Starting phenix.real_space_refine on Fri Sep 27 14:05:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8g_23233/09_2024/7l8g_23233.cif" } resolution = 4.3 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= 0.002 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 9826 2.51 5 N 2656 2.21 5 O 3218 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 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: 15802 Number of models: 1 Model: "" Number of chains: 39 Chain: "C" Number of atoms: 3512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3512 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "D" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3499 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} Chain breaks: 3 Chain: "F" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 952 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "A" Number of atoms: 3497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3497 Classifications: {'peptide': 443} Link IDs: {'PTRANS': 20, 'TRANS': 422} 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: 545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 545 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'TRANS': 108} Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 109 Planarities with less than four sites: {'UNK:plan-1': 109} Unresolved non-hydrogen planarities: 109 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 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: 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: "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: 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: "R" 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: "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: "W" 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: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 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: 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: "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: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" 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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 10.31, per 1000 atoms: 0.65 Number of scatterers: 15802 At special positions: 0 Unit cell: (130.81, 125.66, 145.23, 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 3218 8.00 N 2656 7.00 C 9826 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=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 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=2.07 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=2.11 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.04 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.06 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 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=2.10 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Y 3 " - " MAN Y 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 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 R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 701 " - " ASN A 276 " " NAG A 702 " - " ASN A 386 " " NAG A 703 " - " ASN A 363 " " NAG A 704 " - " ASN A 234 " " NAG A 705 " - " ASN A 133 " " NAG A 706 " - " ASN A 289 " " NAG A 707 " - " ASN A 339 " " NAG A 708 " - " ASN A 355 " " NAG A 709 " - " 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 160 " " NAG C 702 " - " ASN C 276 " " NAG C 703 " - " ASN C 386 " " NAG C 704 " - " ASN C 363 " " NAG C 705 " - " ASN C 133 " " NAG C 706 " - " ASN C 301 " " NAG C 707 " - " ASN C 289 " " NAG C 708 " - " ASN C 339 " " NAG C 709 " - " ASN C 355 " " NAG C 710 " - " 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 160 " " NAG E 702 " - " ASN E 276 " " NAG E 703 " - " ASN E 386 " " NAG E 704 " - " ASN E 363 " " NAG E 705 " - " ASN E 234 " " NAG E 706 " - " ASN E 133 " " NAG E 707 " - " ASN E 301 " " NAG E 708 " - " ASN E 289 " " NAG E 709 " - " ASN E 339 " " NAG E 710 " - " ASN E 355 " " NAG E 711 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 618 " " NAG F 703 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 295 " " NAG K 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 88 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 295 " " NAG U 1 " - " ASN E 197 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 241 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 448 " " NAG a 1 " - " ASN A 295 " " NAG b 1 " - " ASN A 197 " " NAG c 1 " - " ASN A 301 " " NAG d 1 " - " ASN A 88 " " NAG e 1 " - " ASN A 241 " " NAG f 1 " - " ASN A 332 " " NAG g 1 " - " ASN A 160 " Time building additional restraints: 5.19 Conformation dependent library (CDL) restraints added in 1.7 seconds 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3588 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 45 sheets defined 27.7% alpha, 80.