Starting phenix.real_space_refine on Sun Nov 17 00:31:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sgf_25109/11_2024/7sgf_25109.cif" } resolution = 4.41 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= 0.001 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 90 5.16 5 C 7404 2.51 5 N 2031 2.21 5 O 2553 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12078 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "a" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "H" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "L" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "b" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "J" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "K" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1394 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 4, 'TRANS': 173} Chain breaks: 2 Chain: "c" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1137 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "M" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 595 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'PTRANS': 2, 'TRANS': 119} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 386 Unresolved non-hydrogen angles: 511 Unresolved non-hydrogen dihedrals: 340 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'TRP:plan': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 231 Chain: "N" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 523 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 277 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 230 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 145 Chain: "D" 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: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: "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: "I" 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "R" 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: "S" 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: "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: 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: "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: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Z" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "d" 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: "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: 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: "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: 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: "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: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "l" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "m" 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: "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 Time building chain proxies: 8.88, per 1000 atoms: 0.74 Number of scatterers: 12078 At special positions: 0 Unit cell: (143.17, 135.96, 95.79, 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 90 16.00 O 2553 8.00 N 2031 7.00 C 7404 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.08 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.01 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.04 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.08 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.01 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.04 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.08 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.01 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.04 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA F 3 " - " MAN F 4 " " BMA U 3 " - " MAN U 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA F 3 " - " MAN F 5 " " BMA U 3 " - " MAN U 5 " " BMA g 3 " - " MAN g 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " 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 g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG k 2 " - " BMA k 3 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " " NAG m 2 " - " BMA m 3 " BETA1-6 " NAG P 1 " - " FUC P 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG Q 1 " - " FUC Q 3 " " NAG Y 1 " - " FUC Y 4 " " NAG Z 1 " - " FUC Z 3 " " NAG k 1 " - " FUC k 4 " " NAG l 1 " - " FUC l 3 " NAG-ASN " NAG A 701 " - " ASN A 99 " " NAG A 702 " - " ASN A 224 " " NAG B 701 " - " ASN B 99 " " NAG B 702 " - " ASN B 224 " " NAG C 701 " - " ASN C 99 " " NAG C 702 " - " ASN C 224 " " NAG D 1 " - " ASN A 79 " " NAG E 1 " - " ASN A 89 " " NAG F 1 " - " ASN A 109 " " NAG G 1 " - " ASN A 119 " " NAG I 1 " - " ASN A 167 " " NAG O 1 " - " ASN a 373 " " NAG P 1 " - " ASN a 390 " " NAG Q 1 " - " ASN a 395 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN B 79 " " NAG T 1 " - " ASN B 89 " " NAG U 1 " - " ASN B 109 " " NAG V 1 " - " ASN B 119 " " NAG W 1 " - " ASN B 167 " " NAG X 1 " - " ASN b 373 " " NAG Y 1 " - " ASN b 390 " " NAG Z 1 " - " ASN b 395 " " NAG d 1 " - " ASN b 365 " " NAG e 1 " - " ASN C 79 " " NAG f 1 " - " ASN C 89 " " NAG g 1 " - " ASN C 109 " " NAG h 1 " - " ASN C 119 " " NAG i 1 " - " ASN C 167 " " NAG j 1 " - " ASN c 373 " " NAG k 1 " - " ASN c 390 " " NAG l 1 " - " ASN c 395 " " NAG m 1 " - " ASN c 365 " Time building additional restraints: 4.21 Conformation dependent library (CDL) restraints added in 1.8 seconds 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3012 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 27 sheets defined 23.9% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 245 