 current: chain 'U' and resid 284 through 312 removed outlier: 6.898A pdb=" N ASN U 301 " --> pdb=" O ILE U 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE U 323 " --> pdb=" O ASN U 301 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR U 303 " --> pdb=" O GLY U 321 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN U 315 " --> pdb=" O ILE U 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 315 through 323A current: chain 'U' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'U' and resid 381 through 385 current: chain 'U' and resid 466 through 470 Processing sheet with id=30, first strand: chain 'W' and resid 3 through 6 Processing sheet with id=31, first strand: chain 'W' and resid 11 through 12 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 11 through 12 current: chain 'W' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 57 through 59 current: chain 'W' and resid 100H through 103 Processing sheet with id=32, first strand: chain 'X' and resid 12 through 13 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 12 through 13 current: chain 'X' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 45 through 48 current: chain 'X' and resid 96 through 98 No H-bonds generated for sheet with id=32 Processing sheet with id=33, first strand: chain 'X' and resid 19 through 24 516 hydrogen bonds defined for protein. 1368 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: 6.47 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 3288 1.31 - 1.45: 5878 1.45 - 1.58: 10172 1.58 - 1.72: 101 1.72 - 1.86: 160 Bond restraints: 19599 Sorted by residual: bond pdb=" CB ASP L 27B" pdb=" CG ASP L 27B" ideal model delta sigma weight residual 1.516 1.355 0.161 2.50e-02 1.60e+03 4.13e+01 bond pdb=" CB ASP N 27B" pdb=" CG ASP N 27B" ideal model delta sigma weight residual 1.516 1.355 0.161 2.50e-02 1.60e+03 4.12e+01 bond pdb=" CB ASP X 27B" pdb=" CG ASP X 27B" ideal model delta sigma weight residual 1.516 1.356 0.160 2.50e-02 1.60e+03 4.12e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.85e+01 bond pdb=" NE ARG J 503 " pdb=" CZ ARG J 503 " ideal model delta sigma weight residual 1.326 1.394 -0.068 1.10e-02 8.26e+03 3.84e+01 ... (remaining 19594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.80: 26544 7.80 - 15.60: 39 15.60 - 23.40: 0 23.40 - 31.20: 0 31.20 - 39.00: 3 Bond angle restraints: 26586 Sorted by residual: angle pdb=" C2 NAG P 1 " pdb=" N2 NAG P 1 " pdb=" C7 NAG P 1 " ideal model delta sigma weight residual 124.56 163.56 -39.00 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C2 NAG Z 1 " pdb=" N2 NAG Z 1 " pdb=" C7 NAG Z 1 " ideal model delta sigma weight residual 124.56 163.53 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" C2 NAG D 1 " pdb=" N2 NAG D 1 " pdb=" C7 NAG D 1 " ideal model delta sigma weight residual 124.56 163.53 -38.97 3.00e+00 1.11e-01 1.69e+02 angle pdb=" N GLU J 87 " pdb=" CA GLU J 87 " pdb=" C GLU J 87 " ideal model delta sigma weight residual 111.33 121.04 -9.71 1.21e+00 6.83e-01 6.44e+01 angle pdb=" N GLU U 87 " pdb=" CA GLU U 87 " pdb=" C GLU U 87 " ideal model delta sigma weight residual 111.33 121.03 -9.70 1.21e+00 6.83e-01 6.43e+01 ... (remaining 26581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.10: 12357 22.10 - 44.20: 318 44.20 - 66.30: 84 66.30 - 88.40: 36 88.40 - 110.50: 12 Dihedral angle restraints: 12807 sinusoidal: 6180 harmonic: 6627 Sorted by residual: dihedral pdb=" C ASN B 637 " pdb=" N ASN B 637 " pdb=" CA ASN B 637 " pdb=" CB ASN B 637 " ideal model delta harmonic sigma weight residual -122.60 -111.59 -11.01 0 2.50e+00 1.60e-01 1.94e+01 dihedral pdb=" C ASN K 637 " pdb=" N ASN K 637 " pdb=" CA ASN K 637 " pdb=" CB ASN K 637 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 dihedral pdb=" C ASN V 637 " pdb=" N ASN V 637 " pdb=" CA ASN V 637 " pdb=" CB ASN V 637 " ideal model delta harmonic sigma weight residual -122.60 -111.61 -10.99 0 2.50e+00 1.60e-01 1.93e+01 ... (remaining 12804 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2149 0.104 - 0.209: 676 0.209 - 0.313: 252 0.313 - 0.418: 94 0.418 - 0.522: 54 Chirality restraints: 3225 Sorted by residual: chirality pdb=" C1 FUC T 2 " pdb=" O6 NAG T 1 " pdb=" C2 FUC T 2 " pdb=" O5 FUC T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 FUC I 2 " pdb=" O6 NAG I 1 " pdb=" C2 FUC I 2 " pdb=" O5 FUC I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 FUC 3 2 " pdb=" O6 NAG 3 1 " pdb=" C2 FUC 3 2 " pdb=" O5 FUC 3 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.34e+02 ... (remaining 3222 not shown) Planarity restraints: 3339 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG V 702 " -0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG V 702 