Starting phenix.real_space_refine on Mon Feb 19 21:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wm4_32599/02_2024/7wm4_32599.pdb" } resolution = 3.2 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= 0.001 sd= 0.017 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: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 56 5.16 5 C 15795 2.51 5 N 4273 2.21 5 O 5562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 497": "OD1" <-> "OD2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25848 Number of models: 1 Model: "" Number of chains: 38 Chain: "C" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "D" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "E" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5310 Classifications: {'peptide': 661} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 632} Chain breaks: 2 Chain: "F" Number of atoms: 5360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 668, 5360 Classifications: {'peptide': 668} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 639} Chain breaks: 1 Chain: "A" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1702 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 39, 'rna3p_pyr': 39} Link IDs: {'rna2p': 3, 'rna3p': 77} Chain: "B" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1700 Classifications: {'RNA': 81} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 39, 'rna3p_pyr': 41} Link IDs: {'rna2p': 1, 'rna3p': 79} Chain: "G" 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" 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: "L" 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: "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: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: "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: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" 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: 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 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: "g" 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: "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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.35, per 1000 atoms: 0.56 Number of scatterers: 25848 At special positions: 0 Unit cell: (223.344, 181.608, 110.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 162 15.00 O 5562 8.00 N 4273 7.00 C 15795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 38 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 650 " - pdb=" SG CYS C 678 " distance=2.03 Simple disulfide: pdb=" SG CYS C 652 " - pdb=" SG CYS C 697 " distance=2.03 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 38 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 650 " - pdb=" SG CYS D 678 " distance=2.03 Simple disulfide: pdb=" SG CYS D 652 " - pdb=" SG CYS D 697 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 38 " distance=2.03 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 123 " distance=2.03 Simple disulfide: pdb=" SG CYS E 650 " - pdb=" SG CYS E 678 " distance=2.03 Simple disulfide: pdb=" SG CYS E 652 " - pdb=" SG CYS E 697 " distance=2.03 Simple disulfide: pdb=" SG CYS F 29 " - pdb=" SG CYS F 38 " distance=2.03 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 123 " distance=2.03 Simple disulfide: pdb=" SG CYS F 650 " - pdb=" SG CYS F 678 " distance=2.03 Simple disulfide: pdb=" SG CYS F 652 " - pdb=" SG CYS F 697 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied BETA1-4 " 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 J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG C 801 " - " ASN C 71 " " NAG C 802 " - " ASN C 197 " " NAG D 801 " - " ASN D 71 " " NAG D 802 " - " ASN D 197 " " NAG D 803 " - " ASN D 276 " " NAG D 804 " - " ASN D 292 " " NAG E 801 " - " ASN E 71 " " NAG E 802 " - " ASN E 197 " " NAG F 801 " - " ASN F 71 " " NAG F 802 " - " ASN F 197 " " NAG F 803 " - " ASN F 276 " " NAG F 804 " - " ASN F 292 " " NAG G 1 " - " ASN C 248 " " NAG H 1 " - " ASN C 253 " " NAG I 1 " - " ASN C 276 " " NAG J 1 " - " ASN C 292 " " NAG K 1 " - " ASN C 399 " " NAG L 1 " - " ASN C 414 " " NAG M 1 " - " ASN C 425 " " NAG N 1 " - " ASN C 508 " " NAG O 1 " - " ASN D 248 " " NAG P 1 " - " ASN D 253 " " NAG Q 1 " - " ASN D 399 " " NAG R 1 " - " ASN D 414 " " NAG S 1 " - " ASN D 425 " " NAG T 1 " - " ASN D 508 " " NAG U 1 " - " ASN E 248 " " NAG V 1 " - " ASN E 253 " " NAG W 1 " - " ASN E 276 " " NAG X 1 " - " ASN E 292 " " NAG Y 1 " - " ASN E 399 " " NAG Z 1 " - " ASN E 414 " " NAG a 1 " - " ASN E 425 " " NAG b 1 " - " ASN E 508 " " NAG c 1 " - " ASN F 248 " " NAG d 1 " - " ASN F 253 " " NAG e 1 " - " ASN F 399 " " NAG f 1 " - " ASN F 414 " " NAG g 1 " - " ASN F 425 " " NAG h 1 " - " ASN F 508 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.45 Conformation dependent library (CDL) restraints added in 4.4 seconds 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5108 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 39 sheets defined 9.9% alpha, 10.3% beta 65 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 9.61 Creating SS restraints... Processing helix chain 'C' and resid 93 through 99 removed outlier: 3.580A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 3.555A pdb=" N THR C 119 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 121 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 Processing helix chain 'C' and resid 235 through 246 Processing helix chain 'C' and resid 269 through 275 removed outlier: 4.197A pdb=" N TRP C 274 " --> pdb=" O GLY C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 407 removed outlier: 4.160A pdb=" N HIS C 407 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 454 removed outlier: 3.584A pdb=" N TRP C 453 " --> pdb=" O GLY C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 627 through 632 Processing helix chain 'C' and resid 633 through 636 Processing helix chain 'C' and resid 655 through 664 Processing helix chain 'D' and resid 93 through 99 removed outlier: 3.723A pdb=" N GLN D 97 " --> pdb=" O PRO D 93 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 