Processing helix chain 'a' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP a 311 " --> pdb=" O GLU a 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 345 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.539A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 415 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP H 67 " --> pdb=" O TRP H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing helix chain 'B' and resid 74 through 79 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 245 Processing helix chain 'b' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 415 Processing helix chain 'J' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP J 67 " --> pdb=" O TRP J 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 64 through 67' Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'C' and resid 74 through 79 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 245 Processing helix chain 'c' and resid 294 through 304 removed outlier: 4.105A pdb=" N VAL c 298 " --> pdb=" O GLY c 294 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 327 removed outlier: 3.762A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 345 Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.538A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 415 Processing helix chain 'M' and resid 64 through 67 removed outlier: 3.520A pdb=" N ASP M 67 " --> pdb=" O TRP M 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 64 through 67' Processing helix chain 'M' and resid 87 through 91 Processing helix chain 'N' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 87 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY H 16 " --> pdb=" O GLY H 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR H 78 " --> pdb=" O THR H 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR H 74 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 80 " --> pdb=" O SER H 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER H 72 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN H 82 " --> pdb=" O SER H 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS H 96 " --> pdb=" O TRP H 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP H 116 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS H 98 " --> pdb=" O ASP H 114 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG H 109 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL L 11 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN b 365 " --> pdb=" O TRP b 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP b 386 " --> pdb=" O ASN b 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER b 367 " --> pdb=" O LYS b 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS b 384 " --> pdb=" O SER b 367 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB4, first strand: chain 'J' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY J 16 " --> pdb=" O GLY J 85 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR J 78 " --> pdb=" O THR J 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR J 74 " --> pdb=" O THR J 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR J 80 " --> pdb=" O SER J 72 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER J 72 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN J 82 " --> pdb=" O SER J 70 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG J 39 " --> pdb=" O TRP J 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP J 48 " --> pdb=" O ARG J 39 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 10 through 11 removed outlier: 7.287A pdb=" N CYS J 96 " --> pdb=" O TRP J 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP J 116 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS J 98 " --> pdb=" O ASP J 114 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 102 through 103 removed outlier: 3.567A pdb=" N ARG J 109 " --> pdb=" O ARG J 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB9, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL K 11 " --> pdb=" O VAL K 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AC2, first strand: chain 'C' and resid 61 through 62 removed outlier: 4.441A pdb=" N ASN c 365 " --> pdb=" O TRP c 386 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TRP c 386 " --> pdb=" O ASN c 365 " (cutoff:3.500A) removed outlier: 9.167A pdb=" N SER c 367 " --> pdb=" O LYS c 384 " (cutoff:3.500A) removed outlier: 10.553A pdb=" N LYS c 384 " --> pdb=" O SER c 367 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 84 through 87 Processing sheet with id=AC4, first strand: chain 'M' and resid 4 through 7 removed outlier: 5.409A pdb=" N GLY M 16 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR M 78 " --> pdb=" O THR M 74 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N THR M 74 " --> pdb=" O THR M 78 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR M 80 " --> pdb=" O SER M 72 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER M 72 " --> pdb=" O THR M 80 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLN M 82 " --> pdb=" O SER M 70 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.944A pdb=" N ARG M 39 " --> pdb=" O TRP M 48 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TRP M 48 " --> pdb=" O ARG M 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 10 through 11 removed outlier: 7.286A pdb=" N CYS M 96 " --> pdb=" O TRP M 116 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N TRP M 116 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS M 98 " --> pdb=" O ASP M 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 102 through 103 removed outlier: 3.568A pdb=" N ARG M 109 " --> pdb=" O ARG M 103 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AC9, first strand: chain 'N' and resid 10 through 12 removed outlier: 7.595A pdb=" N VAL N 11 " --> pdb=" O VAL N 109 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLN N 39 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU N 48 " --> pdb=" O GLN N 39 " (cutoff:3.500A) 573 hydrogen bonds defined for protein. 