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.04 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 99 through 117 removed outlier: 4.010A pdb=" N GLN C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (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 368 through 373 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.726A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.498A 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 546 removed outlier: 3.719A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 570 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 659 removed outlier: 4.515A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 645 " --> pdb=" O ILE D 641 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 96 through 98 No H-bonds generated for 'chain 'E' and resid 96 through 98' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 139 through 151 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.618A pdb=" N GLN E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 474 through 478 Processing helix chain 'E' and resid 479 through 484 Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 570 through 596 removed outlier: 3.839A pdb=" N LYS F 574 " --> pdb=" O HIS F 570 " (cutoff:3.500A) Processing helix chain 'F' and resid 618 through 626 removed outlier: 4.428A pdb=" N ASP F 624 " --> pdb=" O SER F 620 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 639 through 656 removed outlier: 3.855A pdb=" N GLY F 644 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN F 652 " --> pdb=" O GLU F 648 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N GLN F 653 " --> pdb=" O SER F 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 117 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 351 removed outlier: 3.611A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 425 through 429 removed outlier: 4.236A pdb=" N GLN A 428 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.854A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 removed outlier: 3.926A pdb=" N MET B 535 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.917A pdb=" N GLY B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.385A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.472A 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 53 through 55 removed outlier: 5.029A pdb=" N ILE C 215 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLY C 250 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR C 217 " --> pdb=" O THR C 248 " (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 201 through 203 removed outlier: 6.421A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.648A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.843A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.428A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.367A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.304A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 302 removed outlier: 3.695A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.370A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.291A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 56 removed outlier: 5.054A pdb=" N ILE E 215 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY E 250 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N TYR E 217 " --> pdb=" O THR E 248 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.728A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 3.708A pdb=" N MET E 434 " --> pdb=" O ILE E 424 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 271 through 273 removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 271 through 273 removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 316 through 323A removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) removed outlier: 5.378A pdb=" N LYS E 305 " --> pdb=" O THR E 320 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N THR E 320 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE E 307 " --> pdb=" O TYR E 318 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TYR E 318 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 393 through 396 removed outlier: 6.327A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N GLY E 441 " --> pdb=" O ASN E 300 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N ASN E 300 " --> pdb=" O GLY E 441 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY E 451 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 10.616A pdb=" N GLU E 290 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 11.690A pdb=" N ILE E 453 " --> pdb=" O LEU E 288 " (cutoff:3.500A) removed outlier: 11.628A pdb=" N LEU E 288 " --> pdb=" O ILE E 453 " (cutoff:3.500A) removed outlier: 10.969A pdb=" N THR E 455 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 10.711A pdb=" N VAL E 286 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.395A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AE1, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.100A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AE3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AE4, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.524A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 256 through 257 removed outlier: 3.548A pdb=" N SER A 375 