Starting phenix.real_space_refine on Mon Jul 22 18:21:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tni_41417/07_2024/8tni_41417.cif" } resolution = 3.61 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= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 134 5.16 5 C 12095 2.51 5 N 3303 2.21 5 O 3867 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 368": "OD1" <-> "OD2" Residue "B GLU 584": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C GLU 102": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D ASP 632": "OD1" <-> "OD2" Residue "D GLU 657": "OE1" <-> "OE2" Residue "E PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 584": "OE1" <-> "OE2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "H GLU 30": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 85": "OE1" <-> "OE2" Residue "H PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 85": "OE1" <-> "OE2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "X ASP 30": "OD1" <-> "OD2" Residue "X TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 72": "OD1" <-> "OD2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 100": "OD1" <-> "OD2" Residue "J GLU 30": "OE1" <-> "OE2" Residue "J TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J GLU 85": "OE1" <-> "OE2" Residue "J GLU 101": "OE1" <-> "OE2" Residue "J PHE 1032": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 1086": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 19399 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 1, 'TRANS': 125} Chain breaks: 1 Chain: "C" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "D" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "E" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3567 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 22, 'TRANS': 430} Chain breaks: 2 Chain: "F" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1002 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "H" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "I" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 911 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1143 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TYS:plan-2': 2} Unresolved non-hydrogen planarities: 2 Chain: "J" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1730 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 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: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 10.91, per 1000 atoms: 0.56 Number of scatterers: 19399 At special positions: 0 Unit cell: (135.29, 136.95, 165.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 134 16.00 O 3867 8.00 N 3303 7.00 C 12095 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 201 " - pdb=" SG CYS A 433 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 201 " - pdb=" SG CYS C 433 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.03 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.02 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.04 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 50 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.04 Simple disulfide: pdb=" SG CYS I 50 " - pdb=" SG CYS I 99 " distance=2.03 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.03 Simple disulfide: pdb=" SG CYS X 100A" - pdb=" SG CYS X 100Q" distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.04 Simple disulfide: pdb=" SG CYS J 50 " - pdb=" SG CYS J 99 " distance=2.03 Simple disulfide: pdb=" SG CYS J1023 " - pdb=" SG CYS J1088 " 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 ALPHA1-3 " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 234 " " NAG A 603 " - " ASN A 301 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 392 " " NAG A 606 " - " ASN A 332 " " NAG A 607 " - " ASN A 295 " " NAG A 608 " - " ASN A 339 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 88 " " NAG B 701 " - " ASN B 637 " " NAG C 601 " - " ASN C 133 " " NAG C 602 " - " ASN C 234 " " NAG C 603 " - " ASN C 448 " " NAG C 604 " - " ASN C 301 " " NAG C 605 " - " ASN C 332 " " NAG C 606 " - " ASN C 392 " " NAG C 607 " - " ASN C 339 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 197 " " NAG C 610 " - " ASN C 88 " " NAG E 601 " - " ASN E 234 " " NAG E 602 " - " ASN E 276 " " NAG E 603 " - " ASN E 448 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 133 " " NAG E 606 " - " ASN E 332 " " NAG E 607 " - " ASN E 295 " " NAG E 608 " - " ASN E 301 " " NAG E 609 " - " ASN E 88 " " NAG E 610 " - " ASN E 392 " " NAG E 611 " - " ASN E 339 " " NAG G 1 " - " ASN A 156 " " NAG K 1 " - " ASN A 160 " " NAG L 1 " - " ASN A 262 " " NAG M 1 " - " ASN A 276 " " NAG N 1 " - " ASN A 363 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN C 156 " " NAG Q 1 " - " ASN C 160 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 276 " " NAG T 1 " - " ASN C 363 " " NAG