1458 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: 3.85 Time building geometry restraints manager: 4.68 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: 3101 1.33 - 1.47: 3750 1.47 - 1.60: 5224 1.60 - 1.74: 24 1.74 - 1.88: 132 Bond restraints: 12231 Sorted by residual: bond pdb=" CB TYR C 94 " pdb=" CG TYR C 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR A 94 " pdb=" CG TYR A 94 " ideal model delta sigma weight residual 1.512 1.390 0.122 2.20e-02 2.07e+03 3.06e+01 bond pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 1.512 1.391 0.121 2.20e-02 2.07e+03 3.05e+01 bond pdb=" CB LEU a 415 " pdb=" CG LEU a 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" CB LEU b 415 " pdb=" CG LEU b 415 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.69e+01 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 13416 2.38 - 4.77: 2660 4.77 - 7.15: 458 7.15 - 9.54: 87 9.54 - 11.92: 29 Bond angle restraints: 16650 Sorted by residual: angle pdb=" N VAL A 65 " pdb=" CA VAL A 65 " pdb=" C VAL A 65 " ideal model delta sigma weight residual 112.90 121.94 -9.04 9.60e-01 1.09e+00 8.86e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.84e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 112.90 121.92 -9.02 9.60e-01 1.09e+00 8.83e+01 angle pdb=" N PHE M 104 " pdb=" CA PHE M 104 " pdb=" C PHE M 104 " ideal model delta sigma weight residual 112.92 124.32 -11.40 1.23e+00 6.61e-01 8.59e+01 angle pdb=" N PHE J 104 " pdb=" CA PHE J 104 " pdb=" C PHE J 104 " ideal model delta sigma weight residual 112.92 124.31 -11.39 1.23e+00 6.61e-01 8.58e+01 ... (remaining 16645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.23: 7881 21.23 - 42.46: 240 42.46 - 63.69: 36 63.69 - 84.92: 87 84.92 - 106.16: 75 Dihedral angle restraints: 8319 sinusoidal: 3639 harmonic: 4680 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.62 85.62 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual -86.00 -171.60 85.60 1 1.00e+01 1.00e-02 8.86e+01 ... (remaining 8316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1390 0.105 - 0.209: 495 0.209 - 0.314: 186 0.314 - 0.418: 71 0.418 - 0.523: 60 Chirality restraints: 2202 Sorted by residual: chirality pdb=" C1 BMA e 3 " pdb=" O4 NAG e 2 " pdb=" C2 BMA e 3 " pdb=" O5 BMA e 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.42e+02 chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.39e+02 ... (remaining 2199 not shown) Planarity restraints: 2103 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG W 1 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG W 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG W 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG W 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG i 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.82e+02 pdb=" C7 NAG i 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG i 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG i 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG i 1 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " 0.297 2.00e-02 2.50e+03 2.50e-01 7.81e+02 pdb=" C7 NAG I 1 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " -0.428 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.020 2.00e-02 2.50e+03 ... (remaining 2100 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 4235 2.86 - 3.37: 11353 3.37 - 3.88: 19394 3.88 - 4.39: 22062 4.39 - 4.90: 34281 Nonbonded interactions: 91325 Sorted by model distance: nonbonded pdb=" O3 NAG S 2 " pdb=" O7 NAG S 2 " model vdw 2.354 3.040 nonbonded pdb=" O3 NAG D 2 " pdb=" O7 NAG D 2 " model vdw 2.355 3.040 nonbonded pdb=" O3 NAG e 2 " pdb=" O7 NAG e 2 " model vdw 2.355 3.040 nonbonded pdb=" N TYR C 200 " pdb=" N ILE C 201 " model vdw 2.381 2.560 nonbonded pdb=" N TYR B 200 " pdb=" N ILE B 201 " model vdw 2.382 2.560 ... (remaining 91320 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'i' and resid 1 through 2) selection = (chain 'l' and resid 1 through 2) selection = (chain 'm' and resid 1 through 2) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'O' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'F' selection = chain 'U' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'P' selection = chain 'Y' selection = chain 'k' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 33.020 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.070 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 0.149 12231 Z= 1.451 Angle : 2.044 11.923 16650 Z= 1.323 Chirality : 0.151 0.523 2202 Planarity : 0.014 0.250 2070 Dihedral : 17.976 106.156 5244 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.19), residues: 1605 helix: 0.11 (0.24), residues: 315 sheet: 0.86 (0.27), residues: 333 loop : -0.33 (0.19), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.008 TRP a 370 HIS 0.008 0.002 HIS a 354 PHE 0.031 0.006 PHE b 309 TYR 0.079 0.010 TYR b 363 ARG 0.002 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.456 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: A 125 LYS cc_start: 0.6735 (mttt) cc_final: 0.6479 (mmtt) REVERT: A 144 ILE cc_start: 0.8021 (mt) cc_final: 0.7700 (mt) REVERT: A 200 TYR cc_start: 0.8807 (p90) cc_final: 0.8545 (p90) REVERT: A 217 TYR cc_start: 0.7930 (m-80) cc_final: 0.6916 (m-80) REVERT: A 227 TRP cc_start: 0.7889 (p90) cc_final: 0.7245 (p-90) REVERT: A 228 GLU cc_start: 0.8290 (pm20) cc_final: 0.7973 (pp20) REVERT: A 236 PRO cc_start: 0.8505 (Cg_endo) cc_final: 0.7930 (Cg_exo) REVERT: a 308 GLU cc_start: 0.8539 (mp0) cc_final: 0.8275 (mm-30) REVERT: a 371 TYR cc_start: 0.7382 (m-80) cc_final: 0.7112 (m-80) REVERT: a 396 GLU cc_start: 0.8773 (mp0) cc_final: 0.8567 (mp0) REVERT: B 144 ILE cc_start: 0.8029 (mt) cc_final: 0.7744 (mt) REVERT: B 217 TYR cc_start: 0.7811 (m-80) cc_final: 0.6836 (m-80) REVERT: B 227 TRP cc_start: 0.7911 (p90) cc_final: 0.7378 (p-90) REVERT: B 228 GLU cc_start: 0.8067 (pm20) cc_final: 0.7751 (pp20) REVERT: B 236 PRO cc_start: 0.8579 (Cg_endo) cc_final: 0.8051 (Cg_exo) REVERT: b 311 ASP cc_start: 0.8674 (m-30) cc_final: 0.8204 (t0) REVERT: b 371 TYR cc_start: 0.7389 (m-80) cc_final: 0.7024 (m-80) REVERT: b 396 GLU cc_start: 0.8700 (mp0) cc_final: 0.8468 (mp0) REVERT: C 78 LEU cc_start: 0.8753 (mt) cc_final: 0.8470 (mp) REVERT: C 144 ILE cc_start: 0.8057 (mt) cc_final: 0.7749 (mt) REVERT: C 211 ASP cc_start: 0.8000 (p0) cc_final: 0.7613 (p0) REVERT: C 217 TYR cc_start: 0.7983 (m-80) cc_final: 0.7076 (m-80) REVERT: C 236 PRO cc_start: 0.8575 (Cg_endo) cc_final: 0.7970 (Cg_exo) REVERT: c 311 ASP cc_start: 0.8598 (m-30) cc_final: 0.8211 (t0) REVERT: c 316 PHE cc_start: 0.8584 (m-80) cc_final: 0.8191 (m-10) REVERT: c 321 GLN cc_start: 0.8332 (mt0) cc_final: 0.7953 (mm-40) REVERT: c 396 GLU cc_start: 0.8699 (mp0) cc_final: 0.8497 (mp0) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2707 time to fit residues: 132.0897 Evaluate side-chains 188 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS A 141 HIS ** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 321 GLN a 331 GLN B 92 HIS B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 338 ASN b 405 GLN C 92 HIS C 141 HIS ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 12231 Z= 0.436 Angle : 1.036 9.380 16650 Z= 0.521 Chirality : 0.056 0.392 2202 Planarity : 0.005 0.037 2070 Dihedral : 15.582 105.563 3450 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.70 % Allowed : 6.55 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.39 (0.19), residues: 1605 helix: 0.32 (0.27), residues: 345 sheet: 0.51 (0.30), residues: 300 loop : -0.72 (0.18), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 210 HIS 0.015 0.003 HIS B 230 PHE 0.026 0.003 PHE A 233 TYR 0.034 0.004 TYR B 66 ARG 0.007 0.001 ARG b 325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 242 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7708 (mtm) cc_final: 0.7332 (ppp) REVERT: A 156 ASP cc_start: 0.7418 (t0) cc_final: 0.6943 (t70) REVERT: A 161 LYS cc_start: 0.8771 (ptpp) cc_final: 0.8327 (pttt) REVERT: A 200 TYR cc_start: 0.8574 (p90) cc_final: 0.8316 (p90) REVERT: A 217 TYR cc_start: 0.7590 (m-80) cc_final: 0.7294 (m-80) REVERT: A 228 GLU cc_start: 0.8512 (pm20) cc_final: 0.7694 (pp20) REVERT: A 236 PRO cc_start: 0.9058 (Cg_endo) cc_final: 0.8593 (Cg_exo) REVERT: a 311 ASP cc_start: 0.9005 (m-30) cc_final: 0.8728 (m-30) REVERT: a 335 GLN cc_start: 0.9086 (pm20) cc_final: 0.8620 (pm20) REVERT: a 336 LEU cc_start: 0.9146 (tp) cc_final: 0.8703 (tp) REVERT: a 339 LYS cc_start: 0.9344 (mppt) cc_final: 0.9130 (mptt) REVERT: a 363 TYR cc_start: 0.7606 (p90) cc_final: 0.7215 (p90) REVERT: a 371 TYR cc_start: 0.6780 (m-80) cc_final: 0.6450 (m-80) REVERT: a 396 GLU cc_start: 0.8625 (mp0) cc_final: 0.8251 (mp0) REVERT: a 408 ASP cc_start: 0.7767 (t0) cc_final: 0.7457 (t70) REVERT: a 410 MET cc_start: 0.8931 (mtt) cc_final: 0.8611 (mtp) REVERT: B 96 MET cc_start: 0.7742 (mtm) cc_final: 0.7514 (ppp) REVERT: B 156 ASP cc_start: 0.7186 (t0) cc_final: 0.6914 (t70) REVERT: B 161 LYS cc_start: 0.8660 (ptpp) cc_final: 0.8296 (pttt) REVERT: B 193 ARG cc_start: 0.8576 (mtm180) cc_final: 0.8333 (mtm-85) REVERT: B 217 TYR cc_start: 0.7625 (m-80) cc_final: 0.7331 (m-80) REVERT: B 228 GLU cc_start: 0.8498 (pm20) cc_final: 0.7934 (pp20) REVERT: B 236 PRO cc_start: 0.9208 (Cg_endo) cc_final: 0.8573 (Cg_exo) REVERT: b 311 ASP cc_start: 0.8910 (m-30) cc_final: 0.8676 (m-30) REVERT: b 335 GLN cc_start: 0.8990 (pm20) cc_final: 0.8651 (pm20) REVERT: b 396 GLU cc_start: 0.8672 (mp0) cc_final: 0.8273 (mp0) REVERT: b 408 ASP cc_start: 0.7652 (t0) cc_final: 0.7336 (t70) REVERT: b 410 MET cc_start: 0.9167 (mtt) cc_final: 0.8830 (mtp) REVERT: C 116 LYS cc_start: 0.8128 (mttt) cc_final: 0.7487 (tptt) REVERT: C 134 MET cc_start: 0.7260 (ttp) cc_final: 0.5538 (mtt) REVERT: C 156 ASP cc_start: 0.7263 (t0) cc_final: 0.6818 (t70) REVERT: C 161 LYS cc_start: 0.8746 (ptpp) cc_final: 0.8318 (pttt) REVERT: C 236 PRO cc_start: 0.9091 (Cg_endo) cc_final: 0.8493 (Cg_exo) REVERT: c 396 GLU cc_start: 0.8669 (mp0) cc_final: 0.8415 (mp0) REVERT: c 408 ASP cc_start: 0.7827 (t0) cc_final: 0.7591 (t70) REVERT: c 410 MET cc_start: 0.8906 (mtt) cc_final: 0.8569 (mtp) outliers start: 6 outliers final: 2 residues processed: 246 average time/residue: 0.2569 time to fit residues: 89.0070 Evaluate side-chains 180 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 178 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 30.0000 chunk 120 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 144 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 116 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN a 331 GLN a 338 ASN a 374 HIS ** a 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS b 338 ASN b 374 HIS ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 374 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 12231 Z= 0.314 Angle : 0.871 13.815 16650 Z= 0.431 Chirality : 0.050 0.357 2202 Planarity : 0.004 0.043 2070 Dihedral : 12.619 93.433 3450 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.94 % Allowed : 5.03 % Favored : 94.04 % 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: -0.53 (0.20), residues: 1605 helix: 0.62 (0.29), residues: 339 sheet: 0.41 (0.28), residues: 315 loop : -1.00 (0.19), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP a 386 HIS 0.007 0.002 HIS A 141 PHE 0.034 0.002 PHE b 399 TYR 0.029 0.003 TYR C 66 ARG 0.006 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 241 time to evaluate : 1.543 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: A 71 LEU cc_start: 0.8682 (tt) cc_final: 0.8480 (mp) REVERT: A 156 ASP cc_start: 0.7486 (t0) cc_final: 0.7183 (t70) REVERT: A 200 TYR cc_start: 0.8585 (p90) cc_final: 0.8300 (p90) REVERT: A 217 TYR cc_start: 0.7669 (m-80) cc_final: 0.7324 (m-80) REVERT: A 228 GLU cc_start: 0.8462 (pm20) cc_final: 0.7841 (pp20) REVERT: A 236 PRO cc_start: 0.9191 (Cg_endo) cc_final: 0.8745 (Cg_exo) REVERT: a 308 GLU cc_start: 0.8501 (pm20) cc_final: 0.7943 (mm-30) REVERT: a 331 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: a 335 GLN cc_start: 0.9137 (pm20) cc_final: 0.8917 (pm20) REVERT: a 336 LEU cc_start: 0.9143 (tp) cc_final: 0.8935 (tp) REVERT: a 351 MET cc_start: 0.8855 (mmp) cc_final: 0.8615 (tpp) REVERT: a 363 TYR cc_start: 0.7634 (p90) cc_final: 0.7411 (p90) REVERT: a 371 TYR cc_start: 0.7140 (m-80) cc_final: 0.6937 (m-80) REVERT: a 408 ASP cc_start: 0.7741 (t0) cc_final: 0.7410 (t70) REVERT: a 410 MET cc_start: 0.8987 (mtt) cc_final: 0.8767 (mtp) REVERT: B 156 ASP cc_start: 0.7497 (t0) cc_final: 0.7257 (t70) REVERT: B 193 ARG cc_start: 0.8595 (mtm180) cc_final: 0.8235 (mtm-85) REVERT: B 217 TYR cc_start: 0.7686 (m-80) cc_final: 0.7379 (m-80) REVERT: B 228 GLU cc_start: 0.8344 (pm20) cc_final: 0.7800 (pp20) REVERT: B 236 PRO cc_start: 0.9224 (Cg_endo) cc_final: 0.8811 (Cg_exo) REVERT: b 308 GLU cc_start: 0.8555 (pm20) cc_final: 0.8200 (mm-30) REVERT: b 371 TYR cc_start: 0.7408 (m-80) cc_final: 0.6827 (m-80) REVERT: b 408 ASP cc_start: 0.7546 (t0) cc_final: 0.7236 (t70) REVERT: C 116 LYS cc_start: 0.8154 (mttt) cc_final: 0.7533 (tptt) REVERT: C 134 MET cc_start: 0.6966 (ttp) cc_final: 0.5669 (mtt) REVERT: C 142 LEU cc_start: 0.9132 (pp) cc_final: 0.8887 (mm) REVERT: C 156 ASP cc_start: 0.7268 (t0) cc_final: 0.6098 (t70) REVERT: C 161 LYS cc_start: 0.8713 (ptpp) cc_final: 0.7985 (pttt) REVERT: C 189 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8773 (tp40) REVERT: C 217 TYR cc_start: 0.7385 (m-80) cc_final: 0.7009 (m-80) REVERT: C 236 PRO cc_start: 0.8989 (Cg_endo) cc_final: 0.8667 (Cg_exo) REVERT: c 311 ASP cc_start: 0.8930 (m-30) cc_final: 0.8606 (m-30) REVERT: c 321 GLN cc_start: 0.8523 (mt0) cc_final: 0.8048 (mm-40) REVERT: c 363 TYR cc_start: 0.7286 (p90) cc_final: 0.6746 (p90) REVERT: c 408 ASP cc_start: 0.7609 (t0) cc_final: 0.7344 (t70) REVERT: c 410 MET cc_start: 0.9009 (mtt) cc_final: 0.8779 (mtp) outliers start: 8 outliers final: 1 residues processed: 243 average time/residue: 0.2556 time to fit residues: 88.0633 Evaluate side-chains 185 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 183 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 30.0000 chunk 145 optimal weight: 20.0000 chunk 153 optimal weight: 3.9990 chunk 137 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS b 331 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12231 Z= 0.291 Angle : 0.840 8.659 16650 Z= 0.412 Chirality : 0.049 0.342 2202 Planarity : 0.004 0.045 2070 Dihedral : 10.724 84.000 3450 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.23 % Allowed : 6.32 % Favored : 93.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1605 helix: 0.71 (0.29), residues: 321 sheet: 0.17 (0.29), residues: 318 loop : -1.09 (0.19), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 386 HIS 0.007 0.001 HIS A 124 PHE 0.017 0.002 PHE b 399 TYR 0.035 0.003 TYR b 366 ARG 0.003 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 236 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.7993 (ptm) cc_final: 0.6877 (ppp) REVERT: A 217 TYR cc_start: 0.7539 (m-80) cc_final: 0.7100 (m-80) REVERT: A 228 GLU cc_start: 0.8179 (pm20) cc_final: 0.7840 (pp20) REVERT: a 311 ASP cc_start: 0.9005 (m-30) cc_final: 0.8753 (m-30) REVERT: a 351 MET cc_start: 0.8936 (mmp) cc_final: 0.8494 (tpp) REVERT: a 408 ASP cc_start: 0.7716 (t0) cc_final: 0.7360 (t70) REVERT: B 96 MET cc_start: 0.7730 (ppp) cc_final: 0.7121 (ppp) REVERT: B 217 TYR cc_start: 0.7875 (m-80) cc_final: 0.7518 (m-80) REVERT: B 227 TRP cc_start: 0.7797 (p90) cc_final: 0.7349 (p-90) REVERT: b 308 GLU cc_start: 0.8385 (pm20) cc_final: 0.8100 (mp0) REVERT: b 371 TYR cc_start: 0.7549 (m-80) cc_final: 0.7031 (m-80) REVERT: b 410 MET cc_start: 0.8909 (mtt) cc_final: 0.8672 (mtp) REVERT: C 75 MET cc_start: 0.8317 (mmt) cc_final: 0.7526 (mmt) REVERT: C 96 MET cc_start: 0.8031 (ppp) cc_final: 0.7361 (ppp) REVERT: C 116 LYS cc_start: 0.8161 (mttt) cc_final: 0.7567 (tptt) REVERT: C 134 MET cc_start: 0.7102 (ttp) cc_final: 0.5740 (mtt) REVERT: C 193 ARG cc_start: 0.8481 (mtm-85) cc_final: 0.8021 (mtm-85) REVERT: C 217 TYR cc_start: 0.7584 (m-80) cc_final: 0.7291 (m-80) REVERT: c 284 MET cc_start: 0.8397 (ptp) cc_final: 0.7968 (ptp) REVERT: c 311 ASP cc_start: 0.8871 (m-30) cc_final: 0.8606 (m-30) REVERT: c 321 GLN cc_start: 0.8529 (mt0) cc_final: 0.7970 (mm-40) REVERT: c 332 MET cc_start: 0.7650 (mtp) cc_final: 0.7198 (mtt) REVERT: c 333 SER cc_start: 0.9236 (p) cc_final: 0.8968 (m) REVERT: c 336 LEU cc_start: 0.9053 (tp) cc_final: 0.8764 (tp) REVERT: c 339 LYS cc_start: 0.9271 (mptt) cc_final: 0.9068 (mptt) REVERT: c 363 TYR cc_start: 0.7319 (p90) cc_final: 0.6992 (p90) REVERT: c 408 ASP cc_start: 0.7529 (t0) cc_final: 0.7320 (t70) outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.2599 time to fit residues: 86.1460 Evaluate side-chains 176 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 137 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 189 GLN a 406 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 GLN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.5820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 12231 Z= 0.367 Angle : 0.882 10.058 16650 Z= 0.437 Chirality : 0.049 0.350 2202 Planarity : 0.005 0.061 2070 Dihedral : 10.194 75.641 3450 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.17 (0.20), residues: 1605 helix: 0.02 (0.27), residues: 324 sheet: -0.06 (0.28), residues: 342 loop : -1.38 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP a 386 HIS 0.009 0.002 HIS B 141 PHE 0.026 0.003 PHE B 191 TYR 0.023 0.003 TYR b 366 ARG 0.005 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 211 time to evaluate : 1.307 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: A 96 MET cc_start: 0.7943 (ppp) cc_final: 0.7212 (ppp) REVERT: A 200 TYR cc_start: 0.8567 (p90) cc_final: 0.8325 (p90) REVERT: A 217 TYR cc_start: 0.7577 (m-80) cc_final: 0.6934 (m-80) REVERT: a 308 GLU cc_start: 0.8699 (mp0) cc_final: 0.8073 (mp0) REVERT: a 311 ASP cc_start: 0.9008 (m-30) cc_final: 0.8698 (m-30) REVERT: a 351 MET cc_start: 0.8904 (mmp) cc_final: 0.8462 (tpp) REVERT: a 410 MET cc_start: 0.9186 (mtp) cc_final: 0.8982 (mtp) REVERT: B 75 MET cc_start: 0.8070 (mmm) cc_final: 0.7705 (mmt) REVERT: B 96 MET cc_start: 0.8008 (ppp) cc_final: 0.7446 (ppp) REVERT: B 193 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8565 (mtm-85) REVERT: B 217 TYR cc_start: 0.7991 (m-80) cc_final: 0.7604 (m-80) REVERT: b 308 GLU cc_start: 0.8640 (mp0) cc_final: 0.8261 (mm-30) REVERT: b 371 TYR cc_start: 0.7581 (m-80) cc_final: 0.7119 (m-80) REVERT: b 410 MET cc_start: 0.9008 (mtt) cc_final: 0.8744 (mtp) REVERT: C 75 MET cc_start: 0.8394 (mmt) cc_final: 0.7737 (mmt) REVERT: C 96 MET cc_start: 0.8338 (ppp) cc_final: 0.7673 (ppp) REVERT: C 116 LYS cc_start: 0.8218 (mttt) cc_final: 0.7496 (tptt) REVERT: C 134 MET cc_start: 0.7264 (ttp) cc_final: 0.5829 (mtt) REVERT: c 311 ASP cc_start: 0.9089 (m-30) cc_final: 0.8718 (m-30) REVERT: c 321 GLN cc_start: 0.8509 (mt0) cc_final: 0.7765 (mm-40) REVERT: c 325 ARG cc_start: 0.8706 (mpt180) cc_final: 0.7713 (mpt180) REVERT: c 410 MET cc_start: 0.8791 (mtt) cc_final: 0.8519 (mtp) outliers start: 0 outliers final: 0 residues processed: 211 average time/residue: 0.2593 time to fit residues: 77.4798 Evaluate side-chains 164 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 40.0000 chunk 30 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 50 optimal weight: 30.0000 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12231 Z= 0.261 Angle : 0.813 9.394 16650 Z= 0.397 Chirality : 0.049 0.341 2202 Planarity : 0.004 0.054 2070 Dihedral : 9.737 67.991 3450 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.12 % Allowed : 4.80 % Favored : 95.09 % 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: -1.23 (0.20), residues: 1605 helix: 0.21 (0.28), residues: 327 sheet: -0.25 (0.27), residues: 342 loop : -1.45 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP a 386 HIS 0.020 0.001 HIS B 141 PHE 0.022 0.002 PHE C 191 TYR 0.033 0.002 TYR b 366 ARG 0.007 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.7920 (mmm) cc_final: 0.7456 (mmm) REVERT: A 96 MET cc_start: 0.7935 (ppp) cc_final: 0.7197 (ppp) REVERT: A 217 TYR cc_start: 0.7788 (m-80) cc_final: 0.7201 (m-80) REVERT: a 308 GLU cc_start: 0.8743 (mp0) cc_final: 0.8059 (mp0) REVERT: a 311 ASP cc_start: 0.8945 (m-30) cc_final: 0.8692 (m-30) REVERT: a 351 MET cc_start: 0.8827 (mmp) cc_final: 0.8547 (tpp) REVERT: a 363 TYR cc_start: 0.7552 (p90) cc_final: 0.7332 (p90) REVERT: a 411 ILE cc_start: 0.8514 (mm) cc_final: 0.8291 (tp) REVERT: B 96 MET cc_start: 0.7942 (ppp) cc_final: 0.7338 (ppp) REVERT: B 161 LYS cc_start: 0.8305 (pttm) cc_final: 0.8067 (pttp) REVERT: B 217 TYR cc_start: 0.7949 (m-80) cc_final: 0.7506 (m-80) REVERT: B 227 TRP cc_start: 0.7681 (p90) cc_final: 0.7378 (p90) REVERT: b 284 MET cc_start: 0.8059 (ptp) cc_final: 0.7651 (ptp) REVERT: b 308 GLU cc_start: 0.8690 (mp0) cc_final: 0.8191 (mm-30) REVERT: b 410 MET cc_start: 0.8875 (mtt) cc_final: 0.8563 (mtp) REVERT: C 75 MET cc_start: 0.8202 (mmt) cc_final: 0.7589 (mmt) REVERT: C 82 MET cc_start: 0.9133 (ptp) cc_final: 0.8560 (pmm) REVERT: C 96 MET cc_start: 0.8396 (ppp) cc_final: 0.7759 (ppp) REVERT: C 116 LYS cc_start: 0.8143 (mttt) cc_final: 0.7428 (tptt) REVERT: C 134 MET cc_start: 0.7309 (ttp) cc_final: 0.5930 (mtt) REVERT: C 142 LEU cc_start: 0.9118 (pp) cc_final: 0.8901 (mm) REVERT: c 284 MET cc_start: 0.7811 (ptt) cc_final: 0.7497 (ppp) REVERT: c 311 ASP cc_start: 0.9029 (m-30) cc_final: 0.8686 (m-30) REVERT: c 321 GLN cc_start: 0.8483 (mt0) cc_final: 0.7721 (mm-40) REVERT: c 325 ARG cc_start: 0.8578 (mpt180) cc_final: 0.7569 (mpt180) REVERT: c 333 SER cc_start: 0.9143 (p) cc_final: 0.8785 (m) REVERT: c 335 GLN cc_start: 0.9159 (pm20) cc_final: 0.8911 (pm20) REVERT: c 363 TYR cc_start: 0.7587 (p90) cc_final: 0.7068 (p90) outliers start: 1 outliers final: 0 residues processed: 216 average time/residue: 0.2591 time to fit residues: 78.6859 Evaluate side-chains 163 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 112 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 85 optimal weight: 0.3980 chunk 153 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12231 Z= 0.208 Angle : 0.768 9.610 16650 Z= 0.374 Chirality : 0.047 0.364 2202 Planarity : 0.004 0.057 2070 Dihedral : 9.079 59.571 3450 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -1.08 (0.20), residues: 1605 helix: 0.46 (0.28), residues: 324 sheet: -0.24 (0.28), residues: 318 loop : -1.33 (0.19), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 210 HIS 0.005 0.001 HIS A 141 PHE 0.016 0.001 PHE B 157 TYR 0.025 0.002 TYR b 366 ARG 0.006 0.001 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 223 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8015 (ppp) cc_final: 0.7401 (ppp) REVERT: A 217 TYR cc_start: 0.7652 (m-80) cc_final: 0.7070 (m-80) REVERT: a 284 MET cc_start: 0.7815 (pmm) cc_final: 0.7481 (pmm) REVERT: a 308 GLU cc_start: 0.8624 (mp0) cc_final: 0.7915 (mp0) REVERT: a 311 ASP cc_start: 0.8848 (m-30) cc_final: 0.8641 (m-30) REVERT: a 363 TYR cc_start: 0.7419 (p90) cc_final: 0.7165 (p90) REVERT: a 372 LEU cc_start: 0.6785 (tp) cc_final: 0.5562 (tp) REVERT: a 410 MET cc_start: 0.9087 (mtp) cc_final: 0.8817 (mtp) REVERT: B 82 MET cc_start: 0.8945 (ptp) cc_final: 0.8516 (pmm) REVERT: B 96 MET cc_start: 0.8031 (ppp) cc_final: 0.7438 (ppp) REVERT: B 217 TYR cc_start: 0.7772 (m-80) cc_final: 0.7323 (m-80) REVERT: B 236 PRO cc_start: 0.8940 (Cg_endo) cc_final: 0.8487 (Cg_exo) REVERT: b 284 MET cc_start: 0.8088 (ptp) cc_final: 0.7743 (ptp) REVERT: b 308 GLU cc_start: 0.8613 (mp0) cc_final: 0.8035 (mp0) REVERT: b 410 MET cc_start: 0.8931 (mtt) cc_final: 0.8549 (mtp) REVERT: C 75 MET cc_start: 0.8169 (mmt) cc_final: 0.7159 (mmt) REVERT: C 96 MET cc_start: 0.8250 (ppp) cc_final: 0.7628 (ppp) REVERT: C 116 LYS cc_start: 0.8137 (mttt) cc_final: 0.7408 (tptt) REVERT: C 134 MET cc_start: 0.7254 (ttp) cc_final: 0.5964 (mtt) REVERT: C 142 LEU cc_start: 0.9113 (pp) cc_final: 0.8873 (mm) REVERT: c 311 ASP cc_start: 0.8956 (m-30) cc_final: 0.8593 (m-30) REVERT: c 333 SER cc_start: 0.9140 (p) cc_final: 0.8853 (m) REVERT: c 334 ILE cc_start: 0.8042 (mp) cc_final: 0.7462 (mp) REVERT: c 410 MET cc_start: 0.8791 (mtt) cc_final: 0.8549 (mtp) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.2656 time to fit residues: 83.7627 Evaluate side-chains 163 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 97 optimal weight: 50.0000 chunk 104 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12231 Z= 0.400 Angle : 0.910 9.349 16650 Z= 0.454 Chirality : 0.049 0.343 2202 Planarity : 0.005 0.061 2070 Dihedral : 9.663 60.208 3450 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % 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: -1.69 (0.19), residues: 1605 helix: -0.28 (0.27), residues: 327 sheet: -0.55 (0.26), residues: 357 loop : -1.72 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 210 HIS 0.013 0.002 HIS A 230 PHE 0.028 0.003 PHE b 399 TYR 0.027 0.003 TYR b 366 ARG 0.009 0.001 ARG c 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8204 (ppp) cc_final: 0.7520 (ppp) REVERT: a 284 MET cc_start: 0.7809 (pmm) cc_final: 0.7471 (pmm) REVERT: a 308 GLU cc_start: 0.8753 (mp0) cc_final: 0.8027 (mp0) REVERT: a 311 ASP cc_start: 0.9087 (m-30) cc_final: 0.8724 (m-30) REVERT: a 363 TYR cc_start: 0.7750 (p90) cc_final: 0.7325 (p90) REVERT: a 410 MET cc_start: 0.9057 (mtp) cc_final: 0.8815 (mtp) REVERT: B 96 MET cc_start: 0.8106 (ppp) cc_final: 0.7449 (ppp) REVERT: B 217 TYR cc_start: 0.8105 (m-80) cc_final: 0.7554 (m-80) REVERT: B 236 PRO cc_start: 0.9040 (Cg_endo) cc_final: 0.8483 (Cg_exo) REVERT: b 284 MET cc_start: 0.8106 (ptp) cc_final: 0.7705 (ptp) REVERT: b 308 GLU cc_start: 0.8871 (mp0) cc_final: 0.8276 (mp0) REVERT: b 311 ASP cc_start: 0.8914 (m-30) cc_final: 0.8573 (m-30) REVERT: b 332 MET cc_start: 0.7222 (mtp) cc_final: 0.6727 (mtp) REVERT: b 410 MET cc_start: 0.8982 (mtt) cc_final: 0.8580 (mtp) REVERT: C 75 MET cc_start: 0.8299 (mmt) cc_final: 0.7413 (mmt) REVERT: C 96 MET cc_start: 0.8273 (ppp) cc_final: 0.7499 (ppp) REVERT: C 116 LYS cc_start: 0.8136 (mttt) cc_final: 0.7410 (tptt) REVERT: C 134 MET cc_start: 0.7507 (ttp) cc_final: 0.6398 (mtt) REVERT: c 311 ASP cc_start: 0.9047 (m-30) cc_final: 0.8757 (m-30) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2593 time to fit residues: 72.6592 Evaluate side-chains 155 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 85 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 129 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 151 optimal weight: 0.0060 overall best weight: 5.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 12231 Z= 0.402 Angle : 0.935 10.171 16650 Z= 0.465 Chirality : 0.052 0.389 2202 Planarity : 0.005 0.061 2070 Dihedral : 10.017 59.300 3450 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.04 (0.19), residues: 1605 helix: -0.48 (0.27), residues: 324 sheet: -0.65 (0.26), residues: 315 loop : -1.99 (0.18), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 227 HIS 0.013 0.002 HIS C 230 PHE 0.033 0.003 PHE A 157 TYR 0.031 0.003 TYR c 371 ARG 0.009 0.001 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8188 (ppp) cc_final: 0.7577 (ppp) REVERT: a 284 MET cc_start: 0.7787 (pmm) cc_final: 0.7324 (pmm) REVERT: a 308 GLU cc_start: 0.8897 (mp0) cc_final: 0.8111 (mp0) REVERT: a 311 ASP cc_start: 0.9082 (m-30) cc_final: 0.8648 (m-30) REVERT: a 363 TYR cc_start: 0.7717 (p90) cc_final: 0.7323 (p90) REVERT: a 410 MET cc_start: 0.8962 (mtp) cc_final: 0.8681 (mtp) REVERT: B 82 MET cc_start: 0.8957 (ptp) cc_final: 0.8596 (pmm) REVERT: B 96 MET cc_start: 0.8104 (ppp) cc_final: 0.7453 (ppp) REVERT: B 200 TYR cc_start: 0.8578 (p90) cc_final: 0.8375 (p90) REVERT: B 217 TYR cc_start: 0.8063 (m-80) cc_final: 0.7472 (m-80) REVERT: B 236 PRO cc_start: 0.9052 (Cg_endo) cc_final: 0.8657 (Cg_exo) REVERT: b 284 MET cc_start: 0.8174 (ptp) cc_final: 0.7807 (ptp) REVERT: b 308 GLU cc_start: 0.8929 (mp0) cc_final: 0.8319 (mp0) REVERT: b 311 ASP cc_start: 0.8871 (m-30) cc_final: 0.8420 (m-30) REVERT: b 410 MET cc_start: 0.9103 (mtt) cc_final: 0.8823 (mtp) REVERT: C 75 MET cc_start: 0.8285 (mmt) cc_final: 0.7517 (mmt) REVERT: C 96 MET cc_start: 0.8426 (ppp) cc_final: 0.7666 (ppp) REVERT: C 116 LYS cc_start: 0.8154 (mttt) cc_final: 0.7417 (tptt) REVERT: C 134 MET cc_start: 0.7569 (ttp) cc_final: 0.6505 (mtt) REVERT: c 284 MET cc_start: 0.7541 (pmm) cc_final: 0.7142 (pmm) REVERT: c 311 ASP cc_start: 0.9102 (m-30) cc_final: 0.8774 (m-30) REVERT: c 410 MET cc_start: 0.8889 (mtt) cc_final: 0.8684 (mtp) outliers start: 0 outliers final: 0 residues processed: 200 average time/residue: 0.2715 time to fit residues: 75.9122 Evaluate side-chains 155 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 20.0000 chunk 71 optimal weight: 0.0060 chunk 104 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 145 optimal weight: 30.0000 chunk 126 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 97 optimal weight: 40.0000 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 20.0000 chunk 134 optimal weight: 6.9990 overall best weight: 2.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12231 Z= 0.258 Angle : 0.832 9.120 16650 Z= 0.410 Chirality : 0.049 0.339 2202 Planarity : 0.005 0.074 2070 Dihedral : 9.434 57.343 3450 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.77 (0.19), residues: 1605 helix: -0.05 (0.28), residues: 324 sheet: -0.79 (0.26), residues: 342 loop : -1.79 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 227 HIS 0.007 0.001 HIS C 230 PHE 0.040 0.002 PHE C 233 TYR 0.023 0.002 TYR b 371 ARG 0.010 0.001 ARG A 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3210 Ramachandran restraints generated. 1605 Oldfield, 0 Emsley, 1605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8201 (ppp) cc_final: 0.7721 (ppp) REVERT: A 227 TRP cc_start: 0.7961 (p90) cc_final: 0.7433 (p90) REVERT: a 284 MET cc_start: 0.7813 (pmm) cc_final: 0.7359 (pmm) REVERT: a 308 GLU cc_start: 0.8842 (mp0) cc_final: 0.7962 (mp0) REVERT: a 311 ASP cc_start: 0.9014 (m-30) cc_final: 0.8656 (m-30) REVERT: a 363 TYR cc_start: 0.7622 (p90) cc_final: 0.7215 (p90) REVERT: a 410 MET cc_start: 0.8989 (mtp) cc_final: 0.8740 (mtp) REVERT: B 82 MET cc_start: 0.8895 (ptp) cc_final: 0.8636 (pmm) REVERT: B 96 MET cc_start: 0.8153 (ppp) cc_final: 0.7564 (ppp) REVERT: B 200 TYR cc_start: 0.8468 (p90) cc_final: 0.8183 (p90) REVERT: B 217 TYR cc_start: 0.7849 (m-80) cc_final: 0.7281 (m-80) REVERT: B 236 PRO cc_start: 0.9130 (Cg_endo) cc_final: 0.8678 (Cg_exo) REVERT: b 284 MET cc_start: 0.8109 (ptp) cc_final: 0.7696 (ptp) REVERT: b 308 GLU cc_start: 0.8803 (mp0) cc_final: 0.8168 (mp0) REVERT: b 311 ASP cc_start: 0.8739 (m-30) cc_final: 0.8335 (m-30) REVERT: b 410 MET cc_start: 0.9013 (mtt) cc_final: 0.8791 (mtp) REVERT: C 82 MET cc_start: 0.8949 (ptp) cc_final: 0.8415 (pmm) REVERT: C 96 MET cc_start: 0.8174 (ppp) cc_final: 0.7591 (ppp) REVERT: C 116 LYS cc_start: 0.8111 (mttt) cc_final: 0.7378 (tptt) REVERT: C 134 MET cc_start: 0.7649 (ttp) cc_final: 0.6722 (mtt) REVERT: C 142 LEU cc_start: 0.9143 (pp) cc_final: 0.8835 (mm) REVERT: C 193 ARG cc_start: 0.8596 (mmm-85) cc_final: 0.8353 (mmm-85) REVERT: c 284 MET cc_start: 0.7707 (pmm) cc_final: 0.7279 (pmm) REVERT: c 311 ASP cc_start: 0.9043 (m-30) cc_final: 0.8722 (m-30) outliers start: 0 outliers final: 0 residues processed: 207 average time/residue: 0.2292 time to fit residues: 67.5262 Evaluate side-chains 167 residues out of total 1419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 35 optimal weight: 40.0000 chunk 126 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.069995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.058639 restraints weight = 80315.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.059885 restraints weight = 52525.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.060745 restraints weight = 39436.252| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.7267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12231 Z= 0.432 Angle : 0.968 10.300 16650 Z= 0.483 Chirality : 0.052 0.334 2202 Planarity : 0.005 0.061 2070 Dihedral : 10.229 59.321 3450 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.31 (0.19), residues: 1605 helix: -0.57 (0.27), residues: 321 sheet: -1.05 (0.26), residues: 330 loop : -2.14 (0.18), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 210 HIS 0.015 0.003 HIS C 230 PHE 0.029 0.003 PHE A 233 TYR 0.040 0.003 TYR c 371 ARG 0.008 0.001 ARG C 193 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: