Starting phenix.real_space_refine on Sat Mar 16 23:58:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/03_2024/7l8s_23235_updated.pdb" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 105 5.16 5 C 9978 2.51 5 N 2694 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 560": "OE1" <-> "OE2" Residue "A PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16057 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3482 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 4 Chain: "D" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1027 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "E" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3487 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 4 Chain: "F" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "A" Number of atoms: 3517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3517 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "B" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1036 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 1, 'TRANS': 127} Chain breaks: 1 Chain: "H" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 560 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'TRANS': 111} Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'UNK:plan-1': 112} Unresolved non-hydrogen planarities: 112 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" 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: "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: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "D" Number of atoms: 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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "F" Number of atoms: 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.59, per 1000 atoms: 0.53 Number of scatterers: 16057 At special positions: 0 Unit cell: (128.75, 126.69, 144.2, 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 105 16.00 O 3280 8.00 N 2694 7.00 C 9978 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.04 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS D 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.06 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 74 " - pdb=" SG CYS F 561 " distance=2.07 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.05 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.16 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.02 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.19 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA R 3 " - " MAN R 4 " " BMA Z 3 " - " MAN Z 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA R 3 " - " MAN R 5 " " BMA Z 3 " - " MAN Z 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A 601 " - " ASN A 276 " " NAG A 602 " - " ASN A 386 " " NAG A 603 " - " ASN A 363 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 289 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 355 " " NAG A 608 " - " ASN A 392 " " NAG A 609 " - " ASN A 137 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 601 " - " ASN C 276 " " NAG C 602 " - " ASN C 386 " " NAG C 603 " - " ASN C 363 " " NAG C 604 " - " ASN C 234 " " NAG C 605 " - " ASN C 133 " " NAG C 606 " - " ASN C 88 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 355 " " NAG C 610 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 611 " " NAG E 601 " - " ASN E 276 " " NAG E 602 " - " ASN E 386 " " NAG E 603 " - " ASN E 363 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 88 " " NAG E 608 " - " ASN E 241 " " NAG E 609 " - " ASN E 289 " " NAG E 610 " - " ASN E 339 " " NAG E 611 " - " ASN E 355 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 448 " " NAG J 1 " - " ASN C 160 " " NAG K 1 " - " ASN C 295 " " NAG M 1 " - " ASN C 197 " " NAG N 1 " - " ASN C 156 " " NAG O 1 " - " ASN C 301 " " NAG P 1 " - " ASN C 241 " " NAG Q 1 " - " ASN C 332 " " NAG R 1 " - " ASN E 262 " " NAG S 1 " - " ASN E 448 " " NAG T 1 " - " ASN E 160 " " NAG U 1 " - " ASN E 295 " " NAG V 1 " - " ASN E 197 " " NAG W 1 " - " ASN E 156 " " NAG X 1 " - " ASN E 332 " " NAG Y 1 " - " ASN E 392 " " NAG Z 1 " - " ASN A 262 " " NAG a 1 " - " ASN A 448 " " NAG b 1 " - " ASN A 160 " " NAG c 1 " - " ASN A 295 " " NAG d 1 " - " ASN A 197 " " NAG e 1 " - " ASN A 156 " " NAG f 1 " - " ASN A 301 " " NAG g 1 " - " ASN A 88 " " NAG h 1 " - " ASN A 241 " " NAG i 1 " - " ASN A 332 " " NAG j 1 " - " ASN A 133 " Time building additional restraints: 7.73 Conformation dependent library (CDL) restraints added in 2.2 seconds 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3640 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 34 sheets defined 27.7% alpha, 23.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'C' and resid 68 through 72 Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 99 through 117 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 151 through 153 No H-bonds generated for 'chain 'C' and resid 151 through 153' Processing helix chain 'C' and resid 178 through 180 No H-bonds generated for 'chain 'C' and resid 178 through 180' Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.822A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 No H-bonds generated for 'chain 'C' and resid 369 through 372' Processing helix chain 'C' and resid 378 through 380 No H-bonds generated for 'chain 'C' and resid 378 through 380' Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 475 through 482 removed outlier: 3.742A pdb=" N ARG C 480 " --> pdb=" O ASP C 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 524 through 527 removed outlier: 4.391A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 524 through 527' Processing helix chain 'D' and resid 532 through 544 removed outlier: 4.013A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N THR D 538 " --> pdb=" O MET D 535 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN D 543 " --> pdb=" O GLN D 540 " (cutoff:3.500A) Processing helix chain 'D' and resid 562 through 567 removed outlier: 5.162A pdb=" N LYS D 567 " --> pdb=" O GLN D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 595 Processing helix chain 'D' and resid 619 through 624 Processing helix chain 'D' and resid 628 through 635 removed outlier: 3.668A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 639 through 660 Processing helix chain 'E' and resid 68 through 71 No H-bonds generated for 'chain 'E' and resid 68 through 71' Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 99 through 117 Processing helix chain 'E' and resid 123 through 125 No H-bonds generated for 'chain 'E' and resid 123 through 125' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.974A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 372 No H-bonds generated for 'chain 'E' and resid 369 through 372' Processing helix chain 'E' and resid 388 through 390 No H-bonds generated for 'chain 'E' and resid 388 through 390' Processing helix chain 'E' and resid 475 through 482 removed outlier: 3.628A pdb=" N SER E 481 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 532 through 542 removed outlier: 4.015A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR F 538 " --> pdb=" O MET F 535 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA F 541 " --> pdb=" O THR F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 561 through 567 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 619 through 624 Processing helix chain 'F' and resid 628 through 634 Processing helix chain 'F' and resid 636 through 660 removed outlier: 5.383A pdb=" N GLN F 640 " --> pdb=" O ASN F 637 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 643 " --> pdb=" O GLN F 640 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER F 649 " --> pdb=" O LEU F 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 123 through 125 No H-bonds generated for 'chain 'A' and resid 123 through 125' Processing helix chain 'A' and resid 151 through 153 No H-bonds generated for 'chain 'A' and resid 151 through 153' Processing helix chain 'A' and resid 194 through 197 removed outlier: 4.455A pdb=" N ASN A 197 " --> pdb=" O ILE A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 335 through 353 removed outlier: 3.518A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 372 No H-bonds generated for 'chain 'A' and resid 369 through 372' Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 475 through 485 removed outlier: 3.816A pdb=" N ARG A 480 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS A 485 " --> pdb=" O GLU A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 527 removed outlier: 4.362A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 524 through 527' Processing helix chain 'B' and resid 537 through 544 removed outlier: 3.817A pdb=" N LEU B 544 " --> pdb=" O GLN B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 569 through 595 Processing helix chain 'B' and resid 619 through 625 Processing helix chain 'B' and resid 628 through 634 Processing helix chain 'B' and resid 639 through 661 Processing helix chain 'L' and resid 25 through 27 No H-bonds generated for 'chain 'L' and resid 25 through 27' Processing helix chain 'L' and resid 48 through 50 No H-bonds generated for 'chain 'L' and resid 48 through 50' Processing sheet with id= A, first strand: chain 'C' and resid 35 through 40 Processing sheet with id= B, first strand: chain 'C' and resid 45 through 47 Processing sheet with id= C, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= D, first strand: chain 'C' and resid 130 through 133 Processing sheet with id= E, first strand: chain 'C' and resid 181 through 183 Processing sheet with id= F, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.709A pdb=" N ALA C 433 " --> pdb=" O THR C 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.322A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ALA C 362 " --> pdb=" O PRO C 470 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 374 through 378 removed outlier: 4.215A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 301 through 303 removed outlier: 4.119A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 305 through 312 removed outlier: 6.499A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 35 through 40 Processing sheet with id= L, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.510A pdb=" N ILE E 225 " --> pdb=" O VAL E 245 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= N, first strand: chain 'E' and resid 91 through 94 Processing sheet with id= O, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.819A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.673A pdb=" N ALA E 433 " --> pdb=" O THR E 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 443 through 449 removed outlier: 7.410A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA E 329 " --> pdb=" O CYS E 418 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 301 through 303 removed outlier: 3.893A pdb=" N ASN E 301 " --> pdb=" O ILE E 323A" (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 358 through 362 Processing sheet with id= U, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.241A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 35 through 40 Processing sheet with id= W, first strand: chain 'A' and resid 45 through 47 Processing sheet with id= X, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= Y, first strand: chain 'A' and resid 91 through 93 Processing sheet with id= Z, first strand: chain 'A' and resid 130 through 133 Processing sheet with id= AA, first strand: chain 'A' and resid 181 through 183 Processing sheet with id= AB, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.599A pdb=" N ALA A 433 " --> pdb=" O THR A 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.302A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 374 through 378 removed outlier: 4.643A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'A' and resid 301 through 303 Processing sheet with id= AF, first strand: chain 'A' and resid 305 through 312 removed outlier: 6.816A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 82 through 86 removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N UNK L 36 " --> pdb=" O UNK L 45 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N UNK L 45 " --> pdb=" O UNK L 36 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 87 through 89 528 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 8.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 3908 1.33 - 1.46: 4881 1.46 - 1.60: 7381 1.60 - 1.74: 28 1.74 - 1.87: 131 Bond restraints: 16329 Sorted by residual: bond pdb=" CB LEU F 661 " pdb=" CG LEU F 661 " ideal model delta sigma weight residual 1.530 1.666 -0.136 2.00e-02 2.50e+03 4.64e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.412 0.085 1.40e-02 5.10e+03 3.65e+01 bond pdb=" CB HIS E 374 " pdb=" CG HIS E 374 " ideal model delta sigma weight residual 1.497 1.413 0.084 1.40e-02 5.10e+03 3.59e+01 bond pdb=" CB LEU D 520 " pdb=" CG LEU D 520 " ideal model delta sigma weight residual 1.530 1.642 -0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" CB LEU B 520 " pdb=" CG LEU B 520 " ideal model delta sigma weight residual 1.530 1.630 -0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 16324 not shown) Histogram of bond angle deviations from ideal: 97.34 - 104.70: 240 104.70 - 112.07: 8251 112.07 - 119.43: 6188 119.43 - 126.79: 7275 126.79 - 134.15: 254 Bond angle restraints: 22208 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.07 -8.51 1.02e+00 9.61e-01 6.97e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.87 127.91 -8.04 1.04e+00 9.25e-01 5.98e+01 angle pdb=" C TYR C 319 " pdb=" N THR C 320 " pdb=" CA THR C 320 " ideal model delta sigma weight residual 120.63 133.02 -12.39 1.61e+00 3.86e-01 5.92e+01 angle pdb=" C VAL B 608 " pdb=" N PRO B 609 " pdb=" CA PRO B 609 " ideal model delta sigma weight residual 119.85 127.36 -7.51 1.01e+00 9.80e-01 5.53e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.04 -7.48 1.02e+00 9.61e-01 5.38e+01 ... (remaining 22203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 10823 21.39 - 42.77: 217 42.77 - 64.16: 62 64.16 - 85.55: 34 85.55 - 106.93: 20 Dihedral angle restraints: 11156 sinusoidal: 5568 harmonic: 5588 Sorted by residual: dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -141.52 55.52 1 1.00e+01 1.00e-02 4.16e+01 dihedral pdb=" CB CYS E 501 " pdb=" SG CYS E 501 " pdb=" SG CYS F 605 " pdb=" CB CYS F 605 " ideal model delta sinusoidal sigma weight residual 93.00 145.79 -52.79 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CA UNK H 11 " pdb=" C UNK H 11 " pdb=" N UNK H 12 " pdb=" CA UNK H 12 " ideal model delta harmonic sigma weight residual -180.00 -150.44 -29.56 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 11153 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1963 0.120 - 0.239: 527 0.239 - 0.359: 232 0.359 - 0.478: 120 0.478 - 0.598: 14 Chirality restraints: 2856 Sorted by residual: chirality pdb=" C1 NAG h 2 " pdb=" O4 NAG h 1 " pdb=" C2 NAG h 2 " pdb=" O5 NAG h 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.67 0.27 2.00e-02 2.50e+03 1.85e+02 chirality pdb=" C1 NAG j 2 " pdb=" O4 NAG j 1 " pdb=" C2 NAG j 2 " pdb=" O5 NAG j 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.56e+02 chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.38e+02 ... (remaining 2853 not shown) Planarity restraints: 2772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG f 2 " -0.349 2.00e-02 2.50e+03 3.00e-01 1.13e+03 pdb=" C7 NAG f 2 " 0.086 2.00e-02 2.50e+03 pdb=" C8 NAG f 2 " -0.134 2.00e-02 2.50e+03 pdb=" N2 NAG f 2 " 0.534 2.00e-02 2.50e+03 pdb=" O7 NAG f 2 " -0.137 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 701 " -0.346 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" C7 NAG B 701 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 701 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG B 701 " 0.530 2.00e-02 2.50e+03 pdb=" O7 NAG B 701 " -0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 2 " 0.328 2.00e-02 2.50e+03 2.79e-01 9.76e+02 pdb=" C7 NAG i 2 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG i 2 " 0.174 2.00e-02 2.50e+03 pdb=" N2 NAG i 2 " -0.490 2.00e-02 2.50e+03 pdb=" O7 NAG i 2 " 0.072 2.00e-02 2.50e+03 ... (remaining 2769 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3868 2.81 - 3.33: 15395 3.33 - 3.85: 26272 3.85 - 4.38: 31822 4.38 - 4.90: 48843 Nonbonded interactions: 126200 Sorted by model distance: nonbonded pdb=" O3 NAG b 2 " pdb=" O7 NAG b 2 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASN E 276 " pdb=" N ASN E 279 " model vdw 2.322 2.520 nonbonded pdb=" O HIS E 72 " pdb=" ND1 HIS E 72 " model vdw 2.351 2.520 nonbonded pdb=" N ASN A 425 " pdb=" O ASN A 425 " model vdw 2.379 2.496 nonbonded pdb=" N ILE C 213 " pdb=" O ILE C 213 " model vdw 2.405 2.496 ... (remaining 126195 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 186 or resid 189 through 397 or resid 411 throu \ gh 457 or resid 461 through 505 or resid 601 through 609)) selection = (chain 'C' and (resid 33 through 397 or resid 411 through 505 or resid 602 throu \ gh 610)) selection = (chain 'E' and (resid 33 through 457 or resid 461 through 505 or resid 601 throu \ gh 609)) } ncs_group { reference = (chain 'B' and (resid 520 through 661 or resid 702 through 703)) selection = chain 'D' selection = (chain 'F' and (resid 520 through 546 or resid 561 through 661 or resid 701 thro \ ugh 702)) } ncs_group { reference = chain 'G' selection = chain 'R' selection = chain 'Z' } ncs_group { reference = (chain 'H' and resid 15 through 114) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.840 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 45.130 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.136 16329 Z= 1.360 Angle : 1.741 12.391 22208 Z= 1.111 Chirality : 0.152 0.598 2856 Planarity : 0.014 0.300 2707 Dihedral : 11.451 106.935 7408 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.16 % 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: 1.27 (0.20), residues: 1673 helix: 0.66 (0.23), residues: 415 sheet: 0.99 (0.23), residues: 432 loop : 1.09 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.009 TRP F 571 HIS 0.011 0.003 HIS C 374 PHE 0.031 0.006 PHE C 383 TYR 0.054 0.009 TYR B 638 ARG 0.008 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 474 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8271 (m-80) cc_final: 0.8018 (m-80) REVERT: D 584 GLU cc_start: 0.9125 (mt-10) cc_final: 0.8865 (tm-30) REVERT: D 628 TRP cc_start: 0.7709 (m100) cc_final: 0.7455 (m100) REVERT: D 635 ILE cc_start: 0.9481 (pt) cc_final: 0.9281 (mp) REVERT: D 650 GLN cc_start: 0.8985 (tp40) cc_final: 0.8503 (tm-30) REVERT: D 654 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7563 (tm-30) REVERT: E 39 TYR cc_start: 0.8809 (m-80) cc_final: 0.8501 (m-80) REVERT: E 112 TRP cc_start: 0.8607 (t-100) cc_final: 0.8357 (t-100) REVERT: E 161 MET cc_start: 0.7460 (ppp) cc_final: 0.7028 (ppp) REVERT: E 210 PHE cc_start: 0.8605 (m-80) cc_final: 0.7653 (m-10) REVERT: E 309 ILE cc_start: 0.9394 (pt) cc_final: 0.9047 (tt) REVERT: A 100 MET cc_start: 0.8791 (mtm) cc_final: 0.8549 (mtm) REVERT: A 122 LEU cc_start: 0.9514 (mt) cc_final: 0.9234 (mm) REVERT: A 382 PHE cc_start: 0.9267 (m-80) cc_final: 0.9000 (m-10) REVERT: B 522 PHE cc_start: 0.8449 (t80) cc_final: 0.8171 (t80) REVERT: B 622 ILE cc_start: 0.8721 (mt) cc_final: 0.7796 (mt) REVERT: B 639 THR cc_start: 0.9277 (m) cc_final: 0.8655 (p) REVERT: B 662 GLU cc_start: 0.4533 (mt-10) cc_final: 0.4262 (mt-10) outliers start: 0 outliers final: 0 residues processed: 474 average time/residue: 0.3094 time to fit residues: 207.6905 Evaluate side-chains 217 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 159 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 651 ASN D 653 GLN D 658 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN E 422 GLN F 630 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 422 GLN B 575 GLN B 630 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16329 Z= 0.255 Angle : 0.747 10.595 22208 Z= 0.382 Chirality : 0.049 0.323 2856 Planarity : 0.004 0.033 2707 Dihedral : 9.215 84.119 4163 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.33 % Allowed : 2.15 % Favored : 97.53 % 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: 0.94 (0.20), residues: 1673 helix: 1.07 (0.25), residues: 405 sheet: 0.70 (0.23), residues: 458 loop : 0.51 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 479 HIS 0.006 0.001 HIS E 72 PHE 0.019 0.002 PHE E 53 TYR 0.032 0.002 TYR E 177 ARG 0.007 0.001 ARG F 542 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 303 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.7968 (m-80) cc_final: 0.7755 (m-80) REVERT: C 98 ASN cc_start: 0.9246 (t0) cc_final: 0.8915 (t0) REVERT: C 150 MET cc_start: 0.8472 (mmm) cc_final: 0.8145 (mmm) REVERT: C 195 ASN cc_start: 0.8714 (t0) cc_final: 0.8487 (t0) REVERT: D 530 MET cc_start: 0.8141 (mtp) cc_final: 0.7282 (mtp) REVERT: D 617 ARG cc_start: 0.8632 (ttm-80) cc_final: 0.8378 (mmp80) REVERT: D 654 GLU cc_start: 0.8394 (mt-10) cc_final: 0.7545 (tm-30) REVERT: E 85 HIS cc_start: 0.8053 (m90) cc_final: 0.7677 (m90) REVERT: E 112 TRP cc_start: 0.8555 (t-100) cc_final: 0.8343 (t-100) REVERT: E 161 MET cc_start: 0.7474 (ppp) cc_final: 0.6990 (ppp) REVERT: E 210 PHE cc_start: 0.8481 (m-80) cc_final: 0.7888 (m-10) REVERT: E 303 THR cc_start: 0.8484 (p) cc_final: 0.8131 (p) REVERT: E 492 GLU cc_start: 0.8874 (tt0) cc_final: 0.8332 (pm20) REVERT: F 576 LEU cc_start: 0.9562 (tp) cc_final: 0.9333 (tp) REVERT: F 603 ILE cc_start: 0.9474 (mt) cc_final: 0.9158 (mt) REVERT: F 648 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8867 (mm-30) REVERT: A 95 MET cc_start: 0.9080 (ptt) cc_final: 0.7936 (ppp) REVERT: A 109 ILE cc_start: 0.9490 (mt) cc_final: 0.9047 (tt) REVERT: A 122 LEU cc_start: 0.9475 (mt) cc_final: 0.9247 (mm) REVERT: A 382 PHE cc_start: 0.9187 (m-80) cc_final: 0.8852 (m-10) REVERT: B 568 ASP cc_start: 0.7912 (t0) cc_final: 0.7665 (t0) REVERT: B 592 LEU cc_start: 0.9750 (mt) cc_final: 0.9539 (mm) REVERT: B 596 TRP cc_start: 0.9121 (m-10) cc_final: 0.8577 (m-10) REVERT: B 622 ILE cc_start: 0.8668 (mt) cc_final: 0.8425 (mm) REVERT: B 662 GLU cc_start: 0.4182 (mt-10) cc_final: 0.3822 (mt-10) outliers start: 5 outliers final: 0 residues processed: 306 average time/residue: 0.2638 time to fit residues: 120.4121 Evaluate side-chains 195 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 95 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 171 optimal weight: 30.0000 chunk 185 optimal weight: 20.0000 chunk 153 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 137 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN D 577 GLN D 607 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 16329 Z= 0.452 Angle : 0.854 9.024 22208 Z= 0.424 Chirality : 0.049 0.258 2856 Planarity : 0.005 0.050 2707 Dihedral : 8.922 81.820 4163 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.07 % Allowed : 3.78 % Favored : 96.16 % 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: 0.29 (0.20), residues: 1673 helix: 0.86 (0.25), residues: 395 sheet: 0.25 (0.23), residues: 448 loop : -0.05 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP F 631 HIS 0.009 0.002 HIS A 216 PHE 0.029 0.003 PHE E 53 TYR 0.031 0.003 TYR F 638 ARG 0.006 0.001 ARG C 503 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8457 (m-80) cc_final: 0.8122 (m-80) REVERT: C 104 MET cc_start: 0.9141 (ttt) cc_final: 0.8872 (ttp) REVERT: C 195 ASN cc_start: 0.8757 (t0) cc_final: 0.8538 (t0) REVERT: D 584 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8929 (tm-30) REVERT: D 634 GLU cc_start: 0.9142 (mt-10) cc_final: 0.8852 (mt-10) REVERT: D 647 GLU cc_start: 0.9221 (pp20) cc_final: 0.8805 (pp20) REVERT: D 654 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7722 (tm-30) REVERT: E 85 HIS cc_start: 0.8265 (m90) cc_final: 0.7996 (m90) REVERT: E 210 PHE cc_start: 0.8617 (m-80) cc_final: 0.8177 (m-10) REVERT: F 530 MET cc_start: 0.8206 (mpp) cc_final: 0.7993 (mpp) REVERT: F 568 ASP cc_start: 0.8205 (t0) cc_final: 0.7802 (t70) REVERT: F 603 ILE cc_start: 0.9640 (mt) cc_final: 0.9329 (mp) REVERT: A 95 MET cc_start: 0.9327 (ptt) cc_final: 0.8884 (ppp) REVERT: A 109 ILE cc_start: 0.9565 (mt) cc_final: 0.9318 (tt) REVERT: A 122 LEU cc_start: 0.9390 (mt) cc_final: 0.9138 (mm) REVERT: A 155 LYS cc_start: 0.8746 (mppt) cc_final: 0.8344 (mmmm) REVERT: A 382 PHE cc_start: 0.9184 (m-80) cc_final: 0.8873 (m-10) REVERT: B 535 MET cc_start: 0.8880 (pmm) cc_final: 0.8674 (pmm) REVERT: B 596 TRP cc_start: 0.9362 (m-10) cc_final: 0.8929 (m-10) REVERT: B 662 GLU cc_start: 0.4348 (mt-10) cc_final: 0.3927 (mt-10) outliers start: 1 outliers final: 0 residues processed: 220 average time/residue: 0.2824 time to fit residues: 92.3031 Evaluate side-chains 156 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 169 optimal weight: 40.0000 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS A 411 ASN B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16329 Z= 0.208 Angle : 0.628 10.192 22208 Z= 0.318 Chirality : 0.045 0.462 2856 Planarity : 0.003 0.038 2707 Dihedral : 8.104 73.139 4163 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.07 % Allowed : 1.76 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.20), residues: 1673 helix: 1.14 (0.27), residues: 403 sheet: 0.31 (0.23), residues: 455 loop : -0.06 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 628 HIS 0.004 0.001 HIS A 105 PHE 0.018 0.002 PHE E 53 TYR 0.022 0.002 TYR E 177 ARG 0.006 0.000 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8230 (m-80) cc_final: 0.7966 (m-80) REVERT: D 530 MET cc_start: 0.8577 (mtp) cc_final: 0.7689 (mtp) REVERT: D 537 LEU cc_start: 0.8838 (mt) cc_final: 0.8580 (mt) REVERT: D 584 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8984 (tm-30) REVERT: D 628 TRP cc_start: 0.8027 (m100) cc_final: 0.7381 (m100) REVERT: D 634 GLU cc_start: 0.9126 (mt-10) cc_final: 0.8775 (mt-10) REVERT: D 647 GLU cc_start: 0.9184 (pp20) cc_final: 0.8805 (pp20) REVERT: D 654 GLU cc_start: 0.8295 (mt-10) cc_final: 0.7696 (tm-30) REVERT: E 85 HIS cc_start: 0.8229 (m90) cc_final: 0.7995 (m90) REVERT: E 104 MET cc_start: 0.9259 (ttt) cc_final: 0.8923 (ttm) REVERT: E 210 PHE cc_start: 0.8689 (m-80) cc_final: 0.8121 (m-10) REVERT: F 568 ASP cc_start: 0.7962 (t0) cc_final: 0.7617 (t0) REVERT: F 603 ILE cc_start: 0.9607 (mt) cc_final: 0.9221 (mp) REVERT: A 109 ILE cc_start: 0.9571 (mt) cc_final: 0.9203 (tt) REVERT: A 122 LEU cc_start: 0.9428 (mt) cc_final: 0.9204 (mm) REVERT: B 522 PHE cc_start: 0.8713 (t80) cc_final: 0.8427 (t80) REVERT: B 577 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9086 (tm-30) REVERT: B 596 TRP cc_start: 0.9194 (m-10) cc_final: 0.8775 (m-10) REVERT: B 599 SER cc_start: 0.9482 (t) cc_final: 0.9204 (p) REVERT: B 662 GLU cc_start: 0.4543 (mt-10) cc_final: 0.3798 (mt-10) outliers start: 1 outliers final: 0 residues processed: 246 average time/residue: 0.2651 time to fit residues: 97.5125 Evaluate side-chains 174 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 1.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 152 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 0.0970 chunk 136 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 155 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS C 170 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 440 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 651 ASN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 130 GLN E 188 ASN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 425 ASN ** F 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS A 170 GLN A 352 HIS A 411 ASN B 575 GLN B 651 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 16329 Z= 0.378 Angle : 0.727 8.214 22208 Z= 0.364 Chirality : 0.047 0.251 2856 Planarity : 0.004 0.036 2707 Dihedral : 8.162 71.946 4163 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.07 % Allowed : 2.86 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.20), residues: 1673 helix: 1.10 (0.27), residues: 398 sheet: 0.00 (0.24), residues: 438 loop : -0.38 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 479 HIS 0.006 0.002 HIS E 330 PHE 0.032 0.003 PHE F 522 TYR 0.018 0.002 TYR E 177 ARG 0.003 0.001 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9097 (ttt) cc_final: 0.8831 (ttp) REVERT: C 195 ASN cc_start: 0.8551 (t0) cc_final: 0.8291 (t0) REVERT: D 530 MET cc_start: 0.9025 (mtp) cc_final: 0.8564 (mtp) REVERT: D 537 LEU cc_start: 0.8921 (mt) cc_final: 0.8570 (mt) REVERT: D 577 GLN cc_start: 0.9053 (tt0) cc_final: 0.8795 (tp40) REVERT: D 634 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8887 (mt-10) REVERT: D 647 GLU cc_start: 0.9259 (pp20) cc_final: 0.8849 (pp20) REVERT: D 654 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7798 (tm-30) REVERT: E 85 HIS cc_start: 0.8352 (m90) cc_final: 0.8100 (m90) REVERT: E 104 MET cc_start: 0.9299 (ttt) cc_final: 0.9066 (tpp) REVERT: E 210 PHE cc_start: 0.8813 (m-80) cc_final: 0.8375 (m-10) REVERT: F 530 MET cc_start: 0.7763 (mpp) cc_final: 0.7545 (mpp) REVERT: F 565 LEU cc_start: 0.8947 (mt) cc_final: 0.8583 (tp) REVERT: F 568 ASP cc_start: 0.8170 (t0) cc_final: 0.7833 (t0) REVERT: F 639 THR cc_start: 0.9620 (m) cc_final: 0.8793 (m) REVERT: A 95 MET cc_start: 0.9331 (ptt) cc_final: 0.9116 (ppp) REVERT: A 109 ILE cc_start: 0.9596 (mt) cc_final: 0.9235 (tt) REVERT: A 122 LEU cc_start: 0.9412 (mt) cc_final: 0.9155 (mm) REVERT: B 577 GLN cc_start: 0.9407 (tm-30) cc_final: 0.9185 (tm-30) REVERT: B 596 TRP cc_start: 0.9306 (m-10) cc_final: 0.8974 (m-10) outliers start: 1 outliers final: 0 residues processed: 208 average time/residue: 0.2822 time to fit residues: 86.8652 Evaluate side-chains 146 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 61 optimal weight: 8.9990 chunk 164 optimal weight: 30.0000 chunk 36 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 182 optimal weight: 30.0000 chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 GLN D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 543 ASN F 630 GLN A 85 HIS B 575 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.5291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16329 Z= 0.286 Angle : 0.661 8.980 22208 Z= 0.332 Chirality : 0.046 0.242 2856 Planarity : 0.004 0.038 2707 Dihedral : 7.839 66.694 4163 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.20), residues: 1673 helix: 1.24 (0.27), residues: 393 sheet: -0.05 (0.24), residues: 432 loop : -0.39 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 479 HIS 0.004 0.001 HIS E 330 PHE 0.019 0.002 PHE E 53 TYR 0.014 0.002 TYR E 177 ARG 0.003 0.000 ARG E 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8173 (m-10) cc_final: 0.7703 (m-80) REVERT: C 104 MET cc_start: 0.9153 (ttt) cc_final: 0.8875 (ttp) REVERT: C 195 ASN cc_start: 0.8565 (t0) cc_final: 0.8320 (t0) REVERT: D 584 GLU cc_start: 0.8422 (tm-30) cc_final: 0.7678 (tm-30) REVERT: D 588 ARG cc_start: 0.8651 (ttm170) cc_final: 0.8303 (mtt180) REVERT: D 590 GLN cc_start: 0.9170 (mm110) cc_final: 0.8495 (tm-30) REVERT: D 638 TYR cc_start: 0.8911 (m-80) cc_final: 0.8610 (m-80) REVERT: D 647 GLU cc_start: 0.9237 (pp20) cc_final: 0.8839 (pp20) REVERT: D 654 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7841 (tm-30) REVERT: E 85 HIS cc_start: 0.8307 (m90) cc_final: 0.8083 (m90) REVERT: E 195 ASN cc_start: 0.8925 (t0) cc_final: 0.8697 (t0) REVERT: E 210 PHE cc_start: 0.8821 (m-80) cc_final: 0.8367 (m-10) REVERT: F 568 ASP cc_start: 0.8048 (t0) cc_final: 0.7653 (t0) REVERT: F 603 ILE cc_start: 0.9736 (mp) cc_final: 0.9249 (mp) REVERT: F 639 THR cc_start: 0.9644 (m) cc_final: 0.8936 (m) REVERT: A 109 ILE cc_start: 0.9590 (mt) cc_final: 0.9246 (tt) REVERT: A 122 LEU cc_start: 0.9440 (mt) cc_final: 0.9185 (mm) REVERT: A 382 PHE cc_start: 0.9234 (m-80) cc_final: 0.8868 (m-10) REVERT: B 596 TRP cc_start: 0.9230 (m-10) cc_final: 0.8855 (m-10) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.2791 time to fit residues: 88.2139 Evaluate side-chains 151 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 176 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 153 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 GLN F 630 GLN A 85 HIS B 625 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.5504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16329 Z= 0.278 Angle : 0.654 8.890 22208 Z= 0.329 Chirality : 0.046 0.241 2856 Planarity : 0.003 0.038 2707 Dihedral : 7.661 63.034 4163 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.20), residues: 1673 helix: 1.17 (0.27), residues: 393 sheet: -0.04 (0.24), residues: 438 loop : -0.53 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 479 HIS 0.004 0.001 HIS D 570 PHE 0.021 0.002 PHE D 522 TYR 0.026 0.002 TYR E 217 ARG 0.004 0.000 ARG C 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8278 (m-10) cc_final: 0.7935 (m-80) REVERT: C 104 MET cc_start: 0.9112 (ttt) cc_final: 0.8889 (ttp) REVERT: D 537 LEU cc_start: 0.8928 (mt) cc_final: 0.8513 (mt) REVERT: D 634 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8895 (mt-10) REVERT: D 638 TYR cc_start: 0.8949 (m-80) cc_final: 0.8638 (m-80) REVERT: D 647 GLU cc_start: 0.9227 (pp20) cc_final: 0.8832 (pp20) REVERT: D 654 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7888 (tm-30) REVERT: E 85 HIS cc_start: 0.8350 (m90) cc_final: 0.8067 (m-70) REVERT: E 95 MET cc_start: 0.9473 (ptm) cc_final: 0.8630 (ppp) REVERT: E 104 MET cc_start: 0.9274 (tpp) cc_final: 0.9002 (tpp) REVERT: E 210 PHE cc_start: 0.8835 (m-80) cc_final: 0.8372 (m-10) REVERT: F 530 MET cc_start: 0.7883 (mpp) cc_final: 0.7588 (mpp) REVERT: F 568 ASP cc_start: 0.8023 (t0) cc_final: 0.7614 (t0) REVERT: F 603 ILE cc_start: 0.9725 (mp) cc_final: 0.9277 (mp) REVERT: A 95 MET cc_start: 0.9302 (ppp) cc_final: 0.8955 (ppp) REVERT: A 100 MET cc_start: 0.8605 (mtm) cc_final: 0.8390 (mtm) REVERT: A 109 ILE cc_start: 0.9579 (mt) cc_final: 0.9302 (tt) REVERT: A 122 LEU cc_start: 0.9431 (mt) cc_final: 0.9166 (mm) REVERT: A 382 PHE cc_start: 0.9161 (m-80) cc_final: 0.8885 (m-10) REVERT: B 596 TRP cc_start: 0.9231 (m-10) cc_final: 0.8876 (m-10) outliers start: 0 outliers final: 0 residues processed: 209 average time/residue: 0.2822 time to fit residues: 88.4705 Evaluate side-chains 148 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 112 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 108 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 16329 Z= 0.429 Angle : 0.771 7.288 22208 Z= 0.384 Chirality : 0.048 0.255 2856 Planarity : 0.004 0.039 2707 Dihedral : 8.208 62.573 4163 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.07 % Allowed : 1.04 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.20), residues: 1673 helix: 0.95 (0.27), residues: 381 sheet: -0.31 (0.24), residues: 429 loop : -0.71 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 596 HIS 0.006 0.002 HIS E 330 PHE 0.024 0.003 PHE E 53 TYR 0.033 0.003 TYR E 217 ARG 0.004 0.001 ARG B 617 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 188 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8372 (m-10) cc_final: 0.8166 (m-80) REVERT: C 104 MET cc_start: 0.9211 (ttt) cc_final: 0.8970 (ttp) REVERT: C 195 ASN cc_start: 0.8716 (t0) cc_final: 0.8391 (t0) REVERT: D 584 GLU cc_start: 0.8397 (tm-30) cc_final: 0.8114 (tm-30) REVERT: D 634 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8939 (mt-10) REVERT: D 638 TYR cc_start: 0.9057 (m-80) cc_final: 0.8718 (m-80) REVERT: D 647 GLU cc_start: 0.9233 (pp20) cc_final: 0.8817 (pp20) REVERT: D 654 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7953 (tm-30) REVERT: E 104 MET cc_start: 0.9220 (tpp) cc_final: 0.8869 (tpp) REVERT: E 195 ASN cc_start: 0.9037 (t0) cc_final: 0.8792 (t0) REVERT: F 565 LEU cc_start: 0.8734 (mt) cc_final: 0.8394 (tp) REVERT: F 568 ASP cc_start: 0.8189 (t0) cc_final: 0.7741 (t0) REVERT: F 603 ILE cc_start: 0.9746 (mp) cc_final: 0.9510 (mp) REVERT: A 109 ILE cc_start: 0.9520 (mt) cc_final: 0.9306 (tt) REVERT: A 122 LEU cc_start: 0.9396 (mt) cc_final: 0.9126 (mm) REVERT: A 382 PHE cc_start: 0.9168 (m-80) cc_final: 0.8813 (m-10) REVERT: B 596 TRP cc_start: 0.9286 (m-10) cc_final: 0.8953 (m-10) REVERT: B 647 GLU cc_start: 0.9225 (mt-10) cc_final: 0.9013 (mt-10) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2932 time to fit residues: 84.2114 Evaluate side-chains 140 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 174 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 40.0000 chunk 102 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 133 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 chunk 179 optimal weight: 40.0000 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN D 575 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16329 Z= 0.178 Angle : 0.614 7.199 22208 Z= 0.307 Chirality : 0.045 0.252 2856 Planarity : 0.003 0.037 2707 Dihedral : 7.324 59.326 4163 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.08 (0.21), residues: 1673 helix: 1.15 (0.27), residues: 390 sheet: -0.09 (0.24), residues: 430 loop : -0.54 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 479 HIS 0.003 0.001 HIS D 585 PHE 0.040 0.002 PHE D 522 TYR 0.024 0.002 TYR A 217 ARG 0.003 0.000 ARG B 542 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8197 (m-10) cc_final: 0.7825 (m-80) REVERT: C 104 MET cc_start: 0.9167 (ttt) cc_final: 0.8903 (ttp) REVERT: C 195 ASN cc_start: 0.8685 (t0) cc_final: 0.8442 (t0) REVERT: D 584 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8023 (tm-30) REVERT: D 634 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8886 (mt-10) REVERT: D 638 TYR cc_start: 0.8887 (m-80) cc_final: 0.8595 (m-80) REVERT: D 647 GLU cc_start: 0.9279 (pp20) cc_final: 0.8914 (pp20) REVERT: D 657 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8941 (pt0) REVERT: E 95 MET cc_start: 0.9453 (ptm) cc_final: 0.8665 (ppp) REVERT: E 210 PHE cc_start: 0.8823 (m-80) cc_final: 0.8332 (m-10) REVERT: E 217 TYR cc_start: 0.8647 (m-80) cc_final: 0.8028 (m-80) REVERT: F 565 LEU cc_start: 0.8864 (mt) cc_final: 0.8379 (tp) REVERT: F 568 ASP cc_start: 0.8085 (t0) cc_final: 0.7598 (t0) REVERT: F 603 ILE cc_start: 0.9719 (mp) cc_final: 0.9269 (mp) REVERT: A 109 ILE cc_start: 0.9517 (mt) cc_final: 0.9241 (tt) REVERT: A 122 LEU cc_start: 0.9432 (mt) cc_final: 0.9175 (mm) REVERT: A 382 PHE cc_start: 0.9178 (m-80) cc_final: 0.8899 (m-10) REVERT: B 577 GLN cc_start: 0.9352 (tm-30) cc_final: 0.9116 (tm-30) REVERT: B 596 TRP cc_start: 0.9160 (m-10) cc_final: 0.8765 (m-10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.2637 time to fit residues: 85.4448 Evaluate side-chains 163 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 109 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 188 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 149 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 HIS F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.6041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16329 Z= 0.310 Angle : 0.682 9.267 22208 Z= 0.340 Chirality : 0.046 0.242 2856 Planarity : 0.004 0.035 2707 Dihedral : 7.483 59.929 4163 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.21), residues: 1673 helix: 1.00 (0.27), residues: 386 sheet: -0.14 (0.25), residues: 429 loop : -0.65 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 628 HIS 0.006 0.001 HIS D 585 PHE 0.045 0.002 PHE D 522 TYR 0.025 0.002 TYR A 217 ARG 0.003 0.000 ARG D 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3346 Ramachandran restraints generated. 1673 Oldfield, 0 Emsley, 1673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 104 MET cc_start: 0.9166 (ttt) cc_final: 0.8953 (ttp) REVERT: C 195 ASN cc_start: 0.8756 (t0) cc_final: 0.8524 (t0) REVERT: C 484 TYR cc_start: 0.8342 (p90) cc_final: 0.8099 (p90) REVERT: D 536 THR cc_start: 0.8863 (m) cc_final: 0.8364 (t) REVERT: D 634 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8958 (mt-10) REVERT: D 638 TYR cc_start: 0.9009 (m-80) cc_final: 0.8718 (m-80) REVERT: D 647 GLU cc_start: 0.9236 (pp20) cc_final: 0.8940 (pp20) REVERT: E 95 MET cc_start: 0.9477 (ptm) cc_final: 0.8600 (ppp) REVERT: E 195 ASN cc_start: 0.9003 (t0) cc_final: 0.8752 (t0) REVERT: E 210 PHE cc_start: 0.8832 (m-80) cc_final: 0.8412 (m-10) REVERT: E 217 TYR cc_start: 0.8581 (m-80) cc_final: 0.7996 (m-80) REVERT: F 530 MET cc_start: 0.8083 (mpp) cc_final: 0.7793 (mpp) REVERT: F 565 LEU cc_start: 0.8867 (mt) cc_final: 0.8382 (tp) REVERT: F 568 ASP cc_start: 0.8142 (t0) cc_final: 0.7618 (t0) REVERT: A 100 MET cc_start: 0.8630 (mtm) cc_final: 0.8381 (mtm) REVERT: A 109 ILE cc_start: 0.9567 (mt) cc_final: 0.9317 (tt) REVERT: A 122 LEU cc_start: 0.9381 (mt) cc_final: 0.9107 (mm) REVERT: A 382 PHE cc_start: 0.9182 (m-80) cc_final: 0.8869 (m-10) REVERT: B 577 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9178 (tm-30) REVERT: B 596 TRP cc_start: 0.9208 (m-10) cc_final: 0.8878 (m-10) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 0.2840 time to fit residues: 87.8031 Evaluate side-chains 148 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 189 random chunks: chunk 45 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 0.0270 chunk 41 optimal weight: 0.0030 chunk 150 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 154 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 131 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 overall best weight: 0.5250 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 575 GLN D 577 GLN D 585 HIS ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 630 GLN A 85 HIS ** A 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.069279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.055336 restraints weight = 72600.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.056739 restraints weight = 45291.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.057698 restraints weight = 33328.572| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16329 Z= 0.151 Angle : 0.598 7.229 22208 Z= 0.300 Chirality : 0.044 0.232 2856 Planarity : 0.003 0.034 2707 Dihedral : 6.613 56.827 4163 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.20 % Allowed : 0.39 % Favored : 99.41 % 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: -0.03 (0.21), residues: 1673 helix: 1.17 (0.27), residues: 383 sheet: -0.01 (0.24), residues: 429 loop : -0.51 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 631 HIS 0.003 0.001 HIS D 564 PHE 0.038 0.002 PHE D 522 TYR 0.024 0.002 TYR A 217 ARG 0.003 0.000 ARG E 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2902.66 seconds wall clock time: 53 minutes 53.23 seconds (3233.23 seconds total)