U 1 " - " ASN C 386 " " NAG V 1 " - " ASN E 156 " " NAG W 1 " - " ASN E 262 " " NAG Y 1 " - " ASN E 363 " " NAG Z 1 " - " ASN E 386 " " NAG a 1 " - " ASN E 160 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.94 Conformation dependent library (CDL) restraints added in 3.6 seconds 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 42 sheets defined 18.1% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'A' and resid 58 through 62 removed outlier: 4.557A pdb=" N GLU A 62 " --> pdb=" O LYS A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 removed outlier: 3.511A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 543 removed outlier: 3.762A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 546 No H-bonds generated for 'chain 'B' and resid 544 through 546' Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.935A pdb=" N TRP B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.010A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 663 removed outlier: 3.919A pdb=" N ILE B 642 " --> pdb=" O TYR B 638 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 663 " --> pdb=" O ASP B 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 116 removed outlier: 3.904A pdb=" N HIS C 105 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.897A pdb=" N GLY C 380 " --> pdb=" O ASN C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 543 removed outlier: 3.987A pdb=" N ASN D 543 " --> pdb=" O VAL D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 596 removed outlier: 3.814A pdb=" N TRP D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 removed outlier: 3.579A pdb=" N ASN D 625 " --> pdb=" O GLU D 621 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 removed outlier: 3.513A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU D 634 " --> pdb=" O GLN D 630 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 638 through 664 removed outlier: 3.718A pdb=" N ILE D 642 " --> pdb=" O TYR D 638 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY D 644 " --> pdb=" O GLN D 640 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLU D 647 " --> pdb=" O TYR D 643 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 664 " --> pdb=" O LEU D 660 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 62 removed outlier: 4.509A pdb=" N GLU E 62 " --> pdb=" O LYS E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 4.099A pdb=" N ALA E 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 98 through 116 removed outlier: 4.054A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 350 removed outlier: 3.510A pdb=" N GLY E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 354 removed outlier: 3.853A pdb=" N GLY E 354 " --> pdb=" O LYS E 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 351 through 354' Processing helix chain 'F' and resid 523 through 527 removed outlier: 4.488A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 534 Processing helix chain 'F' and resid 536 through 541 removed outlier: 3.800A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 596 removed outlier: 3.531A pdb=" N TRP F 596 " --> pdb=" O LEU F 592 " (cutoff:3.500A) Processing helix chain 'F' and resid 619 through 625 removed outlier: 3.633A pdb=" N TRP F 623 " --> pdb=" O LEU F 619 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN F 625 " --> pdb=" O GLU F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 641 through 664 removed outlier: 4.212A pdb=" N GLU F 647 " --> pdb=" O TYR F 643 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP F 664 " --> pdb=" O LEU F 660 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 removed outlier: 3.840A pdb=" N THR X 87 " --> pdb=" O PRO X 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 1079 through 1083 Processing sheet with id=AA1, first strand: chain 'A' and resid 495 through 499 removed outlier: 4.641A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR B 606 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.989A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 176 removed outlier: 3.501A pdb=" N CYS A 131 " --> pdb=" O LYS A 189 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS A 189 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.827A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 286 removed outlier: 3.830A pdb=" N LEU A 454 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 393 " --> pdb=" O PHE A 361 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 413 through 417 removed outlier: 3.825A pdb=" N HIS A 330 " --> pdb=" O THR A 297 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 305 through 308 removed outlier: 3.643A pdb=" N ALA A 319 " --> pdb=" O LYS A 305 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.635A pdb=" N VAL C 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 606 