121 Processing helix chain 'D' and resid 235 through 246 removed outlier: 3.699A pdb=" N TRP D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 275 removed outlier: 3.928A pdb=" N TRP D 274 " --> pdb=" O GLY D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 406 removed outlier: 4.430A pdb=" N SER D 404 " --> pdb=" O THR D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 454 Processing helix chain 'D' and resid 627 through 632 removed outlier: 3.536A pdb=" N PHE D 631 " --> pdb=" O GLU D 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 633 through 636 Processing helix chain 'D' and resid 655 through 664 Processing helix chain 'E' and resid 94 through 99 Processing helix chain 'E' and resid 116 through 121 removed outlier: 3.611A pdb=" N THR E 119 " --> pdb=" O SER E 116 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N VAL E 121 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 246 Processing helix chain 'E' and resid 269 through 275 removed outlier: 4.226A pdb=" N TRP E 274 " --> pdb=" O GLY E 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 406 Processing helix chain 'E' and resid 450 through 454 removed outlier: 3.689A pdb=" N TRP E 453 " --> pdb=" O GLY E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 632 Processing helix chain 'E' and resid 633 through 636 Processing helix chain 'E' and resid 655 through 664 Processing helix chain 'F' and resid 93 through 99 removed outlier: 3.772A pdb=" N GLN F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 235 through 246 removed outlier: 3.643A pdb=" N TRP F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 removed outlier: 3.985A pdb=" N TRP F 274 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 407 removed outlier: 4.421A pdb=" N SER F 404 " --> pdb=" O THR F 401 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS F 407 " --> pdb=" O SER F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 454 Processing helix chain 'F' and resid 543 through 547 Processing helix chain 'F' and resid 627 through 632 Processing helix chain 'F' and resid 633 through 636 Processing helix chain 'F' and resid 651 through 664 removed outlier: 3.809A pdb=" N SER F 656 " --> pdb=" O CYS F 652 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TRP F 657 " --> pdb=" O GLU F 653 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N PHE F 658 " --> pdb=" O SER F 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 56 through 58 removed outlier: 6.837A pdb=" N LEU C 57 " --> pdb=" O ASP C 82 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU C 81 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 106 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU C 129 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 154 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 153 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU C 177 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 186 through 187 removed outlier: 3.862A pdb=" N LEU C 187 " --> pdb=" O GLU C 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 199 through 200 Processing sheet with id=AA4, first strand: chain 'C' and resid 226 through 228 removed outlier: 6.939A pdb=" N LEU C 227 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU C 254 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU C 280 " --> pdb=" O SER C 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE C 462 " --> pdb=" O ARG C 485 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET C 487 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU C 486 " --> pdb=" O ASP C 513 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE C 592 " --> pdb=" O ASN C 617 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU C 616 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 263 through 264 Processing sheet with id=AA6, first strand: chain 'C' and resid 313 through 314 removed outlier: 4.053A pdb=" N LEU C 314 " --> pdb=" O ASN C 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 396 through 397 Processing sheet with id=AA8, first strand: chain 'C' and resid 445 through 447 removed outlier: 6.725A pdb=" N GLN C 446 " --> pdb=" O GLN C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 648 through 649 removed outlier: 7.320A pdb=" N PHE C 648 " --> pdb=" O ASN C 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 35 through 37 removed outlier: 6.800A pdb=" N LEU D 57 " --> pdb=" O ASP D 82 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 106 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 152 through 154 removed outlier: 6.695A pdb=" N LEU D 153 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU D 177 " --> pdb=" O ASP D 204 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU D 227 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 254 " --> pdb=" O ASP D 281 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 186 through 187 removed outlier: 3.670A pdb=" N LEU D 187 " --> pdb=" O GLU D 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 199 through 200 Processing sheet with id=AB5, first strand: chain 'D' and resid 263 through 264 Processing sheet with id=AB6, first strand: chain 'D' and resid 313 through 314 removed outlier: 4.111A pdb=" N LEU D 314 " --> pdb=" O ASN D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'D' and resid 360 through 362 removed outlier: 6.981A pdb=" N LEU D 413 " --> pdb=" O ASP D 438 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 396 through 397 Processing sheet with id=AB9, first strand: chain 'D' and resid 445 through 447 removed outlier: 7.530A pdb=" N GLN D 446 " --> pdb=" O GLN D 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 461 through 463 removed outlier: 4.088A pdb=" N MET D 487 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 592 " --> pdb=" O ASN D 617 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 648 through 649 removed outlier: 7.181A pdb=" N PHE D 648 " --> pdb=" O ASN D 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'E' and resid 56 through 58 removed outlier: 6.876A pdb=" N LEU E 57 " --> pdb=" O ASP E 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 104 through 106 removed outlier: 6.747A pdb=" N LEU E 153 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU E 177 " --> pdb=" O ASP E 204 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET E 487 " --> pdb=" O ILE E 462 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU E 486 " --> pdb=" O ASP E 513 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP E 537 " --> pdb=" O LEU E 512 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILE E 592 " --> pdb=" O ASN E 617 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU E 616 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 186 through 187 removed outlier: 3.704A pdb=" N LEU E 187 " --> pdb=" O GLU E 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'E' and resid 199 through 200 Processing sheet with id=AC7, first strand: chain 'E' and resid 263 through 264 Processing sheet with id=AC8, first strand: chain 'E' and resid 313 through 314 removed outlier: 4.206A pdb=" N LEU E 314 " --> pdb=" O ASN E 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 396 through 397 Processing sheet with id=AD1, first strand: chain 'E' and resid 445 through 447 removed outlier: 6.598A pdb=" N GLN E 446 " --> pdb=" O GLN E 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 648 through 649 removed outlier: 7.216A pdb=" N PHE E 648 " --> pdb=" O ASN E 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'F' and resid 35 through 37 removed outlier: 6.548A pdb=" N ALA F 36 " --> pdb=" O ASN F 58 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU F 57 " --> pdb=" O ASP F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'F' and resid 104 through 106 removed outlier: 6.475A pdb=" N LEU F 153 " --> pdb=" O LEU F 178 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU F 177 " --> pdb=" O ASP F 204 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU F 227 " --> pdb=" O SER F 255 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU F 254 " --> pdb=" O ASP F 281 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 186 through 187 removed outlier: 3.668A pdb=" N LEU F 187 " --> pdb=" O GLU F 212 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 199 through 200 Processing sheet with id=AD7, first strand: chain 'F' and resid 263 through 264 Processing sheet with id=AD8, first strand: chain 'F' and resid 313 through 314 removed outlier: 4.154A pdb=" N LEU F 314 " --> pdb=" O ASN F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'F' and resid 396 through 397 Processing sheet with id=AE1, first strand: chain 'F' and resid 436 through 438 removed outlier: 6.999A pdb=" N LEU F 437 " --> pdb=" O TYR F 463 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N MET F 487 " --> pdb=" O ILE F 462 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU F 536 " --> pdb=" O ASN F 569 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE F 592 " --> pdb=" O ASN F 617 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N LEU F 616 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 445 through 447 removed outlier: 7.411A pdb=" N GLN F 446 " --> pdb=" O GLN F 471 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU F 470 " --> pdb=" O LYS F 494 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'F' and resid 648 through 649 removed outlier: 7.244A pdb=" N PHE F 648 " --> pdb=" O ASN F 679 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 221 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 260 hydrogen bond angles 0 basepair planarities 65 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 10.20 Time building geometry restraints manager: 14.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7508 1.34 - 1.46: 5415 1.46 - 1.57: 13380 1.57 - 1.69: 322 1.69 - 1.81: 72 Bond restraints: 26697 Sorted by residual: bond pdb=" C1 NAG I 2 " pdb=" O5 NAG I 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.83e+00 bond pdb=" C1 NAG D 803 " pdb=" O5 NAG D 803 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.97e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.70e+00 bond pdb=" C1 NAG c 1 " pdb=" O5 NAG c 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.57e+00 bond pdb=" C1 NAG D 804 " pdb=" O5 NAG D 804 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.27e+00 ... (remaining 26692 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.22: 1673 107.22 - 114.06: 16153 114.06 - 120.90: 10506 120.90 - 127.75: 8210 127.75 - 134.59: 447 Bond angle restraints: 36989 Sorted by residual: angle pdb=" CA LEU C 394 " pdb=" CB LEU C 394 " pdb=" CG LEU C 394 " ideal model delta sigma weight residual 116.30 128.16 -11.86 3.50e+00 8.16e-02 1.15e+01 angle pdb=" CA LEU F 543 " pdb=" CB LEU F 543 " pdb=" CG LEU F 543 " ideal model delta sigma weight residual 116.30 127.27 -10.97 3.50e+00 8.16e-02 9.82e+00 angle pdb=" CA LEU D 394 " pdb=" CB LEU D 394 " pdb=" CG LEU D 394 " ideal model delta sigma weight residual 116.30 126.98 -10.68 3.50e+00 8.16e-02 9.32e+00 angle pdb=" C ASN C 285 " pdb=" N ASN C 286 " pdb=" CA ASN C 286 " ideal model delta sigma weight residual 121.54 127.20 -5.66 1.91e+00 2.74e-01 8.78e+00 angle pdb=" C ASN E 285 " pdb=" N ASN E 286 " pdb=" CA ASN E 286 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.61e+00 ... (remaining 36984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 16467 35.45 - 70.90: 495 70.90 - 106.35: 168 106.35 - 141.79: 24 141.79 - 177.24: 8 Dihedral angle restraints: 17162 sinusoidal: 9338 harmonic: 7824 Sorted by residual: dihedral pdb=" CB CYS F 652 " pdb=" SG CYS F 652 " pdb=" SG CYS F 697 " pdb=" CB CYS F 697 " ideal model delta sinusoidal sigma weight residual -86.00 -175.22 89.22 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS E 96 " pdb=" SG CYS E 96 " pdb=" SG CYS E 123 " pdb=" CB CYS E 123 " ideal model delta sinusoidal sigma weight residual -86.00 -142.57 56.57 1 1.00e+01 1.00e-02 4.31e+01 dihedral pdb=" CB CYS E 652 " pdb=" SG CYS E 652 " pdb=" SG CYS E 697 " pdb=" CB CYS E 697 " ideal model delta sinusoidal sigma weight residual 93.00 52.41 40.59 1 1.00e+01 1.00e-02 2.31e+01 ... (remaining 17159 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 4169 0.063 - 0.126: 413 0.126 - 0.190: 39 0.190 - 0.253: 13 0.253 - 0.316: 16 Chirality restraints: 4650 Sorted by residual: chirality pdb=" C1 NAG F 802 " pdb=" ND2 ASN F 197 " pdb=" C2 NAG F 802 " pdb=" O5 NAG F 802 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" C5 BMA g 3 " pdb=" C4 BMA g 3 " pdb=" C6 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 4647 not shown) Planarity restraints: 4058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 50 " -0.039 5.00e-02 4.00e+02 6.01e-02 5.79e+00 pdb=" N PRO C 51 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 51 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 51 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 508 " -0.019 2.00e-02 2.50e+03 1.80e-02 4.06e+00 pdb=" CG ASN D 508 " 0.016 2.00e-02 2.50e+03 pdb=" OD1 ASN D 508 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN D 508 " 0.024 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 399 " -0.017 2.00e-02 2.50e+03 1.58e-02 3.12e+00 pdb=" CG ASN C 399 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN C 399 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 399 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG K 1 " -0.015 2.00e-02 2.50e+03 ... (remaining 4055 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 979 2.69 - 3.24: 24782 3.24 - 3.80: 43779 3.80 - 4.35: 56779 4.35 - 4.90: 88672 Nonbonded interactions: 214991 Sorted by model distance: nonbonded pdb=" OG SER D 247 " pdb=" O GLY D 271 " model vdw 2.140 2.440 nonbonded pdb=" O LEU C 171 " pdb=" OG SER C 198 " model vdw 2.181 2.440 nonbonded pdb=" O LEU C 246 " pdb=" OG1 THR C 249 " model vdw 2.201 2.440 nonbonded pdb=" OG SER C 113 " pdb=" O2' U B 50 " model vdw 2.214 2.440 nonbonded pdb=" O4 U A 80 " pdb=" N1 A B 11 " model vdw 2.216 3.120 ... (remaining 214986 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 44 or resid 46 through 85)) selection = (chain 'B' and (resid 6 through 45 or resid 47 through 86)) } ncs_group { reference = chain 'C' selection = (chain 'D' and (resid 29 through 336 or resid 343 through 698 or resid 801 throu \ gh 802)) selection = chain 'E' selection = (chain 'F' and (resid 29 through 336 or resid 343 through 698 or resid 801 throu \ gh 802)) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'e' selection = chain 'f' selection = chain 'g' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'h' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 6.020 Check model and map are aligned: 0.400 Set scattering table: 0.250 Process input model: 80.130 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.400 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 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 : 0.003 0.056 26697 Z= 0.191 Angle : 0.630 11.855 36989 Z= 0.280 Chirality : 0.045 0.316 4650 Planarity : 0.003 0.060 4018 Dihedral : 19.005 177.243 12006 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.85 % Favored : 95.07 % Rotamer: Outliers : 0.08 % Allowed : 0.36 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.73 (0.16), residues: 2638 helix: -1.05 (0.38), residues: 208 sheet: -1.72 (0.26), residues: 430 loop : -1.07 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 274 HIS 0.004 0.000 HIS F 40 PHE 0.012 0.001 PHE C 503 TYR 0.008 0.000 TYR F 469 ARG 0.002 0.000 ARG D 507 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 146 time to evaluate : 2.645 Fit side-chains REVERT: D 144 PHE cc_start: 0.8784 (m-80) cc_final: 0.8513 (m-80) REVERT: D 274 TRP cc_start: 0.8460 (m-90) cc_final: 0.8233 (m-90) REVERT: D 395 GLN cc_start: 0.8695 (mm-40) cc_final: 0.7888 (mm-40) REVERT: D 436 ILE cc_start: 0.3816 (mm) cc_final: 0.3566 (mm) REVERT: E 445 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 488 LEU cc_start: 0.6964 (mm) cc_final: 0.6762 (mt) REVERT: F 120 PHE cc_start: 0.9265 (m-80) cc_final: 0.9033 (m-10) REVERT: F 627 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8149 (mm-30) outliers start: 2 outliers final: 0 residues processed: 148 average time/residue: 0.3113 time to fit residues: 80.1606 Evaluate side-chains 110 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 2.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 6.9990 chunk 212 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 143 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 219 optimal weight: 30.0000 chunk 84 optimal weight: 0.0470 chunk 133 optimal weight: 0.0970 chunk 163 optimal weight: 4.9990 chunk 254 optimal weight: 7.9990 overall best weight: 3.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 446 GLN ** C 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN D 367 ASN D 467 ASN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 585 ASN ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 ASN E 467 ASN E 471 GLN ** E 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 231 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 395 GLN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26697 Z= 0.233 Angle : 0.649 11.643 36989 Z= 0.303 Chirality : 0.044 0.352 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.827 179.837 6760 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.14 % Favored : 93.75 % Rotamer: Outliers : 1.05 % Allowed : 7.68 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.83 (0.16), residues: 2638 helix: -1.09 (0.37), residues: 202 sheet: -1.70 (0.26), residues: 446 loop : -1.16 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 453 HIS 0.008 0.001 HIS C 40 PHE 0.015 0.001 PHE E 428 TYR 0.012 0.001 TYR C 360 ARG 0.003 0.000 ARG F 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 2.927 Fit side-chains REVERT: D 144 PHE cc_start: 0.9034 (m-80) cc_final: 0.8616 (m-80) REVERT: D 274 TRP cc_start: 0.8649 (m-90) cc_final: 0.8355 (m-90) REVERT: D 558 PHE cc_start: 0.6743 (OUTLIER) cc_final: 0.6503 (t80) REVERT: E 445 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7726 (tm-30) REVERT: F 120 PHE cc_start: 0.9408 (m-80) cc_final: 0.9147 (m-10) REVERT: F 558 PHE cc_start: 0.7142 (OUTLIER) cc_final: 0.6843 (t80) REVERT: F 627 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8349 (mm-30) outliers start: 26 outliers final: 15 residues processed: 118 average time/residue: 0.2989 time to fit residues: 63.9884 Evaluate side-chains 110 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 431 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 558 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 7.9990 chunk 78 optimal weight: 9.9990 chunk 211 optimal weight: 50.0000 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 254 optimal weight: 10.0000 chunk 275 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 204 optimal weight: 1.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN C 446 GLN C 471 GLN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 ASN ** D 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 HIS ** D 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 GLN E 109 HIS ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 433 GLN ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN F 231 ASN ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 467 ASN ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 26697 Z= 0.250 Angle : 0.625 12.971 36989 Z= 0.307 Chirality : 0.042 0.343 4650 Planarity : 0.004 0.058 4018 Dihedral : 15.247 177.807 6760 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.37 % Favored : 93.48 % Rotamer: Outliers : 1.65 % Allowed : 10.77 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -1.95 (0.16), residues: 2638 helix: -0.99 (0.37), residues: 202 sheet: -1.67 (0.26), residues: 424 loop : -1.31 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 274 HIS 0.011 0.001 HIS C 540 PHE 0.020 0.002 PHE C 538 TYR 0.018 0.001 TYR C 360 ARG 0.004 0.000 ARG F 507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 98 time to evaluate : 2.786 Fit side-chains REVERT: C 132 MET cc_start: 0.4793 (tpt) cc_final: 0.4555 (tpt) REVERT: C 538 PHE cc_start: 0.8306 (OUTLIER) cc_final: 0.7836 (m-10) REVERT: D 144 PHE cc_start: 0.9038 (m-80) cc_final: 0.8610 (m-80) REVERT: D 274 TRP cc_start: 0.8668 (m-90) cc_final: 0.8338 (m-90) REVERT: D 463 TYR cc_start: 0.7015 (m-10) cc_final: 0.6603 (m-10) REVERT: E 112 LEU cc_start: 0.8547 (mm) cc_final: 0.8288 (mm) REVERT: E 445 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7788 (pp20) REVERT: F 120 PHE cc_start: 0.9504 (m-80) cc_final: 0.9230 (m-10) REVERT: F 627 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8426 (mm-30) outliers start: 41 outliers final: 20 residues processed: 128 average time/residue: 0.2962 time to fit residues: 67.9685 Evaluate side-chains 110 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 268 THR Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 10.0000 chunk 191 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 121 optimal weight: 10.0000 chunk 171 optimal weight: 0.0870 chunk 255 optimal weight: 9.9990 chunk 270 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 242 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 overall best weight: 6.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 GLN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 HIS ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 86 ASN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 542 ASN E 45 HIS ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 ASN E 310 ASN E 419 HIS ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 564 HIS ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 663 ASN E 664 GLN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 230 ASN ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.140 26697 Z= 0.407 Angle : 0.826 13.492 36989 Z= 0.401 Chirality : 0.047 0.346 4650 Planarity : 0.005 0.058 4018 Dihedral : 15.898 177.136 6760 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 27.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.63 % Favored : 90.22 % Rotamer: Outliers : 2.69 % Allowed : 14.31 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.42 (0.16), residues: 2638 helix: -1.21 (0.37), residues: 188 sheet: -2.03 (0.24), residues: 452 loop : -1.65 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 274 HIS 0.016 0.002 HIS E 61 PHE 0.043 0.002 PHE E 558 TYR 0.024 0.002 TYR C 360 ARG 0.012 0.001 ARG C 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 91 time to evaluate : 3.019 Fit side-chains revert: symmetry clash REVERT: C 176 GLU cc_start: 0.6883 (mp0) cc_final: 0.6639 (mp0) REVERT: C 335 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8074 (p) REVERT: C 506 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7772 (mm) REVERT: D 144 PHE cc_start: 0.9116 (m-80) cc_final: 0.8712 (m-80) REVERT: D 274 TRP cc_start: 0.8818 (m-90) cc_final: 0.8465 (m-90) REVERT: D 420 ILE cc_start: 0.9730 (OUTLIER) cc_final: 0.9413 (tp) REVERT: E 112 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8421 (mm) REVERT: E 225 PHE cc_start: 0.7351 (OUTLIER) cc_final: 0.6945 (m-10) REVERT: E 445 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7823 (tm-30) REVERT: E 506 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7837 (mm) REVERT: E 538 PHE cc_start: 0.8678 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: F 120 PHE cc_start: 0.9629 (m-80) cc_final: 0.9367 (m-10) REVERT: F 558 PHE cc_start: 0.7083 (OUTLIER) cc_final: 0.6826 (t80) outliers start: 67 outliers final: 36 residues processed: 146 average time/residue: 0.3107 time to fit residues: 79.4796 Evaluate side-chains 120 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 76 time to evaluate : 2.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 559 LEU Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 243 CYS Chi-restraints excluded: chain E residue 335 THR Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 506 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 576 ASP Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 558 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 30.0000 chunk 153 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 201 optimal weight: 30.0000 chunk 111 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 242 optimal weight: 0.9980 chunk 68 optimal weight: 50.