Starting phenix.real_space_refine on Wed Mar 20 16:37:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymz_33948/03_2024/7ymz_33948.pdb" } resolution = 4.39 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= -0.005 sd= 0.116 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 153 5.16 5 C 17670 2.51 5 N 4515 2.21 5 O 5553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1039": "OE1" <-> "OE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 27891 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "B" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 Chain: "C" Number of atoms: 9020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1166, 9020 Classifications: {'peptide': 1166} Link IDs: {'PTRANS': 57, 'TRANS': 1108} Chain breaks: 5 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: 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 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: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 15.02, per 1000 atoms: 0.54 Number of scatterers: 27891 At special positions: 0 Unit cell: (152.9, 146.3, 160.6, 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 153 16.00 O 5553 8.00 N 4515 7.00 C 17670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 383 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 425 " - pdb=" SG CYS A 478 " distance=2.03 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 585 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.03 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.03 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.03 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=2.03 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.03 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.03 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 30 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 176 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 185 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 383 " - pdb=" SG CYS B 407 " distance=2.03 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.03 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 585 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 654 " distance=2.03 Simple disulfide: pdb=" SG CYS B 620 " - pdb=" SG CYS B 650 " distance=2.03 Simple disulfide: pdb=" SG CYS B 679 " - pdb=" SG CYS B 713 " distance=2.03 Simple disulfide: pdb=" SG CYS B 727 " - pdb=" SG CYS B 736 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.03 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.03 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1106 " - pdb=" SG CYS B1117 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 383 " - pdb=" SG CYS C 407 " distance=2.03 Simple disulfide: pdb=" SG CYS C 425 " - pdb=" SG CYS C 478 " distance=2.03 Simple disulfide: pdb=" SG CYS C 437 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 526 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.03 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.03 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.03 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 806 " - pdb=" SG CYS C 828 " distance=2.03 Simple disulfide: pdb=" SG CYS C 811 " - pdb=" SG CYS C 817 " distance=2.03 Simple disulfide: pdb=" SG CYS C 912 " - pdb=" SG CYS C 925 " distance=2.03 Simple disulfide: pdb=" SG CYS C1106 " - pdb=" SG CYS C1117 " distance=2.03 Simple disulfide: pdb=" SG CYS C1156 " - pdb=" SG CYS C1164 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA M 3 " - " MAN M 4 " " BMA R 3 " - " MAN R 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA M 3 " - " MAN M 5 " " BMA R 3 " - " MAN R 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 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 U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG H 1 " - " FUC H 2 " " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " " NAG S 1 " - " FUC S 2 " " NAG T 1 " - " FUC T 2 " NAG-ASN " NAG A1401 " - " ASN A 166 " " NAG A1402 " - " ASN A 236 " " NAG A1403 " - " ASN A 244 " " NAG A1404 " - " ASN A 785 " " NAG B1401 " - " ASN B 166 " " NAG B1402 " - " ASN B 785 " " NAG B1403 " - " ASN B 236 " " NAG B1404 " - " ASN B 244 " " NAG C1401 " - " ASN C 244 " " NAG C1402 " - " ASN C 785 " " NAG C1403 " - " ASN C 236 " " NAG C1404 " - " ASN C 166 " " NAG D 1 " - " ASN A 66 " " NAG E 1 " - " ASN A 125 " " NAG F 1 " - " ASN A 222 " " NAG G 1 " - " ASN A 619 " " NAG H 1 " - " ASN A 719 " " NAG I 1 " - " ASN A 870 " " NAG J 1 " - " ASN A1213 " " NAG K 1 " - " ASN B 719 " " NAG L 1 " - " ASN B 870 " " NAG M 1 " - " ASN B 125 " " NAG N 1 " - " ASN B1213 " " NAG O 1 " - " ASN B 619 " " NAG P 1 " - " ASN B 222 " " NAG Q 1 " - " ASN B 66 " " NAG R 1 " - " ASN C 125 " " NAG S 1 " - " ASN C 619 " " NAG T 1 " - " ASN C 719 " " NAG U 1 " - " ASN C 222 " " NAG V 1 " - " ASN C 870 " " NAG W 1 " - " ASN C 66 " " NAG X 1 " - " ASN C1213 " Time building additional restraints: 11.62 Conformation dependent library (CDL) restraints added in 5.3 seconds 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6510 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 56 sheets defined 25.4% alpha, 21.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.79 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.462A pdb=" N SER A 106 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.810A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 395 through 399 removed outlier: 4.258A pdb=" N PHE A 399 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 429 through 436 removed outlier: 4.238A pdb=" N ILE A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ALA A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 435 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 removed outlier: 3.675A pdb=" N SER A 457 " --> pdb=" O SER A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 546 through 550 Processing helix chain 'A' and resid 805 through 812 Processing helix chain 'A' and resid 814 through 822 removed outlier: 3.607A pdb=" N GLU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 853 Processing helix chain 'A' and resid 871 through 875 Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 915 Processing helix chain 'A' and resid 924 through 929 removed outlier: 3.938A pdb=" N GLN A 927 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N VAL A 929 " --> pdb=" O ALA A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 956 removed outlier: 3.823A pdb=" N ALA A 956 " --> pdb=" O LEU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 982 removed outlier: 3.566A pdb=" N SER A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1010 removed outlier: 3.680A pdb=" N ILE A 997 " --> pdb=" O ASN A 993 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A1008 " --> pdb=" O ALA A1004 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN A1009 " --> pdb=" O LEU A1005 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A1010 " --> pdb=" O GLY A1006 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1039 removed outlier: 3.539A pdb=" N LEU A1033 " --> pdb=" O ASN A1029 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1106 removed outlier: 4.116A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.791A pdb=" N PHE B 40 " --> pdb=" O GLN B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 Processing helix chain 'B' and resid 104 through 108 removed outlier: 3.520A pdb=" N GLN B 107 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 214 Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.837A pdb=" N TYR B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.877A pdb=" N LEU B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.880A pdb=" N PHE B 399 " --> pdb=" O VAL B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 418 Processing helix chain 'B' and resid 452 through 457 removed outlier: 3.864A pdb=" N SER B 457 " --> pdb=" O SER B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 524 through 529 Processing helix chain 'B' and resid 546 through 550 Processing helix chain 'B' and resid 805 through 812 Processing helix chain 'B' and resid 814 through 820 Processing helix chain 'B' and resid 825 through 853 removed outlier: 4.379A pdb=" N SER B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 875 Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 940 through 959 removed outlier: 3.576A pdb=" N GLU B 944 " --> pdb=" O ASP B 940 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA B 956 " --> pdb=" O LEU B 952 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLY B 957 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLY B 959 " --> pdb=" O ILE B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 removed outlier: 3.903A pdb=" N LEU B 990 " --> pdb=" O THR B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1008 removed outlier: 3.560A pdb=" N ILE B 997 " --> pdb=" O ASN B 993 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET B1008 " --> pdb=" O ALA B1004 " (cutoff:3.500A) Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.780A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1106 removed outlier: 3.581A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.741A pdb=" N PHE C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 4.602A pdb=" N SER C 106 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 223 Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.725A pdb=" N TYR C 231 " --> pdb=" O SER C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 303 through 307 removed outlier: 3.577A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 Processing helix chain 'C' and resid 395 through 399 removed outlier: 3.789A pdb=" N PHE C 399 " --> pdb=" O VAL C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 414 Processing helix chain 'C' and resid 430 through 436 removed outlier: 4.339A pdb=" N ALA C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 removed outlier: 4.145A pdb=" N SER C 457 " --> pdb=" O SER C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'C' and resid 524 through 529 removed outlier: 3.610A pdb=" N ILE C 529 " --> pdb=" O CYS C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 550 Processing helix chain 'C' and resid 805 through 812 Processing helix chain 'C' and resid 814 through 823 removed outlier: 4.155A pdb=" N GLU C 823 " --> pdb=" O GLN C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 854 Processing helix chain 'C' and resid 871 through 875 Processing helix chain 'C' and resid 888 through 898 Processing helix chain 'C' and resid 908 through 915 Processing helix chain 'C' and resid 925 through 930 removed outlier: 4.141A pdb=" N ALA C 930 " --> pdb=" O ALA C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 940 through 958 removed outlier: 4.116A pdb=" N ALA C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY C 957 " --> pdb=" O GLY C 953 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 984 removed outlier: 3.769A pdb=" N GLY C 984 " --> pdb=" O LEU C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 993 removed outlier: 3.814A pdb=" N LEU C 990 " --> pdb=" O THR C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1011 removed outlier: 4.300A pdb=" N MET C1008 " --> pdb=" O ALA C1004 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLN C1009 " --> pdb=" O LEU C1005 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR C1010 " --> pdb=" O GLY C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1016 through 1040 removed outlier: 3.863A pdb=" N LEU C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU C1040 " --> pdb=" O LEU C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1050 through 1058 Processing helix chain 'C' and resid 1059 through 1106 removed outlier: 4.325A pdb=" N ALA C1065 " --> pdb=" O PRO C1061 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 75 removed outlier: 4.514A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.676A pdb=" N TYR A 85 " --> pdb=" O PHE A 313 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 93 removed outlier: 3.573A pdb=" N THR A 93 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR A 96 " --> pdb=" O THR A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 110 through 111 removed outlier: 3.650A pdb=" N LYS A 110 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 293 " --> pdb=" O LYS A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 206 through 208 removed outlier: 5.853A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 removed outlier: 4.252A pdb=" N THR A 669 " --> pdb=" O ASP A 664 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.940A pdb=" N VAL A 374 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N VAL A 631 " --> pdb=" O VAL A 639 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 400 through 404 removed outlier: 6.655A pdb=" N THR A 483 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL A 420 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 513 through 515 removed outlier: 5.094A pdb=" N SER A 498 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 561 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILE A 500 " --> pdb=" O SER A 559 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 559 " --> pdb=" O ILE A 500 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 504 " --> pdb=" O VAL A 555 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 723 through 724 removed outlier: 6.808A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 769 removed outlier: 6.024A pdb=" N ILE A 768 " --> pdb=" O SER B 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 778 through 782 removed outlier: 4.466A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 795 removed outlier: 6.669A pdb=" N GLY A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN A1129 " --> pdb=" O GLY A1133 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR A1135 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N VAL A1127 " --> pdb=" O TYR A1135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N MET A1137 " --> pdb=" O SER A1125 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A1125 " --> pdb=" O MET A1137 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1139 " --> pdb=" O ILE A1123 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A1121 " --> pdb=" O TYR A1141 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AB8, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AB9, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 5.955A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 67 through 75 removed outlier: 4.444A pdb=" N ARG B 335 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 92 through 93 Processing sheet with id=AC3, first strand: chain 'B' and resid 110 through 111 removed outlier: 4.509A pdb=" N ALA B 146 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 280 through 284 removed outlier: 4.817A pdb=" N GLN B 280 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N SER B 267 " --> pdb=" O GLN B 280 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 127 through 129 Processing sheet with id=AC6, first strand: chain 'B' and resid 154 through 155 removed outlier: 5.482A pdb=" N GLY B 154 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 362 removed outlier: 3.931A pdb=" N THR B 669 " --> pdb=" O ASP B 664 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 373 through 374 removed outlier: 6.642A pdb=" N VAL B 374 " --> pdb=" O SER B 607 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 639 " --> pdb=" O LEU B 651 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL B 631 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N PHE B 630 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 400 through 404 removed outlier: 6.654A pdb=" N THR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N VAL B 420 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 408 through 409 Processing sheet with id=AD2, first strand: chain 'B' and resid 513 through 515 removed outlier: 6.911A pdb=" N SER B 557 " --> pdb=" O ASN B 501 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N CYS B 503 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL B 555 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG B 505 " --> pdb=" O TRP B 553 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TRP B 553 " --> pdb=" O ARG B 505 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 723 through 724 removed outlier: 3.740A pdb=" N GLY B 732 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ALA B 737 " --> pdb=" O PRO B 730 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 768 through 769 removed outlier: 6.417A pdb=" N ILE B 768 " --> pdb=" O SER C 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 778 through 782 Processing sheet with id=AD6, first strand: chain 'B' and resid 785 through 796 removed outlier: 5.803A pdb=" N TYR B1141 " --> pdb=" O HIS B1122 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N HIS B1122 " --> pdb=" O TYR B1141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 802 through 803 Processing sheet with id=AD8, first strand: chain 'B' and resid 1155 through 1157 Processing sheet with id=AD9, first strand: chain 'B' and resid 1165 through 1167 Processing sheet with id=AE1, first strand: chain 'B' and resid 1173 through 1174 Processing sheet with id=AE2, first strand: chain 'C' and resid 68 through 75 removed outlier: 4.400A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 92 through 93 removed outlier: 3.903A pdb=" N THR C 93 " --> pdb=" O THR C 96 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR C 96 " --> pdb=" O THR C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.774A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 279 through 284 removed outlier: 5.555A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 119 " --> pdb=" O TYR C 314 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR C 314 " --> pdb=" O ARG C 119 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 127 through 129 removed outlier: 3.605A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 153 through 155 Processing sheet with id=AE8, first strand: chain 'C' and resid 359 through 362 removed outlier: 4.198A pdb=" N THR C 669 " --> pdb=" O ASP C 664 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 373 through 374 removed outlier: 6.875A pdb=" N VAL C 374 " --> pdb=" O SER C 607 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 400 through 404 removed outlier: 6.988A pdb=" N THR C 477 " --> pdb=" O CYS C 425 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N CYS C 425 " --> pdb=" O THR C 477 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N LEU C 479 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N PHE C 423 " --> pdb=" O LEU C 479 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU C 481 " --> pdb=" O ASN C 421 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AF3, first strand: chain 'C' and resid 513 through 515 removed outlier: 5.031A pdb=" N SER C 498 " --> pdb=" O VAL C 561 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 561 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 500 " --> pdb=" O SER C 559 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N SER C 559 " --> pdb=" O ILE C 500 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TRP C 553 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 617 through 618 removed outlier: 4.481A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL C 631 " --> pdb=" O VAL C 639 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 717 through 718 removed outlier: 6.336A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 717 through 718 removed outlier: 6.336A pdb=" N VAL C 718 " --> pdb=" O LEU C 759 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N SER C 761 " --> pdb=" O VAL C 718 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 758 " --> pdb=" O LEU C 738 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY C 732 " --> pdb=" O LEU C 735 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ALA C 737 " --> pdb=" O PRO C 730 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 778 through 782 Processing sheet with id=AF8, first strand: chain 'C' and resid 785 through 796 removed outlier: 6.697A pdb=" N GLY C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASN C1129 " --> pdb=" O GLY C1133 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR C1135 " --> pdb=" O VAL C1127 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL C1127 " --> pdb=" O TYR C1135 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET C1137 " --> pdb=" O SER C1125 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER C1125 " --> pdb=" O MET C1137 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C1139 " --> pdb=" O ILE C1123 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 802 through 804 Processing sheet with id=AG1, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.810A pdb=" N CYS C1164 " --> pdb=" O VAL C1205 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS C1156 " --> pdb=" O ILE C1214 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1170 through 1174 removed outlier: 4.504A pdb=" N GLY C1188 " --> pdb=" O ALA C1193 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ALA C1193 " --> pdb=" O GLY C1188 " (cutoff:3.500A) 1021 hydrogen bonds defined for protein. 2712 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: 12.87 Time building geometry restraints manager: 12.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 4515 1.30 - 1.44: 8044 1.44 - 1.57: 15757 1.57 - 1.71: 1 1.71 - 1.84: 204 Bond restraints: 28521 Sorted by residual: bond pdb=" CA GLU C 252 " pdb=" C GLU C 252 " ideal model delta sigma weight residual 1.521 1.442 0.079 1.17e-02 7.31e+03 4.60e+01 bond pdb=" CA PHE A1019 " pdb=" C PHE A1019 " ideal model delta sigma weight residual 1.523 1.437 0.086 1.35e-02 5.49e+03 4.02e+01 bond pdb=" CA SER A 106 " pdb=" C SER A 106 " ideal model delta sigma weight residual 1.525 1.439 0.086 1.37e-02 5.33e+03 3.93e+01 bond pdb=" C GLU C 252 " pdb=" O GLU C 252 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.14e-02 7.69e+03 3.90e+01 bond pdb=" CA VAL A1022 " pdb=" C VAL A1022 " ideal model delta sigma weight residual 1.524 1.449 0.075 1.23e-02 6.61e+03 3.74e+01 ... (remaining 28516 not shown) Histogram of bond angle deviations from ideal: 96.86 - 104.32: 439 104.32 - 111.78: 13099 111.78 - 119.24: 9923 119.24 - 126.70: 15055 126.70 - 134.16: 286 Bond angle restraints: 38802 Sorted by residual: angle pdb=" N VAL A1022 " pdb=" CA VAL A1022 " pdb=" C VAL A1022 " ideal model delta sigma weight residual 110.53 102.38 8.15 9.40e-01 1.13e+00 7.51e+01 angle pdb=" N ARG B 235 " pdb=" CA ARG B 235 " pdb=" C ARG B 235 " ideal model delta sigma weight residual 108.34 118.52 -10.18 1.31e+00 5.83e-01 6.04e+01 angle pdb=" N PHE A1019 " pdb=" CA PHE A1019 " pdb=" C PHE A1019 " ideal model delta sigma weight residual 111.82 103.30 8.52 1.16e+00 7.43e-01 5.39e+01 angle pdb=" N PHE B 399 " pdb=" CA PHE B 399 " pdb=" C PHE B 399 " ideal model delta sigma weight residual 108.67 118.58 -9.91 1.55e+00 4.16e-01 4.09e+01 angle pdb=" N LEU B 234 " pdb=" CA LEU B 234 " pdb=" C LEU B 234 " ideal model delta sigma weight residual 108.90 118.77 -9.87 1.63e+00 3.76e-01 3.67e+01 ... (remaining 38797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.22: 16719 25.22 - 50.44: 870 50.44 - 75.66: 132 75.66 - 100.88: 65 100.88 - 126.10: 25 Dihedral angle restraints: 17811 sinusoidal: 7620 harmonic: 10191 Sorted by residual: dihedral pdb=" CB CYS B 811 " pdb=" SG CYS B 811 " pdb=" SG CYS B 817 " pdb=" CB CYS B 817 " ideal model delta sinusoidal sigma weight residual -86.00 -167.74 81.74 1 1.00e+01 1.00e-02 8.22e+01 dihedral pdb=" CB CYS C1106 " pdb=" SG CYS C1106 " pdb=" SG CYS C1117 " pdb=" CB CYS C1117 " ideal model delta sinusoidal sigma weight residual 93.00 168.11 -75.11 1 1.00e+01 1.00e-02 7.13e+01 dihedral pdb=" CB CYS C 811 " pdb=" SG CYS C 811 " pdb=" SG CYS C 817 " pdb=" CB CYS C 817 " ideal model delta sinusoidal sigma weight residual -86.00 -160.07 74.07 1 1.00e+01 1.00e-02 6.96e+01 ... (remaining 17808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 4439 0.148 - 0.296: 77 0.296 - 0.444: 8 0.444 - 0.592: 1 0.592 - 0.740: 2 Chirality restraints: 4527 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 125 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.66 -0.74 2.00e-01 2.50e+01 1.37e+01 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN B 222 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.15e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 222 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4524 not shown) Planarity restraints: 4977 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 222 " 0.037 2.00e-02 2.50e+03 3.44e-02 1.48e+01 pdb=" CG ASN A 222 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN A 222 " -0.000 2.00e-02 2.50e+03 pdb=" ND2 ASN A 222 " -0.042 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 221 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG A 221 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG A 221 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN A 222 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 397 " 0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C TYR B 397 " -0.057 2.00e-02 2.50e+03 pdb=" O TYR B 397 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN B 398 " 0.019 2.00e-02 2.50e+03 ... (remaining 4974 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2199 2.74 - 3.28: 27685 3.28 - 3.82: 48607 3.82 - 4.36: 53735 4.36 - 4.90: 90464 Nonbonded interactions: 222690 Sorted by model distance: nonbonded pdb=" OD1 ASN B 421 " pdb=" OG1 THR B 483 " model vdw 2.199 2.440 nonbonded pdb=" O PHE C 399 " pdb=" OH TYR C 523 " model vdw 2.199 2.440 nonbonded pdb=" OH TYR C 824 " pdb=" OD1 ASP C1068 " model vdw 2.231 2.440 nonbonded pdb=" OG SER C 268 " pdb=" O ASP C 272 " model vdw 2.240 2.440 nonbonded pdb=" OG SER A 268 " pdb=" O ASP A 272 " model vdw 2.250 2.440 ... (remaining 222685 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'U' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'W' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 5.040 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 75.490 Find NCS groups from input model: 1.800 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.005 0.086 28521 Z= 0.325 Angle : 0.892 14.162 38802 Z= 0.467 Chirality : 0.059 0.740 4527 Planarity : 0.006 0.079 4944 Dihedral : 16.428 126.102 11157 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.41 % Favored : 93.39 % Rotamer: Outliers : 0.70 % Allowed : 0.63 % Favored : 98.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3462 helix: -0.08 (0.19), residues: 691 sheet: -0.34 (0.19), residues: 702 loop : -1.47 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 253 HIS 0.010 0.001 HIS B 681 PHE 0.038 0.002 PHE A 254 TYR 0.027 0.002 TYR C 71 ARG 0.007 0.000 ARG B 505 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 3.475 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: A 161 MET cc_start: 0.7812 (mmt) cc_final: 0.7574 (mmm) REVERT: A 296 ILE cc_start: 0.8920 (mp) cc_final: 0.8675 (mp) REVERT: A 452 MET cc_start: 0.7393 (pmm) cc_final: 0.7040 (pmm) REVERT: A 563 MET cc_start: 0.8976 (tpt) cc_final: 0.8697 (tpt) REVERT: A 696 MET cc_start: 0.8322 (tpt) cc_final: 0.7892 (mmt) REVERT: B 147 PHE cc_start: 0.8700 (m-80) cc_final: 0.8290 (m-10) REVERT: B 292 TYR cc_start: 0.8951 (m-80) cc_final: 0.8666 (m-80) REVERT: B 452 MET cc_start: 0.7381 (pmm) cc_final: 0.7084 (pmm) REVERT: B 563 MET cc_start: 0.7506 (mmt) cc_final: 0.7218 (mmt) REVERT: B 569 MET cc_start: 0.8714 (pmm) cc_final: 0.7620 (pmm) REVERT: B 686 MET cc_start: 0.6909 (mmp) cc_final: 0.6578 (mmp) REVERT: B 906 MET cc_start: 0.8562 (mmp) cc_final: 0.8249 (pmm) REVERT: B 943 MET cc_start: 0.8615 (mmm) cc_final: 0.7443 (mmm) REVERT: C 563 MET cc_start: 0.8439 (tpt) cc_final: 0.7956 (tpt) REVERT: C 635 TYR cc_start: 0.9109 (m-10) cc_final: 0.8901 (m-10) REVERT: C 695 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.8879 (p) REVERT: C 696 MET cc_start: 0.8225 (tpt) cc_final: 0.7934 (tpt) REVERT: C 757 MET cc_start: 0.8512 (tpt) cc_final: 0.8151 (tpp) outliers start: 21 outliers final: 4 residues processed: 144 average time/residue: 0.3844 time to fit residues: 91.8278 Evaluate side-chains 91 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 2.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 8.9990 chunk 263 optimal weight: 20.0000 chunk 146 optimal weight: 30.0000 chunk 90 optimal weight: 40.0000 chunk 177 optimal weight: 10.0000 chunk 140 optimal weight: 20.0000 chunk 272 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 chunk 165 optimal weight: 7.9990 chunk 203 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 167 HIS ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 796 GLN A 907 GLN A 974 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN B 839 ASN ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 ASN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 HIS C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 ASN C 522 GLN ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 28521 Z= 0.275 Angle : 0.654 11.590 38802 Z= 0.338 Chirality : 0.044 0.521 4527 Planarity : 0.005 0.122 4944 Dihedral : 10.923 118.365 5067 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.86 % Favored : 94.02 % Rotamer: Outliers : 0.10 % Allowed : 4.95 % Favored : 94.95 % 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: -0.90 (0.14), residues: 3462 helix: 0.91 (0.20), residues: 704 sheet: -0.43 (0.19), residues: 693 loop : -1.23 (0.14), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 960 HIS 0.005 0.001 HIS B 670 PHE 0.014 0.002 PHE B 239 TYR 0.018 0.002 TYR B 438 ARG 0.026 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 3.185 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: A 161 MET cc_start: 0.7895 (mmt) cc_final: 0.7665 (mmm) REVERT: A 287 TYR cc_start: 0.6575 (t80) cc_final: 0.6309 (t80) REVERT: A 296 ILE cc_start: 0.9149 (mp) cc_final: 0.8900 (mp) REVERT: A 696 MET cc_start: 0.8479 (tpt) cc_final: 0.8106 (mmt) REVERT: B 147 PHE cc_start: 0.8724 (m-80) cc_final: 0.8330 (m-10) REVERT: B 292 TYR cc_start: 0.9153 (m-80) cc_final: 0.8797 (m-80) REVERT: B 563 MET cc_start: 0.7920 (mmt) cc_final: 0.7623 (mmm) REVERT: B 696 MET cc_start: 0.8669 (mmp) cc_final: 0.8063 (mmp) REVERT: B 906 MET cc_start: 0.8486 (mmp) cc_final: 0.8008 (pmm) REVERT: B 913 MET cc_start: 0.9446 (mtm) cc_final: 0.9054 (mtp) REVERT: B 943 MET cc_start: 0.8514 (mmm) cc_final: 0.8301 (mmm) REVERT: C 84 MET cc_start: 0.8355 (tpt) cc_final: 0.7913 (tpt) REVERT: C 563 MET cc_start: 0.8827 (tpt) cc_final: 0.8368 (tpt) REVERT: C 757 MET cc_start: 0.8788 (tpt) cc_final: 0.8295 (tpp) REVERT: C 906 MET cc_start: 0.8630 (tpt) cc_final: 0.7829 (tmm) outliers start: 3 outliers final: 0 residues processed: 96 average time/residue: 0.4382 time to fit residues: 71.2790 Evaluate side-chains 75 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 30.0000 chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 342 optimal weight: 20.0000 chunk 281 optimal weight: 30.0000 chunk 313 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 253 optimal weight: 0.0980 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN A 796 GLN A 974 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 471 GLN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.081 28521 Z= 0.158 Angle : 0.562 7.896 38802 Z= 0.285 Chirality : 0.044 0.490 4527 Planarity : 0.004 0.136 4944 Dihedral : 9.805 117.549 5067 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 0.07 % Allowed : 3.19 % Favored : 96.74 % 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: -0.69 (0.14), residues: 3462 helix: 1.18 (0.20), residues: 707 sheet: -0.23 (0.19), residues: 663 loop : -1.15 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 44 HIS 0.003 0.001 HIS A 264 PHE 0.037 0.001 PHE A 972 TYR 0.021 0.001 TYR B 689 ARG 0.011 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 3.372 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: A 161 MET cc_start: 0.7894 (mmt) cc_final: 0.7662 (mmm) REVERT: A 296 ILE cc_start: 0.9137 (mp) cc_final: 0.8843 (mp) REVERT: A 696 MET cc_start: 0.8519 (tpt) cc_final: 0.8133 (mmt) REVERT: A 757 MET cc_start: 0.6886 (tpp) cc_final: 0.6528 (tpp) REVERT: A 906 MET cc_start: 0.7205 (mmm) cc_final: 0.6950 (mmm) REVERT: A 939 MET cc_start: 0.8057 (ttp) cc_final: 0.7806 (tmm) REVERT: B 147 PHE cc_start: 0.8756 (m-80) cc_final: 0.8435 (m-10) REVERT: B 292 TYR cc_start: 0.9092 (m-80) cc_final: 0.8758 (m-80) REVERT: B 563 MET cc_start: 0.7866 (mmt) cc_final: 0.7464 (mmt) REVERT: B 569 MET cc_start: 0.9084 (pmm) cc_final: 0.7786 (pmm) REVERT: B 696 MET cc_start: 0.8591 (mmp) cc_final: 0.8016 (mmp) REVERT: B 906 MET cc_start: 0.8367 (mmp) cc_final: 0.7998 (pmm) REVERT: B 913 MET cc_start: 0.9486 (mtm) cc_final: 0.9162 (mtp) REVERT: C 84 MET cc_start: 0.8172 (tpt) cc_final: 0.7935 (tpt) REVERT: C 563 MET cc_start: 0.8823 (tpt) cc_final: 0.8379 (tpt) REVERT: C 757 MET cc_start: 0.8675 (tpt) cc_final: 0.8236 (tpp) REVERT: C 906 MET cc_start: 0.8552 (tpt) cc_final: 0.7782 (tmm) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.3806 time to fit residues: 59.8322 Evaluate side-chains 78 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 20.0000 chunk 238 optimal weight: 30.0000 chunk 164 optimal weight: 50.0000 chunk 35 optimal weight: 30.0000 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 0.0370 chunk 317 optimal weight: 20.0000 chunk 336 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 301 optimal weight: 30.0000 chunk 90 optimal weight: 30.0000 overall best weight: 12.8072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 280 GLN ** A 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 GLN A 832 ASN ** A1104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 599 GLN B 647 ASN B 808 GLN B 832 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 ASN C 522 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 HIS C 733 GLN C 848 ASN C 981 ASN C1028 ASN ** C1097 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1119 GLN C1129 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 28521 Z= 0.418 Angle : 0.797 11.114 38802 Z= 0.413 Chirality : 0.046 0.435 4527 Planarity : 0.005 0.079 4944 Dihedral : 9.596 117.408 5067 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 32.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3462 helix: 0.72 (0.19), residues: 704 sheet: -0.90 (0.19), residues: 686 loop : -1.27 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 44 HIS 0.012 0.002 HIS A 264 PHE 0.028 0.003 PHE B1172 TYR 0.027 0.003 TYR B1171 ARG 0.021 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8089 (mmt) cc_final: 0.7838 (mmm) REVERT: A 296 ILE cc_start: 0.9268 (mp) cc_final: 0.9003 (mp) REVERT: A 696 MET cc_start: 0.8374 (tpt) cc_final: 0.8092 (mmt) REVERT: A 906 MET cc_start: 0.7484 (mmm) cc_final: 0.7219 (mmm) REVERT: A 939 MET cc_start: 0.8055 (ttp) cc_final: 0.7246 (ttm) REVERT: B 147 PHE cc_start: 0.8778 (m-80) cc_final: 0.8345 (m-10) REVERT: B 278 MET cc_start: 0.7217 (tpt) cc_final: 0.6885 (tpt) REVERT: B 292 TYR cc_start: 0.9250 (m-80) cc_final: 0.8927 (m-80) REVERT: B 563 MET cc_start: 0.8475 (mmt) cc_final: 0.8086 (mmt) REVERT: B 696 MET cc_start: 0.8529 (mmp) cc_final: 0.7983 (mmp) REVERT: B 906 MET cc_start: 0.8629 (mmp) cc_final: 0.8115 (pmm) REVERT: B 913 MET cc_start: 0.9539 (mtm) cc_final: 0.9187 (mtp) REVERT: B 939 MET cc_start: 0.8246 (ttp) cc_final: 0.7698 (ttt) REVERT: C 563 MET cc_start: 0.9262 (tpt) cc_final: 0.8927 (tpp) REVERT: C 757 MET cc_start: 0.8952 (tpt) cc_final: 0.8443 (tpp) REVERT: C 906 MET cc_start: 0.8939 (tpt) cc_final: 0.8212 (tmm) outliers start: 2 outliers final: 1 residues processed: 82 average time/residue: 0.3841 time to fit residues: 54.1996 Evaluate side-chains 69 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 30.0000 chunk 190 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 250 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 287 optimal weight: 8.9990 chunk 232 optimal weight: 30.0000 chunk 0 optimal weight: 40.0000 chunk 171 optimal weight: 20.0000 chunk 301 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN A1104 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 GLN C 226 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28521 Z= 0.261 Angle : 0.641 11.391 38802 Z= 0.328 Chirality : 0.044 0.397 4527 Planarity : 0.005 0.108 4944 Dihedral : 9.317 117.108 5067 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3462 helix: 0.94 (0.20), residues: 714 sheet: -0.82 (0.19), residues: 696 loop : -1.28 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 310 HIS 0.007 0.001 HIS A 264 PHE 0.044 0.002 PHE B 164 TYR 0.038 0.002 TYR C 314 ARG 0.017 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 3.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8008 (mmt) cc_final: 0.7750 (mmm) REVERT: A 296 ILE cc_start: 0.9224 (mp) cc_final: 0.8987 (mp) REVERT: A 757 MET cc_start: 0.6967 (tpp) cc_final: 0.6740 (tpp) REVERT: A 906 MET cc_start: 0.7540 (mmm) cc_final: 0.7302 (mmm) REVERT: A 939 MET cc_start: 0.7936 (ttp) cc_final: 0.7349 (ttt) REVERT: A 943 MET cc_start: 0.8618 (tpt) cc_final: 0.8169 (tpp) REVERT: B 84 MET cc_start: 0.8102 (mmp) cc_final: 0.7790 (mmp) REVERT: B 147 PHE cc_start: 0.8729 (m-80) cc_final: 0.8465 (m-10) REVERT: B 292 TYR cc_start: 0.9102 (m-80) cc_final: 0.8846 (m-80) REVERT: B 563 MET cc_start: 0.8490 (mmt) cc_final: 0.8092 (mmt) REVERT: B 569 MET cc_start: 0.9162 (pmm) cc_final: 0.7908 (pmm) REVERT: B 686 MET cc_start: 0.7539 (mmp) cc_final: 0.7177 (mmp) REVERT: B 696 MET cc_start: 0.8629 (mmp) cc_final: 0.8104 (mmp) REVERT: B 906 MET cc_start: 0.8513 (mmp) cc_final: 0.8051 (pmm) REVERT: B 913 MET cc_start: 0.9576 (mtm) cc_final: 0.9244 (mtp) REVERT: B 943 MET cc_start: 0.8555 (tpt) cc_final: 0.8063 (tpt) REVERT: C 278 MET cc_start: 0.6858 (mmp) cc_final: 0.6462 (mmp) REVERT: C 757 MET cc_start: 0.9006 (tpt) cc_final: 0.8452 (tpp) REVERT: C 906 MET cc_start: 0.8828 (tpt) cc_final: 0.8174 (tmm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.3901 time to fit residues: 52.8629 Evaluate side-chains 69 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 20.0000 chunk 302 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 336 optimal weight: 20.0000 chunk 279 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 27 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 176 optimal weight: 20.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28521 Z= 0.207 Angle : 0.604 10.317 38802 Z= 0.306 Chirality : 0.044 0.479 4527 Planarity : 0.004 0.094 4944 Dihedral : 8.797 110.287 5067 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % 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: -0.88 (0.14), residues: 3462 helix: 1.16 (0.20), residues: 715 sheet: -0.72 (0.19), residues: 691 loop : -1.20 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 310 HIS 0.005 0.001 HIS A 264 PHE 0.028 0.001 PHE B 164 TYR 0.026 0.002 TYR C 184 ARG 0.016 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 3.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8070 (mmt) cc_final: 0.7817 (mmm) REVERT: A 296 ILE cc_start: 0.9188 (mp) cc_final: 0.8966 (mp) REVERT: A 939 MET cc_start: 0.7975 (ttp) cc_final: 0.7341 (ttt) REVERT: A 943 MET cc_start: 0.8694 (tpt) cc_final: 0.8248 (tpp) REVERT: B 148 MET cc_start: 0.9355 (tmm) cc_final: 0.9113 (ppp) REVERT: B 278 MET cc_start: 0.7187 (tpt) cc_final: 0.6743 (tpt) REVERT: B 292 TYR cc_start: 0.9124 (m-80) cc_final: 0.8853 (m-80) REVERT: B 563 MET cc_start: 0.8394 (mmt) cc_final: 0.7996 (mmt) REVERT: B 569 MET cc_start: 0.9134 (pmm) cc_final: 0.7835 (pmm) REVERT: B 696 MET cc_start: 0.8582 (mmp) cc_final: 0.8047 (mmp) REVERT: B 906 MET cc_start: 0.8512 (mmp) cc_final: 0.8018 (pmm) REVERT: B 913 MET cc_start: 0.9590 (mtm) cc_final: 0.9270 (mtp) REVERT: B 943 MET cc_start: 0.8527 (tpt) cc_final: 0.7967 (tpp) REVERT: C 278 MET cc_start: 0.6888 (mmp) cc_final: 0.6554 (mmp) REVERT: C 757 MET cc_start: 0.8984 (tpt) cc_final: 0.8467 (tpp) REVERT: C 906 MET cc_start: 0.8763 (tpt) cc_final: 0.8203 (tmm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.3859 time to fit residues: 52.9910 Evaluate side-chains 69 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 191 optimal weight: 30.0000 chunk 245 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 283 optimal weight: 0.0030 chunk 188 optimal weight: 20.0000 chunk 335 optimal weight: 9.9990 chunk 209 optimal weight: 0.0010 chunk 204 optimal weight: 9.9990 chunk 154 optimal weight: 50.0000 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 167 HIS A 466 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 522 GLN ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 28521 Z= 0.223 Angle : 0.606 10.631 38802 Z= 0.308 Chirality : 0.044 0.448 4527 Planarity : 0.004 0.052 4944 Dihedral : 8.630 111.629 5067 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % 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: -0.81 (0.14), residues: 3462 helix: 1.30 (0.20), residues: 714 sheet: -0.75 (0.19), residues: 691 loop : -1.15 (0.14), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 310 HIS 0.005 0.001 HIS A 264 PHE 0.026 0.002 PHE B 164 TYR 0.025 0.002 TYR C 184 ARG 0.010 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 3.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8105 (mmt) cc_final: 0.7856 (mmm) REVERT: A 296 ILE cc_start: 0.9113 (mp) cc_final: 0.8904 (mp) REVERT: A 696 MET cc_start: 0.7842 (mmt) cc_final: 0.7380 (mmm) REVERT: A 939 MET cc_start: 0.7829 (ttp) cc_final: 0.7404 (ttt) REVERT: A 943 MET cc_start: 0.8667 (tpt) cc_final: 0.8302 (tpp) REVERT: B 147 PHE cc_start: 0.8865 (m-80) cc_final: 0.8653 (m-10) REVERT: B 292 TYR cc_start: 0.9132 (m-80) cc_final: 0.8869 (m-80) REVERT: B 563 MET cc_start: 0.8320 (mmt) cc_final: 0.7899 (mmt) REVERT: B 696 MET cc_start: 0.8586 (mmp) cc_final: 0.8053 (mmp) REVERT: B 906 MET cc_start: 0.8586 (mmp) cc_final: 0.8033 (pmm) REVERT: B 913 MET cc_start: 0.9590 (mtm) cc_final: 0.9185 (mtp) REVERT: B 943 MET cc_start: 0.8501 (tpt) cc_final: 0.8077 (tpt) REVERT: C 278 MET cc_start: 0.6961 (mmp) cc_final: 0.6622 (mmp) REVERT: C 757 MET cc_start: 0.8989 (tpt) cc_final: 0.8484 (tpp) REVERT: C 906 MET cc_start: 0.8691 (tpt) cc_final: 0.8189 (tmm) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3768 time to fit residues: 50.5959 Evaluate side-chains 69 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 0.9980 chunk 133 optimal weight: 5.9990 chunk 200 optimal weight: 40.0000 chunk 101 optimal weight: 1.9990 chunk 65 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 228 optimal weight: 8.9990 chunk 165 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 263 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28521 Z= 0.180 Angle : 0.587 9.464 38802 Z= 0.296 Chirality : 0.044 0.456 4527 Planarity : 0.004 0.096 4944 Dihedral : 8.274 106.756 5067 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.71 (0.14), residues: 3462 helix: 1.49 (0.20), residues: 698 sheet: -0.62 (0.19), residues: 684 loop : -1.14 (0.14), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 310 HIS 0.003 0.001 HIS A 670 PHE 0.034 0.001 PHE A 467 TYR 0.019 0.001 TYR B 609 ARG 0.012 0.000 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8176 (mmt) cc_final: 0.7913 (mmm) REVERT: A 696 MET cc_start: 0.7866 (mmt) cc_final: 0.7450 (mmm) REVERT: A 939 MET cc_start: 0.7795 (ttp) cc_final: 0.7383 (ttt) REVERT: A 943 MET cc_start: 0.8649 (tpt) cc_final: 0.8270 (tpp) REVERT: B 147 PHE cc_start: 0.8887 (m-80) cc_final: 0.8641 (m-10) REVERT: B 292 TYR cc_start: 0.9145 (m-80) cc_final: 0.8883 (m-80) REVERT: B 563 MET cc_start: 0.8323 (mmt) cc_final: 0.7925 (mmt) REVERT: B 569 MET cc_start: 0.9063 (pmm) cc_final: 0.7781 (pmm) REVERT: B 696 MET cc_start: 0.8553 (mmp) cc_final: 0.8016 (mmp) REVERT: B 906 MET cc_start: 0.8570 (mmp) cc_final: 0.8005 (pmm) REVERT: B 913 MET cc_start: 0.9593 (mtm) cc_final: 0.9220 (mtp) REVERT: B 943 MET cc_start: 0.8450 (tpt) cc_final: 0.8156 (tpt) REVERT: C 169 LEU cc_start: 0.9507 (mt) cc_final: 0.9299 (mt) REVERT: C 278 MET cc_start: 0.6845 (mmp) cc_final: 0.6536 (mmp) REVERT: C 757 MET cc_start: 0.8914 (tpt) cc_final: 0.8446 (tpp) REVERT: C 906 MET cc_start: 0.8704 (tpt) cc_final: 0.8237 (tmm) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3793 time to fit residues: 50.9474 Evaluate side-chains 66 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 6.9990 chunk 321 optimal weight: 5.9990 chunk 293 optimal weight: 20.0000 chunk 312 optimal weight: 20.0000 chunk 188 optimal weight: 30.0000 chunk 136 optimal weight: 7.9990 chunk 245 optimal weight: 40.0000 chunk 95 optimal weight: 30.0000 chunk 282 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 28521 Z= 0.280 Angle : 0.652 11.252 38802 Z= 0.333 Chirality : 0.044 0.455 4527 Planarity : 0.004 0.078 4944 Dihedral : 8.154 103.564 5067 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 26.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.68 % Favored : 92.29 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.81 (0.14), residues: 3462 helix: 1.37 (0.20), residues: 705 sheet: -0.69 (0.19), residues: 650 loop : -1.18 (0.14), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 310 HIS 0.007 0.002 HIS C 681 PHE 0.032 0.002 PHE A 467 TYR 0.021 0.002 TYR C 184 ARG 0.012 0.001 ARG B 841 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8150 (mmt) cc_final: 0.7914 (mmm) REVERT: A 696 MET cc_start: 0.7943 (mmt) cc_final: 0.7569 (mmm) REVERT: A 939 MET cc_start: 0.7855 (ttp) cc_final: 0.7346 (ttm) REVERT: A 943 MET cc_start: 0.8717 (tpt) cc_final: 0.8440 (tpp) REVERT: B 84 MET cc_start: 0.8120 (mmp) cc_final: 0.7759 (mmp) REVERT: B 147 PHE cc_start: 0.8888 (m-80) cc_final: 0.8602 (m-10) REVERT: B 292 TYR cc_start: 0.9152 (m-80) cc_final: 0.8898 (m-80) REVERT: B 563 MET cc_start: 0.8426 (mmt) cc_final: 0.7972 (mmt) REVERT: B 569 MET cc_start: 0.9073 (pmm) cc_final: 0.7722 (pmm) REVERT: B 696 MET cc_start: 0.8621 (mmp) cc_final: 0.8079 (mmp) REVERT: B 913 MET cc_start: 0.9606 (mtm) cc_final: 0.9266 (mtp) REVERT: B 943 MET cc_start: 0.8396 (tpt) cc_final: 0.7796 (tpp) REVERT: C 278 MET cc_start: 0.7021 (mmp) cc_final: 0.6682 (mmp) REVERT: C 757 MET cc_start: 0.8992 (tpt) cc_final: 0.8475 (tpp) REVERT: C 906 MET cc_start: 0.8766 (tpt) cc_final: 0.8285 (tmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.3536 time to fit residues: 46.7243 Evaluate side-chains 66 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 66 time to evaluate : 3.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 201 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 346 optimal weight: 8.9990 chunk 319 optimal weight: 30.0000 chunk 276 optimal weight: 20.0000 chunk 28 optimal weight: 30.0000 chunk 213 optimal weight: 10.0000 chunk 169 optimal weight: 50.0000 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B 842 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1028 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1031 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 28521 Z= 0.274 Angle : 0.651 13.768 38802 Z= 0.332 Chirality : 0.044 0.445 4527 Planarity : 0.004 0.054 4944 Dihedral : 8.121 101.245 5067 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 26.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.60 % Favored : 92.37 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3462 helix: 1.20 (0.20), residues: 706 sheet: -0.71 (0.20), residues: 625 loop : -1.27 (0.13), residues: 2131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 310 HIS 0.006 0.001 HIS A 298 PHE 0.026 0.002 PHE A 467 TYR 0.022 0.002 TYR C 184 ARG 0.011 0.001 ARG B 841 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6924 Ramachandran restraints generated. 3462 Oldfield, 0 Emsley, 3462 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.8203 (mmt) cc_final: 0.7969 (mmm) REVERT: A 169 LEU cc_start: 0.9441 (tp) cc_final: 0.9214 (tt) REVERT: A 696 MET cc_start: 0.7915 (mmt) cc_final: 0.7545 (mmm) REVERT: A 939 MET cc_start: 0.7831 (ttp) cc_final: 0.7335 (ttm) REVERT: A 943 MET cc_start: 0.8688 (tpt) cc_final: 0.8324 (tpp) REVERT: B 84 MET cc_start: 0.8241 (mmp) cc_final: 0.7939 (mmp) REVERT: B 147 PHE cc_start: 0.8887 (m-80) cc_final: 0.8611 (m-10) REVERT: B 563 MET cc_start: 0.8455 (mmt) cc_final: 0.7960 (mmt) REVERT: B 569 MET cc_start: 0.9092 (pmm) cc_final: 0.7764 (pmm) REVERT: B 696 MET cc_start: 0.8679 (mmp) cc_final: 0.8145 (mmp) REVERT: B 906 MET cc_start: 0.8509 (mmp) cc_final: 0.7941 (pmm) REVERT: B 913 MET cc_start: 0.9610 (mtm) cc_final: 0.9307 (mtp) REVERT: B 943 MET cc_start: 0.8387 (tpt) cc_final: 0.7847 (tpp) REVERT: C 278 MET cc_start: 0.7025 (mmp) cc_final: 0.6674 (mmp) REVERT: C 757 MET cc_start: 0.8970 (tpt) cc_final: 0.8494 (tpp) REVERT: C 906 MET cc_start: 0.8762 (tpt) cc_final: 0.8305 (tmm) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3902 time to fit residues: 48.6572 Evaluate side-chains 64 residues out of total 3009 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 3.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 283 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 50 optimal weight: 40.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 GLN ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 796 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 GLN ** A1029 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 ASN ** B1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1009 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 599 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1063 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.026772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2539 r_free = 0.2539 target = 0.019803 restraints weight = 556295.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.019932 restraints weight = 371318.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2569 r_free = 0.2569 target = 0.020236 restraints weight = 277517.192| |-----------------------------------------------------------------------------| r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.4252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28521 Z= 0.208 Angle : 0.604 11.903 38802 Z= 0.305 Chirality : 0.044 0.450 4527 Planarity : 0.004 0.052 4944 Dihedral : 7.839 100.731 5067 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.22 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -0.79 (0.14), residues: 3462 helix: 1.42 (0.20), residues: 706 sheet: -0.62 (0.20), residues: 629 loop : -1.21 (0.14), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 310 HIS 0.004 0.001 HIS A 298 PHE 0.028 0.002 PHE A 467 TYR 0.019 0.002 TYR C 184 ARG 0.007 0.000 ARG B 841 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.30 seconds wall clock time: 70 minutes 51.80 seconds (4251.80 seconds total)