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.082A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 169 through 175 removed outlier: 3.679A pdb=" N CYS C 131 " --> pdb=" O LYS C 189 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS C 189 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 202 through 203 removed outlier: 7.041A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 271 through 273 removed outlier: 3.691A pdb=" N ARG C 273 " --> pdb=" O LEU C 285 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.780A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 413 through 417 removed outlier: 3.780A pdb=" N HIS C 330 " --> pdb=" O THR C 297 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR C 297 " --> pdb=" O HIS C 330 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 306 through 308 Processing sheet with id=AB7, first strand: chain 'C' and resid 360 through 361 removed outlier: 6.659A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 382 through 383 removed outlier: 4.423A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 495 through 499 Processing sheet with id=AC1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AC2, first strand: chain 'E' and resid 91 through 93 removed outlier: 3.813A pdb=" N GLU E 91 " --> pdb=" O CYS E 239 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 132 through 133 removed outlier: 3.543A pdb=" N THR E 132 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 168 through 169 removed outlier: 7.226A pdb=" N CYS X 100A" --> pdb=" O SER X 100T" (cutoff:3.500A) removed outlier: 6.493A pdb=" N SER X 100T" --> pdb=" O CYS X 100A" (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU X 100C" --> pdb=" O ALA X 100R" (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 181 through 183 Processing sheet with id=AC6, first strand: chain 'E' and resid 271 through 273 removed outlier: 3.629A pdb=" N ARG E 273 " --> pdb=" O LEU E 285 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU E 454 " --> pdb=" O ILE E 284 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 413 through 417 removed outlier: 4.031A pdb=" N HIS E 330 " --> pdb=" O THR E 297 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 297 " --> pdb=" O HIS E 330 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER E 334 " --> pdb=" O GLN E 293 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLN E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 304 through 308 Processing sheet with id=AC9, first strand: chain 'E' and resid 374 through 378 removed outlier: 3.982A pdb=" N PHE E 376 " --> pdb=" O PHE E 383 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AD2, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AD3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AD4, first strand: chain 'H' and resid 47 through 51 removed outlier: 4.566A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE H 34 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AD6, first strand: chain 'I' and resid 10 through 12 removed outlier: 3.841A pdb=" N GLY I 10 " --> pdb=" O GLN I 108 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR I 110 " --> pdb=" O GLY I 10 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 47 through 51 removed outlier: 4.790A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE I 34 " --> pdb=" O LEU I 51 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.764A pdb=" N VAL X 5 " --> pdb=" O ALA X 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'X' and resid 11 through 12 removed outlier: 3.934A pdb=" N ALA X 93 " --> pdb=" O HIS X 35 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS X 35 " --> pdb=" O ALA X 93 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N MET X 34 " --> pdb=" O SER X 50 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N SER X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 4 through 7 removed outlier: 3.596A pdb=" N MET J 82 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 10 through 12 Processing sheet with id=AE3, first strand: chain 'J' and resid 45 through 51 removed outlier: 5.245A pdb=" N GLY J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG J 38 " --> pdb=" O GLY J 47 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE J 34 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 1009 through 1013 removed outlier: 3.661A pdb=" N ALA J1013 " --> pdb=" O ILE J1105 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP J1035 " --> pdb=" O LEU J1047 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 1009 through 1013 removed outlier: 3.661A pdb=" N ALA J1013 " --> pdb=" O ILE J1105 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL J1097 " --> pdb=" O THR J1090 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1019 through 1024 546 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.02 Time building geometry restraints manager: 8.