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 170 GLN ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 569 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26697 Z= 0.201 Angle : 0.618 12.954 36989 Z= 0.301 Chirality : 0.042 0.347 4650 Planarity : 0.004 0.056 4018 Dihedral : 15.595 176.481 6760 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 20.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.97 % Favored : 92.87 % Rotamer: Outliers : 2.41 % Allowed : 15.43 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.27 (0.16), residues: 2638 helix: -1.05 (0.38), residues: 188 sheet: -1.98 (0.25), residues: 444 loop : -1.53 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 430 HIS 0.008 0.001 HIS E 40 PHE 0.014 0.001 PHE E 558 TYR 0.010 0.001 TYR C 360 ARG 0.006 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 91 time to evaluate : 2.807 Fit side-chains revert: symmetry clash REVERT: C 176 GLU cc_start: 0.6779 (mp0) cc_final: 0.6543 (mp0) REVERT: C 239 THR cc_start: 0.8812 (m) cc_final: 0.8545 (p) REVERT: C 480 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8691 (m) REVERT: C 538 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7768 (m-10) REVERT: D 144 PHE cc_start: 0.9141 (m-80) cc_final: 0.8730 (m-80) REVERT: D 153 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9340 (mm) REVERT: D 274 TRP cc_start: 0.8715 (m-90) cc_final: 0.8371 (m-90) REVERT: D 463 TYR cc_start: 0.7137 (m-10) cc_final: 0.6708 (m-10) REVERT: E 112 LEU cc_start: 0.8710 (mm) cc_final: 0.8486 (mm) REVERT: E 445 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7631 (tm-30) REVERT: E 538 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7935 (m-80) REVERT: F 120 PHE cc_start: 0.9598 (m-80) cc_final: 0.9325 (m-10) outliers start: 60 outliers final: 36 residues processed: 140 average time/residue: 0.3134 time to fit residues: 77.1752 Evaluate side-chains 124 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 84 time to evaluate : 2.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 430 TRP Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 310 ASN Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 576 ASP Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 430 TRP Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 30.0000 chunk 243 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 66 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 224 optimal weight: 30.0000 chunk 125 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 495 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 541 ASN C 664 GLN ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 GLN ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 GLN E 310 ASN ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 564 HIS ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 26697 Z= 0.414 Angle : 0.840 12.379 36989 Z= 0.407 Chirality : 0.048 0.433 4650 Planarity : 0.005 0.059 4018 Dihedral : 16.056 176.060 6760 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 31.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.11 % Favored : 88.74 % Rotamer: Outliers : 3.01 % Allowed : 16.24 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.66 (0.16), residues: 2638 helix: -1.05 (0.39), residues: 176 sheet: -2.18 (0.24), residues: 448 loop : -1.86 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 274 HIS 0.012 0.002 HIS E 61 PHE 0.037 0.002 PHE E 558 TYR 0.018 0.002 TYR C 360 ARG 0.010 0.001 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 77 time to evaluate : 2.807 Fit side-chains REVERT: C 176 GLU cc_start: 0.7072 (mp0) cc_final: 0.6828 (mp0) REVERT: C 239 THR cc_start: 0.8652 (m) cc_final: 0.8398 (p) REVERT: C 335 THR cc_start: 0.8512 (OUTLIER) cc_final: 0.8185 (p) REVERT: C 487 MET cc_start: 0.5485 (pmm) cc_final: 0.5164 (pmm) REVERT: D 144 PHE cc_start: 0.9248 (m-80) cc_final: 0.8859 (m-80) REVERT: D 153 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9153 (mm) REVERT: D 274 TRP cc_start: 0.8760 (m-90) cc_final: 0.8414 (m-90) REVERT: D 420 ILE cc_start: 0.9628 (OUTLIER) cc_final: 0.9370 (tp) REVERT: D 497 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7747 (m-30) REVERT: E 112 LEU cc_start: 0.8746 (mm) cc_final: 0.8517 (mm) REVERT: E 225 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7001 (m-10) REVERT: F 120 PHE cc_start: 0.9677 (m-80) cc_final: 0.9426 (m-10) REVERT: F 452 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6995 (mp0) outliers start: 75 outliers final: 51 residues processed: 139 average time/residue: 0.2846 time to fit residues: 71.5972 Evaluate side-chains 126 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 69 time to evaluate : 2.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 482 SER Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 420 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 202 LYS Chi-restraints excluded: chain E residue 225 PHE Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 576 ASP Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 576 ASP Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 197 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 228 optimal weight: 20.0000 chunk 151 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26697 Z= 0.207 Angle : 0.643 13.695 36989 Z= 0.313 Chirality : 0.043 0.350 4650 Planarity : 0.004 0.057 4018 Dihedral : 15.766 178.303 6760 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.28 % Favored : 92.57 % Rotamer: Outliers : 2.65 % Allowed : 17.36 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.40 (0.16), residues: 2638 helix: -0.59 (0.42), residues: 160 sheet: -2.15 (0.26), residues: 400 loop : -1.69 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 430 HIS 0.006 0.001 HIS E 40 PHE 0.017 0.001 PHE E 558 TYR 0.012 0.001 TYR D 466 ARG 0.006 0.000 ARG E 504 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 80 time to evaluate : 3.167 Fit side-chains revert: symmetry clash REVERT: C 239 THR cc_start: 0.8704 (m) cc_final: 0.8428 (p) REVERT: C 335 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8123 (p) REVERT: C 538 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7707 (m-10) REVERT: D 144 PHE cc_start: 0.9234 (m-80) cc_final: 0.8811 (m-80) REVERT: D 153 LEU cc_start: 0.9547 (OUTLIER) cc_final: 0.9327 (mm) REVERT: D 274 TRP cc_start: 0.8662 (m-90) cc_final: 0.8306 (m-90) REVERT: D 497 ASP cc_start: 0.7936 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: D 558 PHE cc_start: 0.6888 (OUTLIER) cc_final: 0.6469 (t80) REVERT: E 112 LEU cc_start: 0.8604 (mm) cc_final: 0.8354 (mm) REVERT: E 118 GLN cc_start: 0.8046 (pp30) cc_final: 0.7821 (mp10) REVERT: E 538 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7985 (m-80) REVERT: F 120 PHE cc_start: 0.9628 (m-80) cc_final: 0.9345 (m-10) outliers start: 66 outliers final: 46 residues processed: 134 average time/residue: 0.3372 time to fit residues: 79.8479 Evaluate side-chains 128 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 76 time to evaluate : 2.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 576 ASP Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 558 PHE Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 81 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 52 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 133 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 495 ASN ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 26697 Z= 0.375 Angle : 0.778 12.158 36989 Z= 0.378 Chirality : 0.046 0.344 4650 Planarity : 0.004 0.059 4018 Dihedral : 16.058 177.913 6760 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 29.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.56 % Favored : 88.29 % Rotamer: Outliers : 3.09 % Allowed : 17.32 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.69 (0.16), residues: 2638 helix: -0.95 (0.39), residues: 176 sheet: -2.20 (0.24), residues: 438 loop : -1.91 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 274 HIS 0.009 0.001 HIS E 61 PHE 0.031 0.002 PHE E 558 TYR 0.013 0.002 TYR E 466 ARG 0.009 0.001 ARG C 504 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 71 time to evaluate : 2.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 THR cc_start: 0.8656 (m) cc_final: 0.8397 (p) REVERT: C 335 THR cc_start: 0.8537 (OUTLIER) cc_final: 0.8128 (p) REVERT: D 144 PHE cc_start: 0.9283 (m-80) cc_final: 0.8909 (m-80) REVERT: D 153 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9178 (mm) REVERT: D 274 TRP cc_start: 0.8733 (m-90) cc_final: 0.8345 (m-90) REVERT: D 497 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7752 (m-30) REVERT: D 543 LEU cc_start: 0.8817 (pp) cc_final: 0.8083 (mp) REVERT: D 558 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6498 (t80) REVERT: E 112 LEU cc_start: 0.8793 (mm) cc_final: 0.8580 (mm) REVERT: E 538 PHE cc_start: 0.8594 (OUTLIER) cc_final: 0.7935 (m-10) REVERT: F 120 PHE cc_start: 0.9653 (m-80) cc_final: 0.9367 (m-10) outliers start: 77 outliers final: 59 residues processed: 137 average time/residue: 0.3097 time to fit residues: 75.0954 Evaluate side-chains 133 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 69 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 403 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 576 ASP Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 490 ARG Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 547 TRP Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 598 ASN Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain E residue 46 ILE Chi-restraints excluded: chain E residue 107 LEU Chi-restraints excluded: chain E residue 113 SER Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 403 VAL Chi-restraints excluded: chain E residue 482 SER Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 497 ASP Chi-restraints excluded: chain E residue 524 GLU Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 576 ASP Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 472 LEU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 522 ILE Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 598 ASN Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 151 optimal weight: 0.0470 chunk 109 optimal weight: 0.9990 chunk 197 optimal weight: 5.9990 chunk 77 optimal weight: 40.0000 chunk 227 optimal weight: 20.0000 chunk 237 optimal weight: 6.9990 chunk 250 optimal weight: 0.9980 overall best weight: 1.3882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 63 GLN C 86 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 ASN ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN D 664 GLN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 58 ASN ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26697 Z= 0.161 Angle : 0.625 13.253 36989 Z= 0.303 Chirality : 0.043 0.347 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.688 179.220 6760 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.60 % Favored : 93.25 % Rotamer: Outliers : 2.37 % Allowed : 18.25 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.29 (0.16), residues: 2638 helix: -0.46 (0.43), residues: 160 sheet: -2.08 (0.24), residues: 470 loop : -1.57 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 453 HIS 0.008 0.001 HIS D 540 PHE 0.012 0.001 PHE C 558 TYR 0.009 0.001 TYR D 463 ARG 0.009 0.000 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 85 time to evaluate : 2.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 THR cc_start: 0.8701 (m) cc_final: 0.8441 (p) REVERT: C 335 THR cc_start: 0.8430 (OUTLIER) cc_final: 0.8065 (p) REVERT: C 480 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8685 (m) REVERT: C 538 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7558 (m-10) REVERT: D 144 PHE cc_start: 0.9285 (m-80) cc_final: 0.8823 (m-80) REVERT: D 153 LEU cc_start: 0.9543 (OUTLIER) cc_final: 0.9306 (mm) REVERT: D 274 TRP cc_start: 0.8581 (m-90) cc_final: 0.8213 (m-90) REVERT: D 497 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: D 543 LEU cc_start: 0.8675 (pp) cc_final: 0.8028 (mp) REVERT: D 558 PHE cc_start: 0.7010 (OUTLIER) cc_final: 0.6584 (t80) REVERT: E 112 LEU cc_start: 0.8778 (mm) cc_final: 0.8533 (mm) REVERT: E 538 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: F 120 PHE cc_start: 0.9607 (m-80) cc_final: 0.9302 (m-80) REVERT: F 452 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6802 (mp0) outliers start: 59 outliers final: 41 residues processed: 134 average time/residue: 0.3121 time to fit residues: 73.5209 Evaluate side-chains 124 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 75 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 547 TRP Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 598 ASN Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 5.9990 chunk 265 optimal weight: 20.0000 chunk 162 optimal weight: 0.6980 chunk 126 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 278 optimal weight: 10.0000 chunk 256 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 171 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 overall best weight: 2.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 585 ASN ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26697 Z= 0.195 Angle : 0.623 12.285 36989 Z= 0.302 Chirality : 0.042 0.342 4650 Planarity : 0.004 0.059 4018 Dihedral : 15.592 179.584 6760 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 21.37 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.61 % Favored : 91.24 % Rotamer: Outliers : 2.01 % Allowed : 18.73 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.37 (0.16), residues: 2638 helix: -0.43 (0.42), residues: 160 sheet: -2.13 (0.26), residues: 386 loop : -1.68 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 453 HIS 0.005 0.001 HIS E 40 PHE 0.014 0.001 PHE E 558 TYR 0.009 0.001 TYR F 469 ARG 0.005 0.000 ARG F 507 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5276 Ramachandran restraints generated. 2638 Oldfield, 0 Emsley, 2638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 78 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 239 THR cc_start: 0.8665 (m) cc_final: 0.8409 (p) REVERT: C 335 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (p) REVERT: C 538 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7627 (m-10) REVERT: D 144 PHE cc_start: 0.9303 (m-80) cc_final: 0.8844 (m-80) REVERT: D 153 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9310 (mm) REVERT: D 274 TRP cc_start: 0.8632 (m-90) cc_final: 0.8279 (m-90) REVERT: D 497 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7785 (m-30) REVERT: D 543 LEU cc_start: 0.8582 (pp) cc_final: 0.8287 (mt) REVERT: D 558 PHE cc_start: 0.7095 (OUTLIER) cc_final: 0.6646 (t80) REVERT: E 112 LEU cc_start: 0.8723 (mm) cc_final: 0.8446 (mm) REVERT: E 538 PHE cc_start: 0.8409 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: F 120 PHE cc_start: 0.9601 (m-80) cc_final: 0.9294 (m-80) REVERT: F 452 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.6970 (mp0) outliers start: 50 outliers final: 40 residues processed: 119 average time/residue: 0.3264 time to fit residues: 69.3646 Evaluate side-chains 121 residues out of total 2488 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 74 time to evaluate : 2.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 117 ASP Chi-restraints excluded: chain C residue 162 SER Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 335 THR Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 538 PHE Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 231 ASN Chi-restraints excluded: chain D residue 298 LEU Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 464 LEU Chi-restraints excluded: chain D residue 480 VAL Chi-restraints excluded: chain D residue 487 MET Chi-restraints excluded: chain D residue 497 ASP Chi-restraints excluded: chain D residue 538 PHE Chi-restraints excluded: chain D residue 558 PHE Chi-restraints excluded: chain D residue 576 ASP Chi-restraints excluded: chain D residue 666 HIS Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 375 THR Chi-restraints excluded: chain E residue 527 LEU Chi-restraints excluded: chain E residue 538 PHE Chi-restraints excluded: chain E residue 558 PHE Chi-restraints excluded: chain E residue 562 LEU Chi-restraints excluded: chain E residue 643 MET Chi-restraints excluded: chain E residue 682 HIS Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 144 PHE Chi-restraints excluded: chain F residue 231 ASN Chi-restraints excluded: chain F residue 439 LEU Chi-restraints excluded: chain F residue 452 GLU Chi-restraints excluded: chain F residue 480 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 538 PHE Chi-restraints excluded: chain F residue 680 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 7.9990 chunk 236 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 204 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 228 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 660 ASN ** D 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 598 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 664 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.060393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.047281 restraints weight = 223196.095| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 5.79 r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 26697 Z= 0.299 Angle : 0.711 12.090 36989 Z= 0.346 Chirality : 0.045 0.335 4650 Planarity : 0.004 0.061 4018 Dihedral : 15.875 179.303 6760 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 26.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.88 % Favored : 88.97 % Rotamer: Outliers : 2.17 % Allowed : 18.65 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: -2.55 (0.16), residues: 2638 helix: -0.49 (0.42), residues: 158 sheet: -2.09 (0.26), residues: 384 loop : -1.86 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 274 HIS 0.007 0.001 HIS E 61 PHE 0.026 0.002 PHE E 558 TYR 0.016 0.002 TYR C 357 ARG 0.008 0.001 ARG C 504 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4293.18 seconds wall clock time: 81 minutes 3.21 seconds (4863.21 seconds total)