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.659A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.050A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.696A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.672A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.407A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.419A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 284 through 298 current: chain 'A' and resid 358 through 361 Processing sheet with id=AE7, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.615A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 21 through 22 Processing sheet with id=AE9, first strand: chain 'L' and resid 11 through 12 removed outlier: 4.051A pdb=" N UNK L 102 " --> pdb=" O UNK L 11 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N UNK L 45 " --> pdb=" O UNK L 37 " (cutoff:3.500A) 844 hydrogen bonds defined for protein. 2262 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: 7.90 Time building geometry restraints manager: 5.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4070 1.33 - 1.47: 4938 1.47 - 1.61: 6917 1.61 - 1.75: 24 1.75 - 1.89: 124 Bond restraints: 16073 Sorted by residual: bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.403 0.094 1.40e-02 5.10e+03 4.52e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.656 -0.126 2.00e-02 2.50e+03 3.97e+01 bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.654 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.303 0.067 1.10e-02 8.26e+03 3.69e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.650 -0.120 2.00e-02 2.50e+03 3.60e+01 ... (remaining 16068 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 19640 2.81 - 5.62: 2018 5.62 - 8.43: 189 8.43 - 11.24: 13 11.24 - 14.05: 3 Bond angle restraints: 21863 Sorted by residual: angle pdb=" N THR C 320 " pdb=" CA THR C 320 " pdb=" C THR C 320 " ideal model delta sigma weight residual 112.54 122.84 -10.30 1.22e+00 6.72e-01 7.13e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.01e+00 9.80e-01 7.11e+01 angle pdb=" N ILE E 424 " pdb=" CA ILE E 424 " pdb=" C ILE E 424 " ideal model delta sigma weight residual 108.11 119.66 -11.55 1.40e+00 5.10e-01 6.81e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.56 -8.00 1.01e+00 9.80e-01 6.28e+01 angle pdb=" N PRO E 437 " pdb=" CA PRO E 437 " pdb=" C PRO E 437 " ideal model delta sigma weight residual 110.70 101.84 8.86 1.22e+00 6.72e-01 5.28e+01 ... (remaining 21858 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.32: 10583 21.32 - 42.65: 218 42.65 - 63.97: 73 63.97 - 85.29: 31 85.29 - 106.61: 15 Dihedral angle restraints: 10920 sinusoidal: 5403 harmonic: 5517 Sorted by residual: dihedral pdb=" CB CYS E 119 " pdb=" SG CYS E 119 " pdb=" SG CYS E 205 " pdb=" CB CYS E 205 " ideal model delta sinusoidal sigma weight residual -86.00 -132.02 46.02 1 1.00e+01 1.00e-02 2.93e+01 dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual -86.00 -41.57 -44.43 1 1.00e+01 1.00e-02 2.74e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -130.05 44.05 1 1.00e+01 1.00e-02 2.70e+01 ... (remaining 10917 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 2441 0.247 - 0.494: 349 0.494 - 0.740: 9 0.740 - 0.987: 0 0.987 - 1.234: 1 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+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 -2.62 0.22 2.00e-02 2.50e+03 1.24e+02 ... (remaining 2797 not shown) Planarity restraints: 2734 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 702 " -0.350 2.00e-02 2.50e+03 3.01e-01 1.14e+03 pdb=" C7 NAG F 702 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG F 702 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG F 702 " 0.536 2.00e-02 2.50e+03 pdb=" O7 NAG F 702 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 702 " 0.347 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG C 702 " -0.086 2.00e-02 2.50e+03 pdb=" C8 NAG C 702 " 0.146 2.00e-02 2.50e+03 pdb=" N2 NAG C 702 " -0.528 2.00e-02 2.50e+03 pdb=" O7 NAG C 702 " 0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 708 " 0.331 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG A 708 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG A 708 " 0.050 2.00e-02 2.50e+03 pdb=" N2 NAG A 708 " -0.502 2.00e-02 2.50e+03 pdb=" O7 NAG A 708 " 0.198 2.00e-02 2.50e+03 ... (remaining 2731 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5183 2.86 - 3.37: 14782 3.37 - 3.88: 26497 3.88 - 4.39: 30686 4.39 - 4.90: 47198 Nonbonded interactions: 124346 Sorted by model distance: nonbonded pdb=" N LEU F 523 " pdb=" OE1 GLN F 540 " model vdw 2.354 3.120 nonbonded pdb=" NZ LYS C 46 " pdb=" OD2 ASP D 632 " model vdw 2.399 3.120 nonbonded pdb=" OD1 ASP E 368 " pdb=" N LEU E 369 " model vdw 2.424 3.120 nonbonded pdb=" NZ LYS A 335 " pdb=" OD2 ASP A 412 " model vdw 2.439 3.120 nonbonded pdb=" N PRO E 437 " pdb=" O PRO E 437 " model vdw 2.439 2.496 ... (remaining 124341 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 709)) selection = (chain 'C' and (resid 33 through 58 or resid 66 through 397 or resid 411 through \ 505 or resid 701 through 709)) selection = (chain 'E' and (resid 33 through 58 or resid 66 through 505 or resid 702 through \ 710)) } ncs_group { reference = (chain 'B' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 520 through 546 or resid 569 through 660 or resid 701 thro \ ugh 703)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Y' } ncs_group { reference = (chain 'H' and resid 11 through 110) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } 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: 0.010 Normalize map: mean=0, sd=1: 7.730 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: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 42.270 Find NCS groups from input model: 1.310 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 0.131 16073 Z= 1.378 Angle : 1.756 14.048 21863 Z= 1.115 Chirality : 0.156 1.234 2800 Planarity : 0.016 0.301 2670 Dihedral : 11.312 106.613 7233 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: 0.64 (0.20), residues: 1659 helix: -0.69 (0.23), residues: 421 sheet: 1.04 (0.23), residues: 438 loop : 0.94 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.010 TRP C 35 HIS 0.017 0.003 HIS C 374 PHE 0.035 0.006 PHE E 353 TYR 0.041 0.008 TYR E 173 ARG 0.006 0.001 ARG E 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 401 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8791 (m-80) cc_final: 0.8410 (m-80) REVERT: C 453 ILE cc_start: 0.9234 (mt) cc_final: 0.8903 (tt) REVERT: D 543 ASN cc_start: 0.9127 (m-40) cc_final: 0.8904 (m110) REVERT: D 571 TRP cc_start: 0.6645 (t60) cc_final: 0.6196 (t60) REVERT: D 588 ARG cc_start: 0.9167 (mmm160) cc_final: 0.8924 (tpp-160) REVERT: D 630 GLN cc_start: 0.9336 (mt0) cc_final: 0.9134 (mt0) REVERT: D 639 THR cc_start: 0.8967 (p) cc_final: 0.8737 (p) REVERT: E 129 LEU cc_start: 0.9176 (mt) cc_final: 0.8942 (mt) REVERT: E 166 ARG cc_start: 0.8740 (mtp85) cc_final: 0.8370 (mtp85) REVERT: E 338 TRP cc_start: 0.8699 (t-100) cc_final: 0.8492 (t-100) REVERT: F 523 LEU cc_start: 0.9265 (mt) cc_final: 0.8915 (mt) REVERT: F 536 THR cc_start: 0.8788 (p) cc_final: 0.8553 (t) REVERT: F 590 GLN cc_start: 0.9317 (mm-40) cc_final: 0.8752 (tm-30) REVERT: F 591 GLN cc_start: 0.9440 (tt0) cc_final: 0.8910 (tt0) REVERT: F 630 GLN cc_start: 0.9445 (mt0) cc_final: 0.8952 (mt0) REVERT: F 634 GLU cc_start: 0.8622 (tp30) cc_final: 0.8275 (tt0) REVERT: F 638 TYR cc_start: 0.7927 (m-80) cc_final: 0.7584 (m-80) REVERT: F 648 GLU cc_start: 0.9157 (mt-10) cc_final: 0.8950 (tm-30) REVERT: F 656 ASN cc_start: 0.9152 (m-40) cc_final: 0.8781 (m-40) REVERT: A 47 ASP cc_start: 0.8793 (m-30) cc_final: 0.8557 (p0) REVERT: B 536 THR cc_start: 0.8870 (p) cc_final: 0.8641 (p) REVERT: B 584 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8904 (tm-30) REVERT: B 585 HIS cc_start: 0.8873 (m-70) cc_final: 0.8597 (m-70) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2956 time to fit residues: 168.7589 Evaluate side-chains 213 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 6.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 302 ASN C 352 HIS C 374 HIS A 283 ASN ** A 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 16073 Z= 0.276 Angle : 0.768 11.331 21863 Z= 0.395 Chirality : 0.050 0.335 2800 Planarity : 0.004 0.039 2670 Dihedral : 8.676 86.640 4041 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.46 % Allowed : 2.31 % Favored : 97.22 % 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: 0.67 (0.20), residues: 1659 helix: 0.38 (0.26), residues: 404 sheet: 0.72 (0.22), residues: 481 loop : 0.50 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 479 HIS 0.010 0.001 HIS A 249 PHE 0.016 0.002 PHE C 53 TYR 0.026 0.002 TYR B 643 ARG 0.004 0.001 ARG E 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8624 (m-80) cc_final: 0.8320 (m-80) REVERT: C 104 MET cc_start: 0.9074 (mmp) cc_final: 0.8836 (mmp) REVERT: C 150 MET cc_start: 0.8051 (mmm) cc_final: 0.7831 (mmt) REVERT: C 333 VAL cc_start: 0.9179 (t) cc_final: 0.8953 (m) REVERT: C 475 MET cc_start: 0.8908 (mmp) cc_final: 0.8687 (mmp) REVERT: D 543 ASN cc_start: 0.8980 (m-40) cc_final: 0.8647 (m110) REVERT: D 626 MET cc_start: 0.8035 (mtp) cc_final: 0.7573 (mtp) REVERT: D 639 THR cc_start: 0.8796 (p) cc_final: 0.8552 (p) REVERT: E 104 MET cc_start: 0.9021 (ttt) cc_final: 0.8661 (ttt) REVERT: E 195 ASN cc_start: 0.8432 (t0) cc_final: 0.8168 (t0) REVERT: E 338 TRP cc_start: 0.8657 (t-100) cc_final: 0.8437 (t-100) REVERT: E 368 ASP cc_start: 0.8538 (p0) cc_final: 0.8306 (p0) REVERT: F 522 PHE cc_start: 0.8508 (t80) cc_final: 0.8012 (t80) REVERT: F 523 LEU cc_start: 0.9248 (mt) cc_final: 0.9038 (mt) REVERT: F 530 MET cc_start: 0.9087 (mtt) cc_final: 0.8804 (mtt) REVERT: F 535 MET cc_start: 0.8437 (mpp) cc_final: 0.8189 (mpp) REVERT: F 536 THR cc_start: 0.8646 (p) cc_final: 0.8352 (t) REVERT: F 589 ASP cc_start: 0.9331 (m-30) cc_final: 0.8946 (m-30) REVERT: F 599 SER cc_start: 0.9291 (p) cc_final: 0.8951 (m) REVERT: F 630 GLN cc_start: 0.9501 (mt0) cc_final: 0.9214 (mt0) REVERT: A 53 PHE cc_start: 0.8196 (m-10) cc_final: 0.7933 (m-10) REVERT: A 104 MET cc_start: 0.8396 (tpt) cc_final: 0.6864 (tpt) REVERT: A 125 LEU cc_start: 0.9427 (mp) cc_final: 0.9071 (mt) REVERT: A 161 MET cc_start: 0.9057 (tpp) cc_final: 0.8737 (tpp) REVERT: A 166 ARG cc_start: 0.8662 (ttm110) cc_final: 0.8290 (ttm110) REVERT: A 217 TYR cc_start: 0.8221 (m-10) cc_final: 0.7755 (m-10) REVERT: A 368 ASP cc_start: 0.8544 (p0) cc_final: 0.7136 (p0) REVERT: A 370 GLU cc_start: 0.8830 (mp0) cc_final: 0.8416 (mp0) REVERT: A 452 LEU cc_start: 0.9225 (mp) cc_final: 0.9023 (mp) REVERT: B 523 LEU cc_start: 0.9144 (mt) cc_final: 0.8741 (mt) REVERT: B 584 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8988 (tm-30) REVERT: B 586 TYR cc_start: 0.9253 (t80) cc_final: 0.9050 (t80) REVERT: B 626 MET cc_start: 0.7925 (tpp) cc_final: 0.7575 (tpp) REVERT: B 630 GLN cc_start: 0.9214 (mt0) cc_final: 0.8893 (mt0) REVERT: B 654 GLU cc_start: 0.9277 (tp30) cc_final: 0.9044 (tp30) outliers start: 7 outliers final: 0 residues processed: 278 average time/residue: 0.2816 time to fit residues: 114.2186 Evaluate side-chains 192 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 94 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 141 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 170 optimal weight: 40.0000 chunk 183 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 168 optimal weight: 40.0000 chunk 57 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 570 HIS D 575 GLN E 183 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN B 570 HIS B 585 HIS B 651 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 16073 Z= 0.522 Angle : 0.876 12.076 21863 Z= 0.443 Chirality : 0.051 0.276 2800 Planarity : 0.005 0.079 2670 Dihedral : 8.406 80.125 4041 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.26 % Allowed : 2.84 % Favored : 96.89 % 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: -0.03 (0.20), residues: 1659 helix: -0.14 (0.25), residues: 413 sheet: 0.40 (0.22), residues: 462 loop : -0.06 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 479 HIS 0.008 0.002 HIS C 330 PHE 0.032 0.003 PHE D 522 TYR 0.026 0.003 TYR C 217 ARG 0.010 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8916 (m-80) cc_final: 0.8265 (m-80) REVERT: C 150 MET cc_start: 0.8178 (mmm) cc_final: 0.7967 (mmp) REVERT: C 475 MET cc_start: 0.9033 (mmp) cc_final: 0.8721 (mmm) REVERT: C 478 ASN cc_start: 0.9098 (m110) cc_final: 0.8862 (m110) REVERT: D 626 MET cc_start: 0.8461 (mtp) cc_final: 0.8125 (mtp) REVERT: E 368 ASP cc_start: 0.8651 (p0) cc_final: 0.8322 (p0) REVERT: E 452 LEU cc_start: 0.9489 (mp) cc_final: 0.8959 (tp) REVERT: F 654 GLU cc_start: 0.9263 (tp30) cc_final: 0.9005 (tp30) REVERT: A 150 MET cc_start: 0.9191 (mmm) cc_final: 0.8869 (mpp) REVERT: B 535 MET cc_start: 0.8952 (mpp) cc_final: 0.8650 (mmm) REVERT: B 584 GLU cc_start: 0.9375 (mt-10) cc_final: 0.9026 (tm-30) REVERT: B 601 LYS cc_start: 0.9351 (pttm) cc_final: 0.9064 (ptpp) REVERT: B 626 MET cc_start: 0.7956 (tpp) cc_final: 0.7649 (tpp) REVERT: B 630 GLN cc_start: 0.9201 (mt0) cc_final: 0.8807 (mt0) REVERT: B 635 ILE cc_start: 0.9253 (pt) cc_final: 0.8986 (pt) REVERT: B 654 GLU cc_start: 0.9295 (tp30) cc_final: 0.8978 (tp30) REVERT: B 657 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8316 (tm-30) outliers start: 4 outliers final: 0 residues processed: 201 average time/residue: 0.2961 time to fit residues: 86.6632 Evaluate side-chains 153 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 168 optimal weight: 30.0000 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 4.9990 chunk 170 optimal weight: 40.0000 chunk 180 optimal weight: 50.0000 chunk 89 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN A 195 ASN A 283 ASN ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 16073 Z= 0.281 Angle : 0.664 11.318 21863 Z= 0.340 Chirality : 0.047 0.298 2800 Planarity : 0.004 0.043 2670 Dihedral : 7.657 73.541 4041 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.33 % Allowed : 2.05 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.20), residues: 1659 helix: 0.26 (0.26), residues: 405 sheet: 0.19 (0.22), residues: 472 loop : -0.10 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 623 HIS 0.006 0.001 HIS A 249 PHE 0.022 0.002 PHE D 522 TYR 0.021 0.002 TYR B 643 ARG 0.005 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8901 (m-80) cc_final: 0.8171 (m-80) REVERT: C 150 MET cc_start: 0.8235 (mmm) cc_final: 0.7971 (mmp) REVERT: C 382 PHE cc_start: 0.8839 (m-80) cc_final: 0.8569 (m-80) REVERT: C 425 ASN cc_start: 0.8834 (t0) cc_final: 0.8527 (t0) REVERT: C 475 MET cc_start: 0.8940 (mmp) cc_final: 0.8695 (mmm) REVERT: C 478 ASN cc_start: 0.9033 (m110) cc_final: 0.8806 (m110) REVERT: D 574 LYS cc_start: 0.9188 (pttp) cc_final: 0.8837 (pttp) REVERT: D 626 MET cc_start: 0.8319 (mtp) cc_final: 0.7821 (mtp) REVERT: E 95 MET cc_start: 0.9036 (ptm) cc_final: 0.7732 (ppp) REVERT: E 161 MET cc_start: 0.8261 (tpp) cc_final: 0.7874 (tpt) REVERT: E 195 ASN cc_start: 0.8263 (t0) cc_final: 0.7943 (t0) REVERT: E 368 ASP cc_start: 0.8633 (p0) cc_final: 0.8417 (p0) REVERT: E 432 GLN cc_start: 0.7930 (pm20) cc_final: 0.7692 (pm20) REVERT: F 599 SER cc_start: 0.9324 (p) cc_final: 0.9032 (m) REVERT: A 125 LEU cc_start: 0.9499 (mp) cc_final: 0.9158 (mt) REVERT: A 150 MET cc_start: 0.9231 (mmm) cc_final: 0.8934 (mpp) REVERT: A 161 MET cc_start: 0.9178 (tpp) cc_final: 0.8831 (tpp) REVERT: A 217 TYR cc_start: 0.8715 (m-10) cc_final: 0.8203 (m-10) REVERT: A 368 ASP cc_start: 0.8299 (p0) cc_final: 0.8041 (p0) REVERT: B 584 GLU cc_start: 0.9366 (mt-10) cc_final: 0.9020 (tm-30) REVERT: B 601 LYS cc_start: 0.9399 (pttm) cc_final: 0.9018 (ptpp) REVERT: B 625 ASN cc_start: 0.8995 (m-40) cc_final: 0.8313 (m110) REVERT: B 626 MET cc_start: 0.7879 (tpp) cc_final: 0.7479 (mmm) REVERT: B 630 GLN cc_start: 0.9218 (mt0) cc_final: 0.8684 (mt0) REVERT: B 654 GLU cc_start: 0.9284 (tp30) cc_final: 0.9043 (tp30) REVERT: B 657 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8400 (tm-30) outliers start: 5 outliers final: 2 residues processed: 199 average time/residue: 0.2692 time to fit residues: 80.0866 Evaluate side-chains 164 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 150 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 0.0770 chunk 45 optimal weight: 10.0000 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN D 575 GLN D 585 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS B 651 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 16073 Z= 0.304 Angle : 0.677 15.623 21863 Z= 0.343 Chirality : 0.047 0.336 2800 Planarity : 0.004 0.046 2670 Dihedral : 7.460 69.385 4041 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.07 % Allowed : 2.71 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.20), residues: 1659 helix: 0.18 (0.26), residues: 405 sheet: 0.22 (0.23), residues: 441 loop : -0.28 (0.22), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 623 HIS 0.007 0.001 HIS D 585 PHE 0.020 0.002 PHE D 522 TYR 0.043 0.002 TYR C 217 ARG 0.006 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 203 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8934 (m-80) cc_final: 0.8147 (m-80) REVERT: C 104 MET cc_start: 0.8870 (mmp) cc_final: 0.8556 (mmp) REVERT: C 150 MET cc_start: 0.8259 (mmm) cc_final: 0.7968 (mmp) REVERT: C 425 ASN cc_start: 0.8945 (t0) cc_final: 0.8601 (t0) REVERT: C 443 ILE cc_start: 0.9032 (tp) cc_final: 0.8779 (tt) REVERT: C 478 ASN cc_start: 0.9162 (m110) cc_final: 0.8902 (m110) REVERT: D 574 LYS cc_start: 0.9161 (pttp) cc_final: 0.8884 (pttp) REVERT: D 626 MET cc_start: 0.8387 (mtp) cc_final: 0.8165 (mtp) REVERT: E 95 MET cc_start: 0.9039 (ptm) cc_final: 0.7811 (ppp) REVERT: E 161 MET cc_start: 0.8402 (tpp) cc_final: 0.8050 (tpp) REVERT: E 195 ASN cc_start: 0.8249 (t0) cc_final: 0.7914 (t0) REVERT: E 368 ASP cc_start: 0.8615 (p0) cc_final: 0.8343 (p0) REVERT: E 452 LEU cc_start: 0.9438 (mp) cc_final: 0.8962 (tp) REVERT: F 599 SER cc_start: 0.9345 (p) cc_final: 0.9050 (m) REVERT: A 125 LEU cc_start: 0.9491 (mp) cc_final: 0.9157 (mt) REVERT: A 150 MET cc_start: 0.9271 (mmm) cc_final: 0.9018 (mpp) REVERT: A 161 MET cc_start: 0.9229 (tpp) cc_final: 0.8881 (tpp) REVERT: A 166 ARG cc_start: 0.8587 (ttm110) cc_final: 0.8324 (ttm110) REVERT: B 584 GLU cc_start: 0.9358 (mt-10) cc_final: 0.8973 (tm-30) REVERT: B 601 LYS cc_start: 0.9362 (pttm) cc_final: 0.9017 (ptpp) outliers start: 1 outliers final: 0 residues processed: 203 average time/residue: 0.2795 time to fit residues: 84.3886 Evaluate side-chains 147 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 60 optimal weight: 2.9990 chunk 162 optimal weight: 0.0040 chunk 35 optimal weight: 8.9990 chunk 106 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 180 optimal weight: 50.0000 chunk 150 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 overall best weight: 4.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 16073 Z= 0.372 Angle : 0.727 12.096 21863 Z= 0.367 Chirality : 0.048 0.284 2800 Planarity : 0.004 0.049 2670 Dihedral : 7.650 66.090 4041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.07 % Allowed : 1.65 % Favored : 98.28 % 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: -0.28 (0.20), residues: 1659 helix: 0.09 (0.26), residues: 411 sheet: 0.15 (0.24), residues: 443 loop : -0.41 (0.22), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 631 HIS 0.006 0.001 HIS A 85 PHE 0.017 0.002 PHE D 522 TYR 0.033 0.002 TYR C 217 ARG 0.007 0.001 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 195 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8971 (m-80) cc_final: 0.8131 (m-80) REVERT: C 104 MET cc_start: 0.8839 (mmp) cc_final: 0.8638 (mmp) REVERT: C 425 ASN cc_start: 0.8866 (t0) cc_final: 0.8506 (t0) REVERT: C 443 ILE cc_start: 0.8974 (tp) cc_final: 0.8736 (tt) REVERT: D 574 LYS cc_start: 0.9223 (pttp) cc_final: 0.8923 (pttp) REVERT: D 626 MET cc_start: 0.8333 (mtp) cc_final: 0.8058 (mtp) REVERT: E 161 MET cc_start: 0.8607 (tpp) cc_final: 0.8149 (tpp) REVERT: E 195 ASN cc_start: 0.8322 (t0) cc_final: 0.7993 (t0) REVERT: E 368 ASP cc_start: 0.8684 (p0) cc_final: 0.8410 (p0) REVERT: E 434 MET cc_start: 0.9072 (ptm) cc_final: 0.8868 (ptt) REVERT: E 475 MET cc_start: 0.9291 (mmm) cc_final: 0.9039 (mmm) REVERT: F 599 SER cc_start: 0.9349 (p) cc_final: 0.9069 (m) REVERT: F 626 MET cc_start: 0.8092 (tpp) cc_final: 0.7641 (tpp) REVERT: F 632 ASP cc_start: 0.8788 (p0) cc_final: 0.8497 (p0) REVERT: A 150 MET cc_start: 0.9302 (mmm) cc_final: 0.9049 (mpp) REVERT: A 161 MET cc_start: 0.9190 (tpp) cc_final: 0.8838 (tpp) REVERT: A 166 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8377 (ttm110) REVERT: B 584 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8997 (tm-30) REVERT: B 601 LYS cc_start: 0.9375 (pttm) cc_final: 0.9082 (ptpp) REVERT: B 626 MET cc_start: 0.8094 (tpt) cc_final: 0.5642 (tmm) REVERT: B 635 ILE cc_start: 0.9236 (pt) cc_final: 0.8935 (pt) outliers start: 1 outliers final: 1 residues processed: 196 average time/residue: 0.2800 time to fit residues: 81.2746 Evaluate side-chains 140 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 174 optimal weight: 30.0000 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 180 optimal weight: 50.0000 chunk 112 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 591 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16073 Z= 0.301 Angle : 0.698 18.825 21863 Z= 0.353 Chirality : 0.048 0.315 2800 Planarity : 0.004 0.045 2670 Dihedral : 7.438 63.949 4041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % 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: -0.26 (0.20), residues: 1659 helix: 0.19 (0.26), residues: 405 sheet: 0.15 (0.24), residues: 444 loop : -0.43 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 112 HIS 0.011 0.001 HIS C 249 PHE 0.013 0.002 PHE D 522 TYR 0.026 0.002 TYR B 643 ARG 0.005 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9019 (m-80) cc_final: 0.8157 (m-80) REVERT: C 201 ILE cc_start: 0.9464 (mt) cc_final: 0.9218 (mt) REVERT: C 425 ASN cc_start: 0.8838 (t0) cc_final: 0.8501 (t0) REVERT: C 443 ILE cc_start: 0.8836 (tp) cc_final: 0.8619 (tt) REVERT: E 195 ASN cc_start: 0.8243 (t0) cc_final: 0.7937 (t0) REVERT: E 452 LEU cc_start: 0.9351 (mp) cc_final: 0.9000 (tp) REVERT: E 475 MET cc_start: 0.9247 (mmm) cc_final: 0.8982 (mmm) REVERT: F 626 MET cc_start: 0.8071 (tpp) cc_final: 0.7590 (tpp) REVERT: F 648 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8869 (tm-30) REVERT: A 150 MET cc_start: 0.9303 (mmm) cc_final: 0.9051 (mpp) REVERT: A 166 ARG cc_start: 0.8611 (ttm110) cc_final: 0.8132 (ttm110) REVERT: B 584 GLU cc_start: 0.9400 (mt-10) cc_final: 0.8964 (tm-30) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.2772 time to fit residues: 81.6588 Evaluate side-chains 151 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 122 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16073 Z= 0.232 Angle : 0.648 16.589 21863 Z= 0.331 Chirality : 0.047 0.280 2800 Planarity : 0.003 0.042 2670 Dihedral : 7.109 61.835 4041 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % 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: -0.13 (0.21), residues: 1659 helix: 0.27 (0.26), residues: 407 sheet: 0.17 (0.23), residues: 464 loop : -0.31 (0.23), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 631 HIS 0.005 0.001 HIS C 249 PHE 0.015 0.001 PHE C 53 TYR 0.035 0.001 TYR C 217 ARG 0.004 0.000 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9005 (m-80) cc_final: 0.8145 (m-80) REVERT: C 104 MET cc_start: 0.8990 (mmp) cc_final: 0.8661 (mmp) REVERT: C 425 ASN cc_start: 0.8784 (t0) cc_final: 0.8350 (t0) REVERT: C 443 ILE cc_start: 0.8800 (tp) cc_final: 0.8577 (tt) REVERT: D 542 ARG cc_start: 0.8734 (ptp-170) cc_final: 0.8415 (ptt-90) REVERT: D 545 LEU cc_start: 0.8266 (tp) cc_final: 0.8045 (tp) REVERT: E 95 MET cc_start: 0.9108 (ptm) cc_final: 0.8793 (ppp) REVERT: E 161 MET cc_start: 0.8600 (tpp) cc_final: 0.8184 (tpt) REVERT: E 195 ASN cc_start: 0.8103 (t0) cc_final: 0.7796 (t0) REVERT: E 452 LEU cc_start: 0.9343 (mp) cc_final: 0.9023 (tp) REVERT: E 475 MET cc_start: 0.9170 (mmm) cc_final: 0.8938 (mmm) REVERT: E 478 ASN cc_start: 0.9022 (m-40) cc_final: 0.8566 (t0) REVERT: A 104 MET cc_start: 0.8500 (tpp) cc_final: 0.8248 (tpt) REVERT: A 112 TRP cc_start: 0.8847 (t-100) cc_final: 0.8546 (t-100) REVERT: A 150 MET cc_start: 0.9282 (mmm) cc_final: 0.9039 (mpp) REVERT: A 166 ARG cc_start: 0.8617 (ttm110) cc_final: 0.8130 (ttm110) REVERT: B 584 GLU cc_start: 0.9416 (mt-10) cc_final: 0.8988 (tm-30) REVERT: B 626 MET cc_start: 0.7559 (tpp) cc_final: 0.7269 (tpt) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2687 time to fit residues: 84.5378 Evaluate side-chains 150 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 163 optimal weight: 5.9990 chunk 172 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 101 optimal weight: 8.9990 chunk 73 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 110 optimal weight: 7.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 577 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 585 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 16073 Z= 0.288 Angle : 0.676 16.230 21863 Z= 0.344 Chirality : 0.048 0.281 2800 Planarity : 0.004 0.044 2670 Dihedral : 7.190 60.469 4041 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -0.20 (0.21), residues: 1659 helix: 0.19 (0.26), residues: 401 sheet: 0.18 (0.23), residues: 467 loop : -0.37 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 631 HIS 0.008 0.001 HIS A 216 PHE 0.018 0.002 PHE C 53 TYR 0.035 0.002 TYR C 217 ARG 0.005 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9015 (m-80) cc_final: 0.8161 (m-80) REVERT: C 104 MET cc_start: 0.8870 (mmp) cc_final: 0.8663 (mmp) REVERT: C 425 ASN cc_start: 0.8780 (t0) cc_final: 0.8407 (t0) REVERT: C 443 ILE cc_start: 0.8792 (tp) cc_final: 0.8569 (tt) REVERT: D 626 MET cc_start: 0.7914 (mtp) cc_final: 0.7587 (mtp) REVERT: E 95 MET cc_start: 0.9091 (ptm) cc_final: 0.8809 (ppp) REVERT: E 104 MET cc_start: 0.8389 (tmm) cc_final: 0.7941 (tmm) REVERT: E 452 LEU cc_start: 0.9347 (mp) cc_final: 0.9007 (tp) REVERT: E 478 ASN cc_start: 0.9078 (m-40) cc_final: 0.8631 (t0) REVERT: E 479 TRP cc_start: 0.8916 (m-10) cc_final: 0.8563 (m-10) REVERT: F 626 MET cc_start: 0.7786 (tpp) cc_final: 0.7503 (tpp) REVERT: A 150 MET cc_start: 0.9282 (mmm) cc_final: 0.9060 (mpp) REVERT: A 166 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8360 (ttm110) REVERT: B 584 GLU cc_start: 0.9419 (mt-10) cc_final: 0.8976 (tm-30) REVERT: B 625 ASN cc_start: 0.8247 (m-40) cc_final: 0.8018 (m-40) REVERT: B 626 MET cc_start: 0.7317 (tpp) cc_final: 0.7001 (tpt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2755 time to fit residues: 80.5216 Evaluate side-chains 142 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 177 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 84 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 186 optimal weight: 40.0000 chunk 171 optimal weight: 40.0000 chunk 148 optimal weight: 0.9980 chunk 15 optimal weight: 7.9990 chunk 114 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN ** C 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 577 GLN D 591 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 ASN ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 550 GLN ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16073 Z= 0.248 Angle : 0.647 15.954 21863 Z= 0.331 Chirality : 0.047 0.278 2800 Planarity : 0.004 0.043 2670 Dihedral : 6.972 57.940 4041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.14 (0.21), residues: 1659 helix: 0.21 (0.26), residues: 403 sheet: 0.16 (0.23), residues: 464 loop : -0.28 (0.23), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 631 HIS 0.005 0.001 HIS C 249 PHE 0.012 0.001 PHE D 522 TYR 0.037 0.001 TYR C 217 ARG 0.005 0.000 ARG D 588 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3318 Ramachandran restraints generated. 1659 Oldfield, 0 Emsley, 1659 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.9035 (m-80) cc_final: 0.8185 (m-80) REVERT: C 104 MET cc_start: 0.8782 (mmp) cc_final: 0.8046 (mmt) REVERT: C 425 ASN cc_start: 0.8813 (t0) cc_final: 0.8471 (t0) REVERT: E 95 MET cc_start: 0.9052 (ptm) cc_final: 0.8771 (ppp) REVERT: E 104 MET cc_start: 0.8259 (tmm) cc_final: 0.7937 (tmm) REVERT: E 150 MET cc_start: 0.8436 (mpp) cc_final: 0.8229 (mpp) REVERT: E 195 ASN cc_start: 0.8248 (t0) cc_final: 0.7942 (t0) REVERT: E 217 TYR cc_start: 0.8757 (m-80) cc_final: 0.8466 (m-10) REVERT: E 452 LEU cc_start: 0.9318 (mp) cc_final: 0.8913 (tp) REVERT: E 478 ASN cc_start: 0.9055 (m-40) cc_final: 0.8614 (t0) REVERT: E 479 TRP cc_start: 0.8844 (m-10) cc_final: 0.8560 (m-10) REVERT: F 535 MET cc_start: 0.8429 (mmm) cc_final: 0.8065 (mpp) REVERT: F 626 MET cc_start: 0.7718 (tpp) cc_final: 0.7483 (tpp) REVERT: A 112 TRP cc_start: 0.8848 (t-100) cc_final: 0.8393 (t-100) REVERT: A 150 MET cc_start: 0.9271 (mmm) cc_final: 0.9050 (mpp) REVERT: A 166 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8362 (ttm110) REVERT: A 210 PHE cc_start: 0.8698 (m-10) cc_final: 0.8480 (m-10) REVERT: A 217 TYR cc_start: 0.8201 (m-10) cc_final: 0.7608 (m-10) REVERT: B 584 GLU cc_start: 0.9375 (mt-10) cc_final: 0.8924 (tm-30) REVERT: B 601 LYS cc_start: 0.9033 (pttm) cc_final: 0.8776 (pttt) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.2755 time to fit residues: 80.3336 Evaluate side-chains 151 residues out of total 1513 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 0.0770 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN C 425 ASN D 575 GLN D 577 GLN ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.060838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047155 restraints weight = 76250.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.048591 restraints weight = 44337.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049566 restraints weight = 31228.742| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16073 Z= 0.243 Angle : 0.638 15.907 21863 Z= 0.327 Chirality : 0.047 0.277 2800 Planarity : 0.004 0.043 2670 Dihedral : 6.901 56.216 4041 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % 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: -0.09 (0.21), residues: 1659 helix: 0.27 (0.26), residues: 402 sheet: 0.22 (0.23), residues: 457 loop : -0.28 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 596 HIS 0.007 0.001 HIS A 249 PHE 0.013 0.001 PHE C 53 TYR 0.017 0.001 TYR A 217 ARG 0.004 0.000 ARG C 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2924.51 seconds wall clock time: 53 minutes 44.80 seconds (3224.80 seconds total)