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6243 1.35 - 1.48: 5039 1.48 - 1.61: 8317 1.61 - 1.74: 2 1.74 - 1.87: 174 Bond restraints: 19775 Sorted by residual: bond pdb=" O3 TYS X 100I" pdb=" S TYS X 100I" ideal model delta sigma weight residual 1.458 1.636 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" O2 TYS X 100H" pdb=" S TYS X 100H" ideal model delta sigma weight residual 1.461 1.632 -0.171 2.00e-02 2.50e+03 7.30e+01 bond pdb=" OH TYS X 100I" pdb=" S TYS X 100I" ideal model delta sigma weight residual 1.679 1.536 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" OH TYS X 100H" pdb=" S TYS X 100H" ideal model delta sigma weight residual 1.679 1.554 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C1 MAN R 4 " pdb=" O5 MAN R 4 " ideal model delta sigma weight residual 1.399 1.480 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 19770 not shown) Histogram of bond angle deviations from ideal: 83.78 - 93.85: 3 93.85 - 103.92: 214 103.92 - 113.99: 11966 113.99 - 124.06: 14038 124.06 - 134.13: 611 Bond angle restraints: 26832 Sorted by residual: angle pdb=" O1 TYS X 100H" pdb=" S TYS X 100H" pdb=" O2 TYS X 100H" ideal model delta sigma weight residual 114.11 83.78 30.33 3.00e+00 1.11e-01 1.02e+02 angle pdb=" O2 TYS X 100H" pdb=" S TYS X 100H" pdb=" O3 TYS X 100H" ideal model delta sigma weight residual 115.38 88.75 26.63 3.00e+00 1.11e-01 7.88e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O2 TYS X 100H" ideal model delta sigma weight residual 104.74 85.59 19.15 3.00e+00 1.11e-01 4.07e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O1 TYS X 100H" ideal model delta sigma weight residual 104.92 123.18 -18.26 3.00e+00 1.11e-01 3.71e+01 angle pdb=" OH TYS X 100H" pdb=" S TYS X 100H" pdb=" O3 TYS X 100H" ideal model delta sigma weight residual 100.21 117.11 -16.90 3.00e+00 1.11e-01 3.17e+01 ... (remaining 26827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 11460 24.83 - 49.65: 1072 49.65 - 74.48: 174 74.48 - 99.30: 48 99.30 - 124.13: 20 Dihedral angle restraints: 12774 sinusoidal: 6034 harmonic: 6740 Sorted by residual: dihedral pdb=" CB CYS C 119 " pdb=" SG CYS C 119 " pdb=" SG CYS C 205 " pdb=" CB CYS C 205 " ideal model delta sinusoidal sigma weight residual 93.00 -178.41 -88.59 1 1.00e+01 1.00e-02 9.36e+01 dihedral pdb=" CB CYS E 54 " pdb=" SG CYS E 54 " pdb=" SG CYS E 74 " pdb=" CB CYS E 74 " ideal model delta sinusoidal sigma weight residual 93.00 10.99 82.01 1 1.00e+01 1.00e-02 8.26e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 74 " pdb=" CB CYS A 74 " ideal model delta sinusoidal sigma weight residual 93.00 13.71 79.29 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 12771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 3167 0.181 - 0.362: 21 0.362 - 0.542: 3 0.542 - 0.723: 0 0.723 - 0.904: 1 Chirality restraints: 3192 Sorted by residual: chirality pdb=" C1 NAG A 604 " pdb=" ND2 ASN A 197 " pdb=" C2 NAG A 604 " pdb=" O5 NAG A 604 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.04e+01 chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 133 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB VAL J 100C" pdb=" CA VAL J 100C" pdb=" CG1 VAL J 100C" pdb=" CG2 VAL J 100C" both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 3189 not shown) Planarity restraints: 3406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 166 " -0.493 9.50e-02 1.11e+02 2.22e-01 3.29e+01 pdb=" NE ARG E 166 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG E 166 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG E 166 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG E 166 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 276 " 0.054 2.00e-02 2.50e+03 5.03e-02 3.16e+01 pdb=" CG ASN A 276 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASN A 276 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 276 " -0.060 2.00e-02 2.50e+03 pdb=" C1 NAG M 1 " 0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 133 " -0.007 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN E 133 " 0.063 2.00e-02 2.50e+03 pdb=" OD1 ASN E 133 " -0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN E 133 " 0.044 2.00e-02 2.50e+03 pdb=" C1 NAG E 605 " -0.044 2.00e-02 2.50e+03 ... (remaining 3403 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 866 2.70 - 3.25: 19216 3.25 - 3.80: 29741 3.80 - 4.35: 36650 4.35 - 4.90: 62845 Nonbonded interactions: 149318 Sorted by model distance: nonbonded pdb=" OG1 THR A 303 " pdb=" O GLY A 321 " model vdw 2.151 2.440 nonbonded pdb=" OG SER D 612 " pdb=" OD1 ASN D 616 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR C 37 " pdb=" O CYS D 604 " model vdw 2.195 2.440 nonbonded pdb=" O ALA A 55 " pdb=" ND1 HIS A 216 " model vdw 2.215 2.520 nonbonded pdb=" OG1 THR J1090 " pdb=" O ALA J1095C" model vdw 2.217 2.440 ... (remaining 149313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = (chain 'E' and (resid 31 through 505 or resid 601 through 610)) } ncs_group { reference = (chain 'B' and resid 519 through 664) selection = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'Z' selection = chain 'a' } ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'O' selection = chain 'W' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 53.450 Find NCS groups from input model: 2.110 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.178 19775 Z= 0.344 Angle : 0.878 30.326 26832 Z= 0.428 Chirality : 0.054 0.904 3192 Planarity : 0.006 0.222 3357 Dihedral : 18.761 124.130 8313 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.86 % Favored : 89.71 % Rotamer: Outliers : 0.54 % Allowed : 31.87 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.94 (0.17), residues: 2312 helix: 0.62 (0.29), residues: 371 sheet: -0.76 (0.23), residues: 536 loop : -2.15 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 69 HIS 0.006 0.001 HIS C 374 PHE 0.014 0.002 PHE B 522 TYR 0.019 0.001 TYR H 100B ARG 0.030 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 220 time to evaluate : 2.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 369 LEU cc_start: 0.7905 (tp) cc_final: 0.7668 (tt) REVERT: E 427 TRP cc_start: 0.6495 (m100) cc_final: 0.6161 (m100) REVERT: F 584 GLU cc_start: 0.7122 (tm-30) cc_final: 0.6822 (tm-30) REVERT: H 32 TYR cc_start: 0.7912 (m-10) cc_final: 0.7653 (m-80) REVERT: H 82 LEU cc_start: 0.8110 (mp) cc_final: 0.7718 (tt) REVERT: X 108 MET cc_start: 0.6123 (tpt) cc_final: 0.5819 (tpt) outliers start: 11 outliers final: 3 residues processed: 230 average time/residue: 0.3771 time to fit residues: 124.9337 Evaluate side-chains 143 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain H residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.7980 chunk 175 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 0.0970 chunk 70 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 chunk 135 optimal weight: 0.7980 chunk 210 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19775 Z= 0.201 Angle : 0.691 9.644 26832 Z= 0.347 Chirality : 0.045 0.428 3192 Planarity : 0.004 0.070 3357 Dihedral : 11.980 112.974 4022 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.56 % Favored : 90.01 % Rotamer: Outliers : 4.29 % Allowed : 30.00 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.92 (0.17), residues: 2312 helix: 0.61 (0.29), residues: 372 sheet: -0.77 (0.22), residues: 551 loop : -2.13 (0.16), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 78 HIS 0.004 0.001 HIS C 374 PHE 0.022 0.001 PHE F 519 TYR 0.017 0.001 TYR H 100B ARG 0.011 0.001 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 161 time to evaluate : 2.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 82 MET cc_start: 0.3323 (mmp) cc_final: 0.3077 (mmp) REVERT: X 108 MET cc_start: 0.6007 (tpt) cc_final: 0.5783 (tpt) outliers start: 87 outliers final: 30 residues processed: 240 average time/residue: 0.3284 time to fit residues: 119.3394 Evaluate side-chains 163 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 657 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain I residue 77 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.8980 chunk 65 optimal weight: 0.1980 chunk 175 optimal weight: 10.0000 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 209 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19775 Z= 0.227 Angle : 0.679 9.892 26832 Z= 0.338 Chirality : 0.045 0.343 3192 Planarity : 0.004 0.040 3357 Dihedral : 10.454 112.312 4022 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.34 % Favored : 90.22 % Rotamer: Outliers : 4.19 % Allowed : 28.72 % Favored : 67.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.17), residues: 2312 helix: 0.71 (0.29), residues: 372 sheet: -0.77 (0.22), residues: 579 loop : -2.07 (0.16), residues: 1361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 628 HIS 0.003 0.001 HIS C 374 PHE 0.014 0.001 PHE H 67 TYR 0.016 0.001 TYR H 100B ARG 0.006 0.000 ARG E 166 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 147 time to evaluate : 2.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 ASN cc_start: 0.6844 (t0) cc_final: 0.6620 (t0) REVERT: I 82 MET cc_start: 0.7176 (mpp) cc_final: 0.6935 (mpp) REVERT: X 82 MET cc_start: 0.3693 (mmp) cc_final: 0.3357 (mmp) REVERT: X 108 MET cc_start: 0.5975 (tpt) cc_final: 0.5701 (tpt) outliers start: 85 outliers final: 47 residues processed: 224 average time/residue: 0.3053 time to fit residues: 105.4247 Evaluate side-chains 174 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 100 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 211 optimal weight: 7.9990 chunk 224 optimal weight: 0.0020 chunk 110 optimal weight: 0.0970 chunk 200 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN D 590 GLN ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 31 ASN H 76 ASN ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 19775 Z= 0.235 Angle : 0.673 11.150 26832 Z= 0.333 Chirality : 0.044 0.288 3192 Planarity : 0.004 0.041 3357 Dihedral : 9.442 111.944 4022 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.82 % Favored : 89.75 % Rotamer: Outliers : 4.14 % Allowed : 29.90 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2312 helix: 0.76 (0.29), residues: 372 sheet: -0.86 (0.21), residues: 600 loop : -2.02 (0.17), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 479 HIS 0.005 0.001 HIS C 66 PHE 0.011 0.001 PHE E 382 TYR 0.015 0.001 TYR H 100B ARG 0.004 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 143 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 377 ASN cc_start: 0.6877 (t0) cc_final: 0.6610 (t0) REVERT: H 30 GLU cc_start: 0.7860 (pm20) cc_final: 0.7655 (pm20) REVERT: X 82 MET cc_start: 0.3831 (mmp) cc_final: 0.3438 (mmp) REVERT: X 108 MET cc_start: 0.5998 (tpt) cc_final: 0.5760 (tpt) REVERT: J 1098 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.3022 (m-80) outliers start: 84 outliers final: 56 residues processed: 218 average time/residue: 0.3297 time to fit residues: 109.4880 Evaluate side-chains 183 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 126 time to evaluate : 2.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 135 THR Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 ASN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 191 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19775 Z= 0.379 Angle : 0.727 10.364 26832 Z= 0.362 Chirality : 0.044 0.274 3192 Planarity : 0.004 0.043 3357 Dihedral : 9.007 111.204 4022 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.39 % Allowed : 10.99 % Favored : 88.62 % Rotamer: Outliers : 6.16 % Allowed : 27.88 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.12 % Twisted General : 0.09 % 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: -1.84 (0.17), residues: 2312 helix: 0.50 (0.28), residues: 390 sheet: -0.86 (0.22), residues: 575 loop : -1.99 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 427 HIS 0.006 0.001 HIS A 352 PHE 0.014 0.002 PHE A 288 TYR 0.015 0.001 TYR H 100B ARG 0.008 0.001 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 142 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.6521 (p0) cc_final: 0.6266 (p0) REVERT: C 377 ASN cc_start: 0.7158 (t0) cc_final: 0.6895 (t0) REVERT: E 171 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8144 (tptm) REVERT: E 427 TRP cc_start: 0.7062 (m100) cc_final: 0.6840 (m100) REVERT: H 82 MET cc_start: 0.8220 (mmm) cc_final: 0.8008 (mmm) REVERT: X 82 MET cc_start: 0.4002 (mmp) cc_final: 0.3573 (mmp) REVERT: X 108 MET cc_start: 0.6083 (tpt) cc_final: 0.5819 (tpt) REVERT: J 1098 PHE cc_start: 0.3852 (OUTLIER) cc_final: 0.3109 (m-80) outliers start: 125 outliers final: 77 residues processed: 259 average time/residue: 0.3111 time to fit residues: 125.0858 Evaluate side-chains 203 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 124 time to evaluate : 2.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 387 THR Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 171 LYS Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1053 LYS Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 224 optimal weight: 20.0000 chunk 186 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 591 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 HIS ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 100NGLN J 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 19775 Z= 0.286 Angle : 0.699 10.025 26832 Z= 0.348 Chirality : 0.044 0.251 3192 Planarity : 0.004 0.045 3357 Dihedral : 8.651 110.632 4022 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.52 % Favored : 90.05 % Rotamer: Outliers : 5.02 % Allowed : 29.46 % Favored : 65.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2312 helix: 0.45 (0.28), residues: 390 sheet: -0.86 (0.23), residues: 527 loop : -1.96 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 427 HIS 0.004 0.001 HIS C 216 PHE 0.012 0.001 PHE E 382 TYR 0.016 0.001 TYR H 100B ARG 0.005 0.000 ARG A 327 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 136 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.6430 (p0) cc_final: 0.6169 (p0) REVERT: E 426 MET cc_start: 0.7227 (tpp) cc_final: 0.6951 (tpp) REVERT: H 82 MET cc_start: 0.8237 (mmm) cc_final: 0.7963 (mmm) REVERT: I 102 PHE cc_start: 0.7316 (OUTLIER) cc_final: 0.6667 (m-80) REVERT: X 82 MET cc_start: 0.3997 (mmp) cc_final: 0.3599 (mmp) REVERT: X 108 MET cc_start: 0.6118 (tpt) cc_final: 0.5838 (tpt) REVERT: J 1098 PHE cc_start: 0.3758 (OUTLIER) cc_final: 0.3082 (m-80) outliers start: 102 outliers final: 74 residues processed: 229 average time/residue: 0.2974 time to fit residues: 106.9241 Evaluate side-chains 200 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 124 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 369 LEU Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 198 THR Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain C residue 460 SER Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 639 THR Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 188 optimal weight: 0.1980 chunk 125 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19775 Z= 0.187 Angle : 0.687 10.371 26832 Z= 0.340 Chirality : 0.044 0.237 3192 Planarity : 0.004 0.050 3357 Dihedral : 8.257 109.289 4022 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.47 % Favored : 90.10 % Rotamer: Outliers : 3.89 % Allowed : 30.30 % Favored : 65.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.18), residues: 2312 helix: 0.47 (0.28), residues: 384 sheet: -0.78 (0.22), residues: 574 loop : -1.86 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 427 HIS 0.004 0.001 HIS C 216 PHE 0.011 0.001 PHE J 37 TYR 0.016 0.001 TYR H 100B ARG 0.014 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 142 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 589 ASP cc_start: 0.6323 (p0) cc_final: 0.6041 (p0) REVERT: E 150 MET cc_start: 0.6937 (mtm) cc_final: 0.6597 (pmm) REVERT: E 161 MET cc_start: 0.7156 (tmm) cc_final: 0.6935 (tmm) REVERT: I 102 PHE cc_start: 0.7178 (OUTLIER) cc_final: 0.6644 (m-80) REVERT: X 82 MET cc_start: 0.4089 (mmp) cc_final: 0.3736 (mmp) REVERT: X 108 MET cc_start: 0.6104 (tpt) cc_final: 0.5813 (tpt) REVERT: J 1098 PHE cc_start: 0.3707 (OUTLIER) cc_final: 0.3084 (m-80) outliers start: 79 outliers final: 58 residues processed: 213 average time/residue: 0.3012 time to fit residues: 99.8450 Evaluate side-chains 186 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 126 time to evaluate : 2.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 203 optimal weight: 6.9990 chunk 214 optimal weight: 0.0980 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN ** A 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19775 Z= 0.332 Angle : 0.732 11.999 26832 Z= 0.362 Chirality : 0.044 0.245 3192 Planarity : 0.004 0.047 3357 Dihedral : 8.292 107.910 4022 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.23 Ramachandran Plot: Outliers : 0.43 % Allowed : 10.03 % Favored : 89.53 % Rotamer: Outliers : 4.53 % Allowed : 30.54 % Favored : 64.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.18), residues: 2312 helix: 0.51 (0.28), residues: 384 sheet: -0.75 (0.22), residues: 573 loop : -1.87 (0.17), residues: 1355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 427 HIS 0.005 0.001 HIS A 374 PHE 0.011 0.001 PHE E 382 TYR 0.016 0.001 TYR H 100B ARG 0.010 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 130 time to evaluate : 2.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7521 (OUTLIER) cc_final: 0.7205 (tpp) REVERT: B 589 ASP cc_start: 0.6394 (p0) cc_final: 0.6179 (p0) REVERT: H 18 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8886 (mm) REVERT: I 102 PHE cc_start: 0.7297 (OUTLIER) cc_final: 0.6703 (m-80) REVERT: X 82 MET cc_start: 0.4139 (mmp) cc_final: 0.3765 (mmp) REVERT: X 108 MET cc_start: 0.6207 (tpt) cc_final: 0.5907 (tpt) REVERT: J 1098 PHE cc_start: 0.3667 (OUTLIER) cc_final: 0.3048 (m-80) outliers start: 92 outliers final: 75 residues processed: 210 average time/residue: 0.2986 time to fit residues: 98.8811 Evaluate side-chains 204 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 125 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 274 SER Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 373 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 573 ILE Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 595 ILE Chi-restraints excluded: chain F residue 615 SER Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 55 LYS Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 0.3980 chunk 208 optimal weight: 20.0000 chunk 214 optimal weight: 0.2980 chunk 125 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 188 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19775 Z= 0.197 Angle : 0.709 11.685 26832 Z= 0.351 Chirality : 0.044 0.238 3192 Planarity : 0.004 0.050 3357 Dihedral : 8.024 107.526 4022 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.43 % Favored : 90.14 % Rotamer: Outliers : 3.79 % Allowed : 31.43 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.18), residues: 2312 helix: 0.50 (0.28), residues: 384 sheet: -0.61 (0.23), residues: 543 loop : -1.84 (0.16), residues: 1385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP C 427 HIS 0.003 0.001 HIS C 216 PHE 0.011 0.001 PHE E 382 TYR 0.016 0.001 TYR H 100B ARG 0.008 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 141 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.7090 (tpp) REVERT: H 18 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8853 (mm) REVERT: I 102 PHE cc_start: 0.7119 (OUTLIER) cc_final: 0.6587 (m-80) REVERT: X 82 MET cc_start: 0.4101 (mmp) cc_final: 0.3737 (mmp) REVERT: X 108 MET cc_start: 0.6150 (tpt) cc_final: 0.5882 (tpt) REVERT: J 1098 PHE cc_start: 0.3769 (OUTLIER) cc_final: 0.3194 (m-80) outliers start: 77 outliers final: 63 residues processed: 207 average time/residue: 0.3086 time to fit residues: 99.1315 Evaluate side-chains 193 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 126 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 457 ASP Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 7.9990 chunk 134 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 231 optimal weight: 50.0000 chunk 212 optimal weight: 0.0270 chunk 184 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19775 Z= 0.211 Angle : 0.714 11.401 26832 Z= 0.355 Chirality : 0.044 0.239 3192 Planarity : 0.004 0.051 3357 Dihedral : 7.928 105.946 4022 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.43 % Allowed : 9.47 % Favored : 90.10 % Rotamer: Outliers : 3.74 % Allowed : 31.77 % Favored : 64.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.65 (0.18), residues: 2312 helix: 0.41 (0.28), residues: 384 sheet: -0.60 (0.23), residues: 546 loop : -1.82 (0.16), residues: 1382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP A 427 HIS 0.004 0.001 HIS A 216 PHE 0.011 0.001 PHE E 382 TYR 0.017 0.001 TYR H 100B ARG 0.009 0.000 ARG B 542 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4624 Ramachandran restraints generated. 2312 Oldfield, 0 Emsley, 2312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 130 time to evaluate : 2.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.7102 (tpp) REVERT: H 18 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8862 (mm) REVERT: I 102 PHE cc_start: 0.7059 (OUTLIER) cc_final: 0.6584 (m-80) REVERT: X 82 MET cc_start: 0.4094 (mmp) cc_final: 0.3735 (mmp) REVERT: X 108 MET cc_start: 0.6181 (tpt) cc_final: 0.5886 (tpt) REVERT: J 1098 PHE cc_start: 0.3565 (OUTLIER) cc_final: 0.3071 (m-80) outliers start: 76 outliers final: 64 residues processed: 195 average time/residue: 0.3113 time to fit residues: 96.2267 Evaluate side-chains 191 residues out of total 2031 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 123 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 104 MET Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 132 THR Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 195 ASN Chi-restraints excluded: chain C residue 197 ASN Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 330 HIS Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 475 MET Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 494 LEU Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 126 CYS Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 242 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 296 CYS Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain E residue 501 CYS Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 593 LEU Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain F residue 639 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 19 ARG Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 94 THR Chi-restraints excluded: chain I residue 100 VAL Chi-restraints excluded: chain I residue 102 PHE Chi-restraints excluded: chain J residue 37 PHE Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 1098 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 0.0970 chunk 56 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.0980 chunk 184 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100AASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.049233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.034430 restraints weight = 132793.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.035648 restraints weight = 71894.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.036470 restraints weight = 49929.733| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19775 Z= 0.195 Angle : 0.701 11.535 26832 Z= 0.347 Chirality : 0.044 0.240 3192 Planarity : 0.004 0.055 3357 Dihedral : 7.800 104.509 4022 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.39 % Allowed : 9.52 % Favored : 90.10 % Rotamer: Outliers : 3.55 % Allowed : 31.87 % Favored : 64.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.65 (0.18), residues: 2312 helix: 0.62 (0.29), residues: 366 sheet: -0.65 (0.22), residues: 573 loop : -1.85 (0.17), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP A 427 HIS 0.003 0.001 HIS C 216 PHE 0.011 0.001 PHE E 382 TYR 0.016 0.001 TYR H 100B ARG 0.009 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4127.39 seconds wall clock time: 75 minutes 23.04 seconds (4523.04 seconds total)