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG V 702 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG V 702 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG V 702 " -0.172 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 702 " 0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG K 702 " -0.053 2.00e-02 2.50e+03 pdb=" C8 NAG K 702 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG K 702 " -0.413 2.00e-02 2.50e+03 pdb=" O7 NAG K 702 " 0.171 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 702 " -0.263 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" C7 NAG B 702 " 0.053 2.00e-02 2.50e+03 pdb=" C8 NAG B 702 " -0.031 2.00e-02 2.50e+03 pdb=" N2 NAG B 702 " 0.413 2.00e-02 2.50e+03 pdb=" O7 NAG B 702 " -0.171 2.00e-02 2.50e+03 ... (remaining 3336 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 4205 2.80 - 3.32: 16580 3.32 - 3.85: 31609 3.85 - 4.37: 39357 4.37 - 4.90: 63668 Nonbonded interactions: 155419 Sorted by model distance: nonbonded pdb=" NH2 ARG M 53 " pdb=" OD1 ASN V 656 " model vdw 2.271 3.120 nonbonded pdb=" OD1 ASN B 656 " pdb=" NH2 ARG W 53 " model vdw 2.272 3.120 nonbonded pdb=" NH2 ARG H 53 " pdb=" OD1 ASN K 656 " model vdw 2.272 3.120 nonbonded pdb=" N ASP M 84 " pdb=" OD1 ASP M 84 " model vdw 2.371 3.120 nonbonded pdb=" N ASP H 84 " pdb=" OD1 ASP H 84 " model vdw 2.371 3.120 ... (remaining 155414 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 '0' selection = chain 'E' selection = chain 'Q' } ncs_group { reference = (chain '1' and resid 1) selection = (chain '2' and resid 1) selection = (chain '3' and resid 1) selection = (chain 'C' and resid 1) selection = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'Y' and resid 1) selection = (chain 'Z' and resid 1) } ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'B' selection = chain 'K' selection = chain 'V' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'W' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.840 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: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 44.780 Find NCS groups from input model: 1.110 Set up NCS constraints: 0.110 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:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.161 19599 Z= 1.423 Angle : 1.827 38.997 26586 Z= 1.177 Chirality : 0.139 0.522 3225 Planarity : 0.014 0.234 3276 Dihedral : 11.787 110.504 8451 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.79 % Allowed : 2.51 % Favored : 96.69 % Rotamer: Outliers : 0.90 % Allowed : 0.85 % Favored : 98.26 % Cbeta Deviations : 0.56 % 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: 0.58 (0.17), residues: 2268 helix: -0.64 (0.24), residues: 372 sheet: 0.90 (0.20), residues: 714 loop : 0.58 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.009 TRP J 96 HIS 0.012 0.003 HIS J 85 PHE 0.040 0.007 PHE A 353 TYR 0.064 0.008 TYR L 96 ARG 0.014 0.001 ARG M 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 414 time to evaluate : 2.031 Fit side-chains REVERT: A 142 MET cc_start: 0.6882 (mmm) cc_final: 0.6439 (mmm) REVERT: L 94 ARG cc_start: 0.6858 (mmm160) cc_final: 0.5553 (mtt180) REVERT: N 94 ARG cc_start: 0.6826 (mmm160) cc_final: 0.5335 (mtt-85) REVERT: U 142 MET cc_start: 0.6788 (mmm) cc_final: 0.6542 (mmm) REVERT: X 94 ARG cc_start: 0.6982 (mmm160) cc_final: 0.5462 (ptp-170) outliers start: 18 outliers final: 4 residues processed: 426 average time/residue: 1.6511 time to fit residues: 775.0857 Evaluate side-chains 231 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 227 time to evaluate : 2.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain U residue 189 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 189 optimal weight: 0.6980 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 115 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 176 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 258 GLN A 280 ASN A 302 ASN A 348 GLN B 652 GLN H 100BGLN H 105 GLN J 280 ASN J 302 ASN J 348 GLN K 653 GLN M 100BGLN U 302 ASN U 348 GLN V 630 GLN V 653 GLN X 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19599 Z= 0.227 Angle : 0.652 11.736 26586 Z= 0.344 Chirality : 0.047 0.279 3225 Planarity : 0.004 0.052 3276 Dihedral : 8.751 76.628 4277 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.40 % Allowed : 2.43 % Favored : 97.18 % Rotamer: Outliers : 3.14 % Allowed : 9.67 % Favored : 87.19 % 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: 0.65 (0.17), residues: 2268 helix: 1.23 (0.27), residues: 375 sheet: 0.74 (0.19), residues: 708 loop : 0.07 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP J 479 HIS 0.005 0.001 HIS J 85 PHE 0.016 0.002 PHE A 176 TYR 0.011 0.001 TYR X 96 ARG 0.007 0.001 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 248 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8841 (mtp) cc_final: 0.8599 (mtp) REVERT: A 142 MET cc_start: 0.6572 (mmm) cc_final: 0.6051 (mmm) REVERT: L 94 ARG cc_start: 0.6925 (mmm160) cc_final: 0.5533 (mtt180) REVERT: J 348 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8102 (mp-120) REVERT: M 23 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7109 (tmt170) REVERT: N 85 ASP cc_start: 0.8060 (m-30) cc_final: 0.7837 (m-30) REVERT: N 94 ARG cc_start: 0.6817 (mmm160) cc_final: 0.5391 (mtt-85) REVERT: U 83 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7071 (tt0) REVERT: U 106 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: U 348 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7413 (mp-120) REVERT: X 94 ARG cc_start: 0.6841 (mmm160) cc_final: 0.5412 (mtt-85) outliers start: 63 outliers final: 30 residues processed: 294 average time/residue: 1.6145 time to fit residues: 525.6043 Evaluate side-chains 233 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 GLU Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 244 THR Chi-restraints excluded: chain J residue 340 GLU Chi-restraints excluded: chain J residue 348 GLN Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain U residue 46 LYS Chi-restraints excluded: chain U residue 83 GLU Chi-restraints excluded: chain U residue 106 GLU Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 348 GLN Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain W residue 46 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 170 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 204 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 chunk 182 optimal weight: 0.9980 chunk 202 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 164 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN B 653 GLN H 105 GLN L 31 ASN J 283 ASN K 653 GLN U 283 ASN X 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19599 Z= 0.178 Angle : 0.572 9.494 26586 Z= 0.295 Chirality : 0.045 0.276 3225 Planarity : 0.004 0.043 3276 Dihedral : 7.571 59.913 4277 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.69 % Favored : 97.05 % Rotamer: Outliers : 3.19 % Allowed : 10.51 % Favored : 86.30 % 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: 0.65 (0.18), residues: 2268 helix: 1.95 (0.28), residues: 357 sheet: 0.66 (0.19), residues: 717 loop : -0.12 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 479 HIS 0.004 0.001 HIS A 105 PHE 0.013 0.002 PHE U 353 TYR 0.020 0.001 TYR A 173 ARG 0.010 0.001 ARG U 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 212 time to evaluate : 2.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8845 (mtp) cc_final: 0.8602 (mtp) REVERT: A 142 MET cc_start: 0.6593 (mmm) cc_final: 0.6193 (mmm) REVERT: B 533 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7954 (mtt) REVERT: L 94 ARG cc_start: 0.6872 (mmm160) cc_final: 0.5488 (mtt-85) REVERT: M 23 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7055 (tmt170) REVERT: N 85 ASP cc_start: 0.8079 (m-30) cc_final: 0.7848 (m-30) REVERT: N 94 ARG cc_start: 0.6812 (mmm160) cc_final: 0.5338 (mtt-85) REVERT: U 143 ARG cc_start: 0.7002 (mtp85) cc_final: 0.6775 (tpp-160) REVERT: X 94 ARG cc_start: 0.6858 (mmm160) cc_final: 0.5366 (mtt180) outliers start: 64 outliers final: 30 residues processed: 260 average time/residue: 1.5366 time to fit residues: 446.0765 Evaluate side-chains 220 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 188 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 128 THR Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain W residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 202 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 97 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 0.8980 chunk 217 optimal weight: 0.2980 chunk 107 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN J 258 GLN J 348 GLN M 52 ASN N 31 ASN U 348 GLN X 31 ASN X 95 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19599 Z= 0.182 Angle : 0.550 10.215 26586 Z= 0.281 Chirality : 0.045 0.263 3225 Planarity : 0.004 0.036 3276 Dihedral : 6.357 59.686 4277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.82 % Favored : 96.91 % Rotamer: Outliers : 3.34 % Allowed : 11.16 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2268 helix: 2.18 (0.27), residues: 360 sheet: 0.63 (0.19), residues: 717 loop : -0.23 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.013 0.002 PHE M 29 TYR 0.020 0.001 TYR A 173 ARG 0.005 0.000 ARG J 143 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 213 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8828 (mtp) cc_final: 0.8475 (mtp) REVERT: A 142 MET cc_start: 0.6458 (mmm) cc_final: 0.6071 (mmm) REVERT: A 428 GLN cc_start: 0.6755 (OUTLIER) cc_final: 0.5971 (mt0) REVERT: A 475 MET cc_start: 0.8188 (mmp) cc_final: 0.7938 (mmt) REVERT: B 533 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8016 (mtt) REVERT: L 94 ARG cc_start: 0.6791 (mmm160) cc_final: 0.5501 (mtt180) REVERT: K 533 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7899 (mtp) REVERT: M 23 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7041 (tmt170) REVERT: M 52 ASN cc_start: 0.7845 (t0) cc_final: 0.7431 (t0) REVERT: N 94 ARG cc_start: 0.6735 (mmm160) cc_final: 0.5264 (mtt-85) REVERT: X 94 ARG cc_start: 0.6749 (mmm160) cc_final: 0.5321 (mtt180) outliers start: 67 outliers final: 34 residues processed: 262 average time/residue: 1.5386 time to fit residues: 448.7127 Evaluate side-chains 233 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 290 THR Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 106 GLU Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 364 SER Chi-restraints excluded: chain J residue 388 SER Chi-restraints excluded: chain J residue 426 MET Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 371 VAL Chi-restraints excluded: chain U residue 388 SER Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 612 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 181 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.0030 chunk 195 optimal weight: 2.9990 chunk 54 optimal weight: 0.0980 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 GLN A 348 GLN J 348 GLN U 348 GLN X 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19599 Z= 0.185 Angle : 0.543 10.943 26586 Z= 0.276 Chirality : 0.044 0.260 3225 Planarity : 0.004 0.034 3276 Dihedral : 5.879 59.301 4277 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.78 % Favored : 96.96 % Rotamer: Outliers : 2.54 % Allowed : 12.66 % Favored : 84.80 % 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: 0.68 (0.18), residues: 2268 helix: 2.28 (0.27), residues: 360 sheet: 0.78 (0.20), residues: 699 loop : -0.28 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 479 HIS 0.003 0.001 HIS A 105 PHE 0.013 0.002 PHE M 29 TYR 0.022 0.001 TYR A 173 ARG 0.008 0.000 ARG U 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 203 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 MET cc_start: 0.8787 (mtp) cc_final: 0.8417 (mtp) REVERT: A 142 MET cc_start: 0.6426 (mmm) cc_final: 0.6068 (mmm) REVERT: A 428 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6058 (mt0) REVERT: B 533 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.8035 (mtt) REVERT: L 94 ARG cc_start: 0.6867 (mmm160) cc_final: 0.5550 (mtt180) REVERT: K 533 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.7913 (mtp) REVERT: M 23 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7073 (tmt170) REVERT: N 94 ARG cc_start: 0.6633 (mmm160) cc_final: 0.5306 (mtt-85) REVERT: U 138 ILE cc_start: 0.7705 (OUTLIER) cc_final: 0.7329 (tt) REVERT: W 100 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.8450 (mt0) REVERT: X 94 ARG cc_start: 0.6724 (mmm160) cc_final: 0.5289 (mtt-85) outliers start: 51 outliers final: 29 residues processed: 237 average time/residue: 1.3663 time to fit residues: 360.6193 Evaluate side-chains 233 residues out of total 2007 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LYS Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 189 THR Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 428 GLN Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 639 THR Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain J residue 117 LYS Chi-restraints excluded: chain J residue 138 ILE Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 201 ILE Chi-restraints excluded: chain J residue 213 ILE Chi-restraints excluded: chain J residue 333 VAL Chi-restraints excluded: chain K residue 533 MET Chi-restraints excluded: chain K residue 581 LEU Chi-restraints excluded: chain K residue 595 ILE Chi-restraints excluded: chain K residue 612 SER Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 23 ARG Chi-restraints excluded: chain U residue 138 ILE Chi-restraints excluded: chain U residue 189 THR Chi-restraints excluded: chain U residue 201 ILE Chi-restraints excluded: chain U residue 213 ILE Chi-restraints excluded: chain U residue 333 VAL Chi-restraints excluded: chain U residue 412 ASP Chi-restraints excluded: chain U residue 465 THR Chi-restraints excluded: chain V residue 536 THR Chi-restraints excluded: chain V residue 581 LEU Chi-restraints excluded: chain W residue 100 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 225 random chunks: chunk 73 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 217 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: