Starting phenix.real_space_refine on Mon Jul 22 00:54:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/07_2024/7l8s_23235.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/07_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_23235/07_2024/7l8s_23235.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/07_2024/7l8s_23235.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/07_2024/7l8s_23235.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l8s_23235/07_2024/7l8s_23235.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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-5388/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: 9.40, per 1000 atoms: 0.59 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: 7.91 Conformation dependent library (CDL) restraints added in 2.5 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... Secondary structure from input PDB file: 53 helices and 34 sheets defined 31.1% alpha, 38.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.024A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 335 through 354 removed outlier: 3.822A pdb=" N HIS C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 377 through 381 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 425 through 429 removed outlier: 4.427A pdb=" N GLN C 428 " --> pdb=" O ASN C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 483 removed outlier: 4.118A pdb=" N SER C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.391A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 removed outlier: 4.013A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 543 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 568 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 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 638 through 661 Processing helix chain 'E' and resid 67 through 72 Processing helix chain 'E' and resid 98 through 117 removed outlier: 4.124A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 removed outlier: 3.974A pdb=" N HIS E 352 " --> pdb=" O GLN E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.569A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 4.015A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 541 Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 568 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.175A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.518A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.842A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.362A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 543 Processing helix chain 'B' and resid 562 through 568 Processing helix chain 'B' and resid 568 through 596 Processing helix chain 'B' and resid 618 through 626 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'L' and resid 24 through 28 Processing helix chain 'L' and resid 48 through 51 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.160A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 92 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.668A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 394 through 395 removed outlier: 10.328A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.072A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.892A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.466A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'C' and resid 315 through 323A removed outlier: 6.499A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.261A pdb=" N VAL E 36 " --> pdb=" O THR F 606 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'E' and resid 75 through 76 removed outlier: 4.499A pdb=" N VAL E 75 " --> pdb=" O CYS E 54 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB6, first strand: chain 'E' and resid 169 through 177 removed outlier: 3.819A pdb=" N LYS E 189 " --> pdb=" O CYS E 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.623A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 259 through 261 removed outlier: 6.503A pdb=" N LEU E 260 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 9.989A pdb=" N ARG E 444 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 11.567A pdb=" N ILE E 294 " --> pdb=" O ARG E 444 " (cutoff:3.500A) removed outlier: 9.342A pdb=" N VAL E 446 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 10.198A pdb=" N VAL E 292 " --> pdb=" O VAL E 446 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N ASN E 448 " --> pdb=" O GLU E 290 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N GLU E 290 " --> pdb=" O ASN E 448 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR E 450 " --> pdb=" O LEU E 288 " (cutoff:3.500A) 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) removed outlier: 4.370A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 301 through 308 removed outlier: 7.071A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 394 through 395 removed outlier: 6.358A pdb=" N ILE E 358 " --> pdb=" O GLU E 466 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N PHE E 468 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ARG E 360 " --> pdb=" O PHE E 468 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.716A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AC6, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AC7, first strand: chain 'A' and resid 169 through 176 Processing sheet with id=AC8, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.635A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLN A 432 " --> pdb=" O MET A 426 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N MET A 426 " --> pdb=" O GLN A 432 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 394 through 396 removed outlier: 10.428A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.132A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.072A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.716A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.602A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.577A pdb=" N ASN A 448 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.133A pdb=" N GLU A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR A 450 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 259 through 261 Processing sheet with id=AD2, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AD3, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.264A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 34 through 35 Processing sheet with id=AD5, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'L' and resid 44 through 47 removed outlier: 6.603A pdb=" N UNK L 34 " --> pdb=" O UNK L 46 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N UNK L 35 " --> pdb=" O UNK L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N UNK L 84 " --> pdb=" O UNK L 35 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK L 82 " --> pdb=" O UNK L 37 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N UNK L 99 " --> pdb=" O UNK L 83 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 62 through 63 removed outlier: 3.921A pdb=" N UNK L 63 " --> pdb=" O UNK L 70 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N UNK L 70 " --> pdb=" O UNK L 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 600 hydrogen bonds defined for protein. 1599 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: 5.72 Time building geometry restraints manager: 8.54 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: 3860 2.81 - 3.33: 15336 3.33 - 3.85: 26238 3.85 - 4.38: 31694 4.38 - 4.90: 48832 Nonbonded interactions: 125960 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 125955 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: 1.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 46.460 Find NCS groups from input model: 2.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.750 ------------------------------------------------------------------------------- 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= 1.355 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 : 1.800 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: 0.3127 time to fit residues: 209.6347 Evaluate side-chains 217 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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: 2.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 76 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 90 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 HIS ** E 170 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 16329 Z= 0.240 Angle : 0.746 10.740 22208 Z= 0.383 Chirality : 0.049 0.330 2856 Planarity : 0.004 0.033 2707 Dihedral : 9.222 84.573 4163 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.61 % Favored : 98.33 % Rotamer: Outliers : 0.20 % Allowed : 2.34 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.20), residues: 1673 helix: 1.34 (0.25), residues: 415 sheet: 0.71 (0.22), residues: 468 loop : 0.49 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 479 HIS 0.006 0.001 HIS E 72 PHE 0.018 0.002 PHE E 53 TYR 0.030 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 311 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 308 time to evaluate : 1.825 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 98 ASN cc_start: 0.9212 (t0) cc_final: 0.8848 (t0) REVERT: C 150 MET cc_start: 0.8507 (mmm) cc_final: 0.8209 (mmm) REVERT: D 530 MET cc_start: 0.8365 (mtp) cc_final: 0.7623 (mtp) REVERT: D 537 LEU cc_start: 0.8642 (mt) cc_final: 0.8327 (mt) REVERT: D 617 ARG cc_start: 0.8636 (ttm-80) cc_final: 0.8410 (mmp80) REVERT: D 654 GLU cc_start: 0.8406 (mt-10) cc_final: 0.7560 (tm-30) REVERT: E 85 HIS cc_start: 0.7987 (m90) cc_final: 0.7644 (m90) REVERT: E 112 TRP cc_start: 0.8555 (t-100) cc_final: 0.8323 (t-100) REVERT: E 161 MET cc_start: 0.7447 (ppp) cc_final: 0.6956 (ppp) REVERT: E 210 PHE cc_start: 0.8373 (m-80) cc_final: 0.7879 (m-10) REVERT: E 303 THR cc_start: 0.8447 (p) cc_final: 0.8140 (t) REVERT: F 568 ASP cc_start: 0.8194 (t0) cc_final: 0.7832 (t0) REVERT: F 576 LEU cc_start: 0.9559 (tp) cc_final: 0.9347 (tp) REVERT: F 603 ILE cc_start: 0.9449 (mt) cc_final: 0.9110 (mt) REVERT: A 95 MET cc_start: 0.9027 (ptt) cc_final: 0.8001 (ppp) REVERT: A 109 ILE cc_start: 0.9482 (mt) cc_final: 0.9084 (tt) REVERT: A 122 LEU cc_start: 0.9398 (mt) cc_final: 0.9185 (mm) REVERT: A 382 PHE cc_start: 0.9202 (m-80) cc_final: 0.8876 (m-10) REVERT: B 568 ASP cc_start: 0.7703 (t0) cc_final: 0.7310 (t0) REVERT: B 584 GLU cc_start: 0.9235 (mt-10) cc_final: 0.9019 (mt-10) REVERT: B 596 TRP cc_start: 0.9250 (m-10) cc_final: 0.8822 (m-10) REVERT: B 626 MET cc_start: 0.7796 (mmm) cc_final: 0.7350 (mpp) REVERT: B 662 GLU cc_start: 0.4320 (mt-10) cc_final: 0.4014 (mt-10) outliers start: 3 outliers final: 0 residues processed: 309 average time/residue: 0.2684 time to fit residues: 123.8257 Evaluate side-chains 199 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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: 8.9990 chunk 53 optimal weight: 10.0000 chunk 142 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 47 optimal weight: 0.0970 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: 10.0000 chunk 137 optimal weight: 4.9990 overall best weight: 4.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 HIS ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 577 GLN D 658 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS B 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16329 Z= 0.391 Angle : 0.794 9.745 22208 Z= 0.399 Chirality : 0.049 0.348 2856 Planarity : 0.004 0.056 2707 Dihedral : 8.638 80.400 4163 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 3.19 % Favored : 96.68 % 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: 0.61 (0.20), residues: 1673 helix: 1.39 (0.26), residues: 406 sheet: 0.40 (0.23), residues: 473 loop : 0.00 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 479 HIS 0.008 0.002 HIS A 216 PHE 0.027 0.003 PHE E 53 TYR 0.041 0.003 TYR A 217 ARG 0.004 0.001 ARG C 429 *********************** 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 237 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 39 TYR cc_start: 0.8152 (m-10) cc_final: 0.7715 (m-80) REVERT: C 195 ASN cc_start: 0.8682 (t0) cc_final: 0.8177 (t0) REVERT: C 427 TRP cc_start: 0.8681 (m100) cc_final: 0.8406 (m100) REVERT: D 522 PHE cc_start: 0.8671 (t80) cc_final: 0.8470 (t80) REVERT: D 584 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8920 (tm-30) REVERT: D 632 ASP cc_start: 0.8700 (m-30) cc_final: 0.8038 (m-30) REVERT: D 634 GLU cc_start: 0.9115 (mt-10) cc_final: 0.8820 (mt-10) REVERT: D 647 GLU cc_start: 0.9192 (pp20) cc_final: 0.8808 (pp20) REVERT: D 654 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7681 (tm-30) REVERT: E 85 HIS cc_start: 0.8206 (m90) cc_final: 0.7890 (m90) REVERT: E 104 MET cc_start: 0.9364 (ttt) cc_final: 0.9042 (ttm) REVERT: E 210 PHE cc_start: 0.8563 (m-80) cc_final: 0.8030 (m-10) REVERT: E 302 ASN cc_start: 0.7803 (m110) cc_final: 0.7570 (m110) REVERT: E 381 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8756 (mm-30) REVERT: F 568 ASP cc_start: 0.8085 (t0) cc_final: 0.7619 (t0) REVERT: F 603 ILE cc_start: 0.9574 (mt) cc_final: 0.9296 (mt) REVERT: A 100 MET cc_start: 0.8586 (mtm) cc_final: 0.8243 (mtt) REVERT: A 109 ILE cc_start: 0.9553 (mt) cc_final: 0.9178 (tt) REVERT: A 122 LEU cc_start: 0.9332 (mt) cc_final: 0.9095 (mm) REVERT: A 155 LYS cc_start: 0.8579 (mppt) cc_final: 0.8241 (mmmm) REVERT: A 382 PHE cc_start: 0.9211 (m-80) cc_final: 0.8928 (m-10) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.2696 time to fit residues: 95.7620 Evaluate side-chains 167 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.742 ------------------------------------------------------------------------------- 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: 3.9990 chunk 89 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 182 optimal weight: 30.0000 chunk 90 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 49 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 103 GLN ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 GLN A 85 HIS A 170 GLN B 575 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16329 Z= 0.295 Angle : 0.685 9.346 22208 Z= 0.345 Chirality : 0.046 0.350 2856 Planarity : 0.004 0.052 2707 Dihedral : 8.196 74.645 4163 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.20 % Allowed : 2.21 % Favored : 97.59 % 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: 0.45 (0.20), residues: 1673 helix: 1.57 (0.26), residues: 405 sheet: 0.25 (0.23), residues: 457 loop : -0.24 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP E 479 HIS 0.006 0.001 HIS C 85 PHE 0.023 0.002 PHE F 522 TYR 0.016 0.002 TYR F 586 ARG 0.003 0.000 ARG B 542 *********************** 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 226 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 223 time to evaluate : 1.721 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: 0.7954 (m-10) cc_final: 0.7521 (m-80) REVERT: C 104 MET cc_start: 0.9108 (ttt) cc_final: 0.8822 (ttp) REVERT: C 195 ASN cc_start: 0.8591 (t0) cc_final: 0.8168 (t0) REVERT: D 522 PHE cc_start: 0.8770 (t80) cc_final: 0.8314 (t80) REVERT: D 523 LEU cc_start: 0.9247 (mt) cc_final: 0.8656 (mt) REVERT: D 584 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8967 (tm-30) REVERT: D 634 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8818 (mt-10) REVERT: D 647 GLU cc_start: 0.9144 (pp20) cc_final: 0.8744 (pp20) REVERT: D 654 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7699 (tm-30) REVERT: E 85 HIS cc_start: 0.8202 (m90) cc_final: 0.7922 (m90) REVERT: E 210 PHE cc_start: 0.8545 (m-80) cc_final: 0.8159 (m-10) REVERT: F 565 LEU cc_start: 0.8859 (mt) cc_final: 0.8567 (tp) REVERT: F 568 ASP cc_start: 0.8067 (t0) cc_final: 0.7491 (t0) REVERT: F 596 TRP cc_start: 0.8887 (m-10) cc_final: 0.8514 (m-10) REVERT: F 603 ILE cc_start: 0.9568 (mt) cc_final: 0.9160 (mp) REVERT: A 100 MET cc_start: 0.8535 (mtm) cc_final: 0.8175 (mtt) REVERT: A 109 ILE cc_start: 0.9577 (mt) cc_final: 0.9219 (tt) REVERT: A 122 LEU cc_start: 0.9301 (mt) cc_final: 0.9079 (mm) REVERT: B 584 GLU cc_start: 0.9045 (pt0) cc_final: 0.8574 (tm-30) REVERT: B 599 SER cc_start: 0.9461 (t) cc_final: 0.9227 (p) REVERT: B 646 LEU cc_start: 0.9466 (mt) cc_final: 0.9200 (mt) outliers start: 3 outliers final: 1 residues processed: 225 average time/residue: 0.2684 time to fit residues: 90.5757 Evaluate side-chains 161 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 160 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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: 0.9990 chunk 103 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 163 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 651 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** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS B 575 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16329 Z= 0.243 Angle : 0.631 8.189 22208 Z= 0.319 Chirality : 0.045 0.240 2856 Planarity : 0.003 0.036 2707 Dihedral : 7.602 68.849 4163 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.07 % Allowed : 1.89 % 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: 0.47 (0.20), residues: 1673 helix: 1.69 (0.26), residues: 408 sheet: 0.18 (0.23), residues: 474 loop : -0.25 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP E 479 HIS 0.003 0.001 HIS E 330 PHE 0.021 0.002 PHE E 53 TYR 0.025 0.002 TYR E 217 ARG 0.004 0.000 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 234 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 233 time to evaluate : 2.274 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: 0.8025 (m-10) cc_final: 0.7577 (m-80) REVERT: C 104 MET cc_start: 0.9177 (ttt) cc_final: 0.8917 (ttp) REVERT: C 195 ASN cc_start: 0.8536 (t0) cc_final: 0.8249 (t0) REVERT: D 522 PHE cc_start: 0.8872 (t80) cc_final: 0.8451 (t80) REVERT: D 523 LEU cc_start: 0.9239 (mt) cc_final: 0.8668 (mt) REVERT: D 638 TYR cc_start: 0.8938 (m-80) cc_final: 0.8617 (m-80) REVERT: D 641 ILE cc_start: 0.9297 (mt) cc_final: 0.8981 (tt) REVERT: D 647 GLU cc_start: 0.9201 (pp20) cc_final: 0.8857 (pp20) REVERT: D 654 GLU cc_start: 0.8288 (mt-10) cc_final: 0.7734 (tm-30) REVERT: E 85 HIS cc_start: 0.8209 (m90) cc_final: 0.7938 (m90) REVERT: E 210 PHE cc_start: 0.8683 (m-80) cc_final: 0.8146 (m-10) REVERT: F 565 LEU cc_start: 0.9086 (mt) cc_final: 0.8582 (tp) REVERT: F 568 ASP cc_start: 0.7961 (t0) cc_final: 0.7340 (t0) REVERT: F 603 ILE cc_start: 0.9549 (mt) cc_final: 0.9177 (mp) REVERT: F 628 TRP cc_start: 0.7938 (m100) cc_final: 0.7729 (m100) REVERT: F 655 LYS cc_start: 0.8748 (pttm) cc_final: 0.8327 (pttm) REVERT: A 100 MET cc_start: 0.8640 (mtm) cc_final: 0.8148 (mtt) REVERT: A 109 ILE cc_start: 0.9581 (mt) cc_final: 0.9227 (tt) REVERT: A 122 LEU cc_start: 0.9314 (mt) cc_final: 0.9089 (mm) REVERT: A 378 CYS cc_start: 0.7704 (t) cc_final: 0.7458 (t) REVERT: B 577 GLN cc_start: 0.9305 (tm-30) cc_final: 0.9092 (tm-30) REVERT: B 599 SER cc_start: 0.9463 (t) cc_final: 0.9230 (p) REVERT: B 626 MET cc_start: 0.8030 (mpp) cc_final: 0.7542 (mpp) REVERT: B 646 LEU cc_start: 0.9487 (mt) cc_final: 0.9139 (mt) REVERT: B 662 GLU cc_start: 0.4817 (mt-10) cc_final: 0.4586 (mt-10) outliers start: 1 outliers final: 0 residues processed: 233 average time/residue: 0.2715 time to fit residues: 94.3859 Evaluate side-chains 169 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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: 9.9990 chunk 164 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 182 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 170 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN ** 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 425 ASN A 85 HIS B 575 GLN B 652 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16329 Z= 0.247 Angle : 0.628 8.073 22208 Z= 0.317 Chirality : 0.045 0.237 2856 Planarity : 0.003 0.031 2707 Dihedral : 7.307 64.224 4163 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.13 % Allowed : 1.76 % Favored : 98.11 % 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: 0.33 (0.20), residues: 1673 helix: 1.58 (0.26), residues: 408 sheet: 0.05 (0.23), residues: 480 loop : -0.31 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP F 596 HIS 0.005 0.001 HIS F 585 PHE 0.021 0.002 PHE C 317 TYR 0.015 0.001 TYR E 217 ARG 0.005 0.000 ARG D 542 *********************** 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 236 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 1.570 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: 0.8089 (m-10) cc_final: 0.7608 (m-80) REVERT: C 104 MET cc_start: 0.9206 (ttt) cc_final: 0.8946 (ttp) REVERT: C 150 MET cc_start: 0.7533 (mpp) cc_final: 0.7266 (mtt) REVERT: C 195 ASN cc_start: 0.8533 (t0) cc_final: 0.8221 (t0) REVERT: D 522 PHE cc_start: 0.8975 (t80) cc_final: 0.8545 (t80) REVERT: D 523 LEU cc_start: 0.9203 (mt) cc_final: 0.8712 (mt) REVERT: D 584 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8112 (tm-30) REVERT: D 638 TYR cc_start: 0.8932 (m-80) cc_final: 0.8620 (m-80) REVERT: D 647 GLU cc_start: 0.9189 (pp20) cc_final: 0.8793 (pp20) REVERT: D 650 GLN cc_start: 0.9101 (tp40) cc_final: 0.8772 (mm-40) REVERT: D 654 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7744 (tm-30) REVERT: E 85 HIS cc_start: 0.8275 (m90) cc_final: 0.8019 (m90) REVERT: E 95 MET cc_start: 0.9473 (ptm) cc_final: 0.8667 (ppp) REVERT: E 210 PHE cc_start: 0.8701 (m-80) cc_final: 0.8235 (m-10) REVERT: F 565 LEU cc_start: 0.9086 (mt) cc_final: 0.8530 (tp) REVERT: F 593 LEU cc_start: 0.9714 (tp) cc_final: 0.9493 (tt) REVERT: F 603 ILE cc_start: 0.9574 (mt) cc_final: 0.9208 (mp) REVERT: F 655 LYS cc_start: 0.8759 (pttm) cc_final: 0.8342 (pttm) REVERT: A 109 ILE cc_start: 0.9579 (mt) cc_final: 0.9219 (tt) REVERT: A 122 LEU cc_start: 0.9327 (mt) cc_final: 0.9087 (mm) REVERT: B 542 ARG cc_start: 0.9304 (ttm-80) cc_final: 0.8787 (tpt90) REVERT: B 577 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9107 (tm-30) REVERT: B 646 LEU cc_start: 0.9488 (mt) cc_final: 0.9092 (mt) REVERT: B 662 GLU cc_start: 0.5064 (mt-10) cc_final: 0.4858 (mt-10) outliers start: 2 outliers final: 0 residues processed: 235 average time/residue: 0.2688 time to fit residues: 94.3615 Evaluate side-chains 165 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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: 8.9990 chunk 104 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 111 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 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 328 GLN A 85 HIS B 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16329 Z= 0.266 Angle : 0.634 8.315 22208 Z= 0.319 Chirality : 0.045 0.237 2856 Planarity : 0.003 0.031 2707 Dihedral : 7.084 60.133 4163 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % 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: 1.52 (0.26), residues: 414 sheet: -0.07 (0.23), residues: 477 loop : -0.34 (0.23), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP F 596 HIS 0.003 0.001 HIS A 105 PHE 0.021 0.002 PHE E 53 TYR 0.020 0.002 TYR C 40 ARG 0.004 0.000 ARG B 542 *********************** 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 221 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.673 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: 0.8052 (m-10) cc_final: 0.7593 (m-80) REVERT: C 104 MET cc_start: 0.9218 (ttt) cc_final: 0.8935 (ttp) REVERT: C 195 ASN cc_start: 0.8570 (t0) cc_final: 0.8355 (t0) REVERT: D 569 THR cc_start: 0.8324 (m) cc_final: 0.8123 (m) REVERT: D 584 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8183 (tm-30) REVERT: D 588 ARG cc_start: 0.8607 (ttm170) cc_final: 0.8390 (mtt90) REVERT: D 626 MET cc_start: 0.8066 (tpt) cc_final: 0.6964 (tpp) REVERT: D 638 TYR cc_start: 0.8885 (m-80) cc_final: 0.8586 (m-80) REVERT: D 647 GLU cc_start: 0.9192 (pp20) cc_final: 0.8804 (pp20) REVERT: D 650 GLN cc_start: 0.9102 (tp40) cc_final: 0.8805 (mm-40) REVERT: D 654 GLU cc_start: 0.8299 (mt-10) cc_final: 0.7764 (tm-30) REVERT: E 85 HIS cc_start: 0.8286 (m90) cc_final: 0.8058 (m90) REVERT: E 95 MET cc_start: 0.9474 (ptm) cc_final: 0.8667 (ppp) REVERT: E 210 PHE cc_start: 0.8860 (m-80) cc_final: 0.8396 (m-10) REVERT: F 565 LEU cc_start: 0.9096 (mt) cc_final: 0.8630 (tp) REVERT: F 603 ILE cc_start: 0.9589 (mt) cc_final: 0.9225 (mp) REVERT: F 631 TRP cc_start: 0.9270 (t-100) cc_final: 0.8911 (t-100) REVERT: F 655 LYS cc_start: 0.8763 (pttm) cc_final: 0.8331 (pttm) REVERT: A 109 ILE cc_start: 0.9577 (mt) cc_final: 0.9314 (tt) REVERT: A 122 LEU cc_start: 0.9368 (mt) cc_final: 0.9115 (mm) REVERT: A 382 PHE cc_start: 0.9249 (m-80) cc_final: 0.8874 (m-10) REVERT: B 577 GLN cc_start: 0.9364 (tm-30) cc_final: 0.9100 (tm-30) REVERT: B 626 MET cc_start: 0.7953 (mpp) cc_final: 0.7583 (mpp) REVERT: B 646 LEU cc_start: 0.9495 (mt) cc_final: 0.9188 (mt) REVERT: B 654 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8484 (tm-30) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.2818 time to fit residues: 92.2902 Evaluate side-chains 162 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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: 4.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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 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** A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16329 Z= 0.277 Angle : 0.649 9.264 22208 Z= 0.326 Chirality : 0.045 0.237 2856 Planarity : 0.003 0.031 2707 Dihedral : 7.117 58.765 4163 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % 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: 0.07 (0.21), residues: 1673 helix: 1.52 (0.26), residues: 407 sheet: -0.14 (0.23), residues: 471 loop : -0.55 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP F 596 HIS 0.004 0.001 HIS D 585 PHE 0.021 0.002 PHE E 53 TYR 0.019 0.002 TYR E 217 ARG 0.007 0.000 ARG D 542 *********************** 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 215 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.722 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: 0.8120 (m-10) cc_final: 0.7645 (m-80) REVERT: C 104 MET cc_start: 0.9219 (ttt) cc_final: 0.8918 (ttp) REVERT: D 638 TYR cc_start: 0.8895 (m-80) cc_final: 0.8633 (m-80) REVERT: D 647 GLU cc_start: 0.9204 (pp20) cc_final: 0.8823 (pp20) REVERT: D 654 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7898 (tm-30) REVERT: E 85 HIS cc_start: 0.8302 (m90) cc_final: 0.8096 (m90) REVERT: E 95 MET cc_start: 0.9475 (ptm) cc_final: 0.8654 (ppp) REVERT: F 565 LEU cc_start: 0.9069 (mt) cc_final: 0.8645 (tp) REVERT: F 603 ILE cc_start: 0.9598 (mt) cc_final: 0.9289 (mt) REVERT: F 654 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8820 (tm-30) REVERT: F 655 LYS cc_start: 0.8756 (pttm) cc_final: 0.8250 (pttm) REVERT: A 95 MET cc_start: 0.9381 (ppp) cc_final: 0.9016 (ppp) REVERT: A 100 MET cc_start: 0.8590 (mtm) cc_final: 0.8294 (mtm) REVERT: A 109 ILE cc_start: 0.9580 (mt) cc_final: 0.9247 (tt) REVERT: A 122 LEU cc_start: 0.9352 (mt) cc_final: 0.9091 (mm) REVERT: A 382 PHE cc_start: 0.9194 (m-80) cc_final: 0.8951 (m-10) REVERT: B 577 GLN cc_start: 0.9381 (tm-30) cc_final: 0.9125 (tm-30) REVERT: B 626 MET cc_start: 0.7770 (mpp) cc_final: 0.7550 (mpp) REVERT: B 646 LEU cc_start: 0.9476 (mt) cc_final: 0.9197 (mt) REVERT: B 654 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8612 (tm-30) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.2856 time to fit residues: 90.9850 Evaluate side-chains 159 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.661 ------------------------------------------------------------------------------- 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: 9.9990 chunk 169 optimal weight: 40.0000 chunk 102 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 153 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 8.9990 chunk 179 optimal weight: 30.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS A 352 HIS B 575 GLN B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.5781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16329 Z= 0.366 Angle : 0.718 9.139 22208 Z= 0.358 Chirality : 0.046 0.248 2856 Planarity : 0.004 0.031 2707 Dihedral : 7.484 59.938 4163 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.07 % Allowed : 0.78 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.20), residues: 1673 helix: 1.29 (0.26), residues: 407 sheet: -0.32 (0.23), residues: 456 loop : -0.76 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 427 HIS 0.007 0.001 HIS D 585 PHE 0.026 0.003 PHE D 522 TYR 0.018 0.002 TYR E 217 ARG 0.006 0.001 ARG D 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 198 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 197 time to evaluate : 1.835 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: C 39 TYR cc_start: 0.8261 (m-10) cc_final: 0.7742 (m-80) REVERT: C 104 MET cc_start: 0.9251 (ttt) cc_final: 0.8983 (ttp) REVERT: C 195 ASN cc_start: 0.8468 (t0) cc_final: 0.8170 (t0) REVERT: D 536 THR cc_start: 0.8627 (m) cc_final: 0.8052 (t) REVERT: D 584 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8268 (tm-30) REVERT: D 638 TYR cc_start: 0.8978 (m-80) cc_final: 0.8696 (m-80) REVERT: D 647 GLU cc_start: 0.9230 (pp20) cc_final: 0.8848 (pp20) REVERT: D 654 GLU cc_start: 0.8424 (mt-10) cc_final: 0.7945 (tm-30) REVERT: E 95 MET cc_start: 0.9472 (ptm) cc_final: 0.8569 (ppp) REVERT: F 565 LEU cc_start: 0.9093 (mt) cc_final: 0.8677 (tp) REVERT: F 603 ILE cc_start: 0.9614 (mt) cc_final: 0.9295 (mp) REVERT: A 109 ILE cc_start: 0.9539 (mt) cc_final: 0.9323 (tt) REVERT: A 122 LEU cc_start: 0.9356 (mt) cc_final: 0.9080 (mm) REVERT: A 382 PHE cc_start: 0.9199 (m-80) cc_final: 0.8883 (m-10) REVERT: B 577 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9161 (tm-30) REVERT: B 626 MET cc_start: 0.7673 (mpp) cc_final: 0.7424 (mpp) REVERT: B 646 LEU cc_start: 0.9493 (mt) cc_final: 0.9237 (mt) outliers start: 1 outliers final: 0 residues processed: 198 average time/residue: 0.2799 time to fit residues: 83.2733 Evaluate side-chains 148 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 chunk 149 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 115 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 ASN A 85 HIS A 183 GLN B 575 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.5901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16329 Z= 0.265 Angle : 0.661 9.248 22208 Z= 0.329 Chirality : 0.046 0.279 2856 Planarity : 0.003 0.032 2707 Dihedral : 7.278 57.919 4163 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % 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: -0.19 (0.20), residues: 1673 helix: 1.40 (0.27), residues: 407 sheet: -0.33 (0.23), residues: 457 loop : -0.74 (0.22), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP E 479 HIS 0.004 0.001 HIS D 570 PHE 0.044 0.002 PHE D 522 TYR 0.013 0.002 TYR C 40 ARG 0.005 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 200 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 1.605 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: 0.8205 (m-10) cc_final: 0.7957 (m-80) REVERT: C 195 ASN cc_start: 0.8444 (t0) cc_final: 0.8096 (t0) REVERT: D 536 THR cc_start: 0.8611 (m) cc_final: 0.8038 (t) REVERT: D 584 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8215 (tm-30) REVERT: D 638 TYR cc_start: 0.8963 (m-80) cc_final: 0.8690 (m-80) REVERT: D 647 GLU cc_start: 0.9193 (pp20) cc_final: 0.8818 (pp20) REVERT: D 654 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8039 (tm-30) REVERT: E 95 MET cc_start: 0.9468 (ptm) cc_final: 0.8637 (ppp) REVERT: E 161 MET cc_start: 0.8954 (tpt) cc_final: 0.8671 (tpp) REVERT: F 565 LEU cc_start: 0.9085 (mt) cc_final: 0.8599 (tp) REVERT: F 603 ILE cc_start: 0.9656 (mt) cc_final: 0.9340 (mp) REVERT: F 654 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8828 (tm-30) REVERT: F 655 LYS cc_start: 0.8763 (pttm) cc_final: 0.8501 (pttm) REVERT: A 109 ILE cc_start: 0.9552 (mt) cc_final: 0.9269 (tt) REVERT: A 122 LEU cc_start: 0.9299 (mt) cc_final: 0.9028 (mm) REVERT: A 382 PHE cc_start: 0.9169 (m-80) cc_final: 0.8810 (m-10) REVERT: B 577 GLN cc_start: 0.9409 (tm-30) cc_final: 0.9126 (tm-30) REVERT: B 654 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8577 (tm-30) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2666 time to fit residues: 79.7485 Evaluate side-chains 155 residues out of total 1536 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.596 ------------------------------------------------------------------------------- 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: 6.9990 chunk 138 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 19 optimal weight: 20.0000 chunk 27 optimal weight: 0.5980 chunk 131 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.053546 restraints weight = 73843.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.054924 restraints weight = 45819.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.055878 restraints weight = 33748.328| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16329 Z= 0.220 Angle : 0.632 9.249 22208 Z= 0.316 Chirality : 0.045 0.242 2856 Planarity : 0.003 0.031 2707 Dihedral : 6.937 57.327 4163 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.20), residues: 1673 helix: 1.47 (0.27), residues: 407 sheet: -0.28 (0.23), residues: 455 loop : -0.70 (0.22), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP E 45 HIS 0.003 0.001 HIS D 564 PHE 0.040 0.002 PHE D 522 TYR 0.028 0.001 TYR F 638 ARG 0.005 0.000 ARG D 542 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2937.36 seconds wall clock time: 54 minutes 3.15 seconds (3243.15 seconds total)