Starting phenix.real_space_refine on Fri Feb 16 04:07:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dmh_27538/02_2024/8dmh_27538.pdb" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 8988 2.51 5 N 2379 2.21 5 O 2790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 214": "OD1" <-> "OD2" Residue "a GLU 313": "OE1" <-> "OE2" Residue "a ASP 323": "OD1" <-> "OD2" Residue "a TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 402": "OE1" <-> "OE2" Residue "a GLU 419": "OE1" <-> "OE2" Residue "a TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 61": "OD1" <-> "OD2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "b ASP 317": "OD1" <-> "OD2" Residue "b GLU 419": "OE1" <-> "OE2" Residue "C TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "c TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 402": "OE1" <-> "OE2" Residue "c GLU 410": "OE1" <-> "OE2" Residue "c GLU 412": "OE1" <-> "OE2" Residue "c ASP 414": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14259 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "E" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "a" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "B" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "G" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "b" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "C" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1521 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 2, 'TRANS': 187} Chain breaks: 1 Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 822 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Chain: "J" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 938 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "c" Number of atoms: 1265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1265 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 4, 'TRANS': 151} Chain breaks: 1 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 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: "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: 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: "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: 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "a" 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: "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: "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: 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: 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 Time building chain proxies: 7.34, per 1000 atoms: 0.51 Number of scatterers: 14259 At special positions: 0 Unit cell: (118.8, 128.4, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2790 8.00 N 2379 7.00 C 8988 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 123 " - pdb=" SG CYS A 160 " distance=2.04 Simple disulfide: pdb=" SG CYS A 184 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 366 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 98 " distance=2.03 Simple disulfide: pdb=" SG CYS a 285 " - pdb=" SG CYS a 298 " distance=2.04 Simple disulfide: pdb=" SG CYS a 307 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 370 " - pdb=" SG CYS a 391 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 239 " distance=2.03 Simple disulfide: pdb=" SG CYS B 123 " - pdb=" SG CYS B 160 " distance=2.04 Simple disulfide: pdb=" SG CYS B 184 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 366 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS b 285 " - pdb=" SG CYS b 298 " distance=2.04 Simple disulfide: pdb=" SG CYS b 307 " - pdb=" SG CYS b 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 370 " - pdb=" SG CYS b 391 " distance=2.03 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 123 " - pdb=" SG CYS C 160 " distance=2.03 Simple disulfide: pdb=" SG CYS C 184 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 366 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 98 " distance=2.03 Simple disulfide: pdb=" SG CYS c 285 " - pdb=" SG CYS c 298 " distance=2.04 Simple disulfide: pdb=" SG CYS c 307 " - pdb=" SG CYS c 316 " distance=2.03 Simple disulfide: pdb=" SG CYS c 370 " - pdb=" SG CYS c 391 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " 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 V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " NAG-ASN " NAG A 301 " - " ASN A 124 " " NAG B 301 " - " ASN B 124 " " NAG C 301 " - " ASN C 124 " " NAG D 1 " - " ASN A 85 " " NAG K 1 " - " ASN A 95 " " NAG L 1 " - " ASN A 114 " " NAG M 1 " - " ASN A 171 " " NAG N 1 " - " ASN A 232 " " NAG O 1 " - " ASN a 401 " " NAG P 1 " - " ASN B 85 " " NAG Q 1 " - " ASN B 95 " " NAG R 1 " - " ASN B 114 " " NAG S 1 " - " ASN B 171 " " NAG T 1 " - " ASN B 232 " " NAG U 1 " - " ASN b 401 " " NAG V 1 " - " ASN C 85 " " NAG W 1 " - " ASN C 95 " " NAG X 1 " - " ASN C 114 " " NAG Y 1 " - " ASN C 171 " " NAG Z 1 " - " ASN C 232 " " NAG a 701 " - " ASN a 371 " " NAG b 701 " - " ASN b 371 " " NAG c 701 " - " ASN c 371 " " NAG d 1 " - " ASN c 401 " Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 2.6 seconds 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3198 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 26 sheets defined 25.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.551A pdb=" N ASN A 85 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LEU A 86 " --> pdb=" O HIS A 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 82 through 86' Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.692A pdb=" N ILE A 141 " --> pdb=" O THR A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.573A pdb=" N MET A 194 " --> pdb=" O ARG A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.674A pdb=" N TRP A 210 " --> pdb=" O CYS A 207 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR A 211 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 207 through 212' Processing helix chain 'A' and resid 244 through 254 removed outlier: 3.804A pdb=" N LEU A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'F' and resid 89 through 93 removed outlier: 3.509A pdb=" N THR F 93 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 308 removed outlier: 3.523A pdb=" N VAL a 304 " --> pdb=" O GLY a 300 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS a 306 " --> pdb=" O THR a 302 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 332 removed outlier: 3.976A pdb=" N ASP a 317 " --> pdb=" O GLU a 313 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET a 318 " --> pdb=" O GLU a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 346 removed outlier: 3.755A pdb=" N HIS a 341 " --> pdb=" O GLU a 337 " (cutoff:3.500A) Processing helix chain 'a' and resid 347 through 351 Processing helix chain 'a' and resid 352 through 365 Processing helix chain 'a' and resid 401 through 404 Processing helix chain 'a' and resid 405 through 427 removed outlier: 3.667A pdb=" N LYS a 423 " --> pdb=" O GLU a 419 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE a 426 " --> pdb=" O ARG a 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.069A pdb=" N ASN B 130 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 Processing helix chain 'B' and resid 186 through 200 Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.509A pdb=" N ARG B 249 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE B 250 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 32 No H-bonds generated for 'chain 'G' and resid 30 through 32' Processing helix chain 'H' and resid 89 through 93 removed outlier: 3.611A pdb=" N THR H 93 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'b' and resid 287 through 291 removed outlier: 3.530A pdb=" N ILE b 291 " --> pdb=" O LYS b 288 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 308 removed outlier: 3.928A pdb=" N LYS b 306 " --> pdb=" O THR b 302 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N CYS b 307 " --> pdb=" O ALA b 303 " (cutoff:3.500A) Processing helix chain 'b' and resid 313 through 332 removed outlier: 3.951A pdb=" N ASP b 317 " --> pdb=" O GLU b 313 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET b 318 " --> pdb=" O GLU b 314 " (cutoff:3.500A) Processing helix chain 'b' and resid 335 through 346 Processing helix chain 'b' and resid 347 through 351 Processing helix chain 'b' and resid 352 through 365 removed outlier: 3.504A pdb=" N HIS b 360 " --> pdb=" O LEU b 356 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU b 361 " --> pdb=" O MET b 357 " (cutoff:3.500A) Processing helix chain 'b' and resid 401 through 404 Processing helix chain 'b' and resid 405 through 427 removed outlier: 3.500A pdb=" N GLU b 412 " --> pdb=" O GLN b 408 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 423 " --> pdb=" O GLU b 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.565A pdb=" N ILE C 141 " --> pdb=" O THR C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 207 through 211 removed outlier: 3.917A pdb=" N TRP C 210 " --> pdb=" O CYS C 207 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR C 211 " --> pdb=" O TRP C 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 211' Processing helix chain 'C' and resid 244 through 253 removed outlier: 3.673A pdb=" N LEU C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER C 253 " --> pdb=" O ARG C 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 30 through 32 No H-bonds generated for 'chain 'I' and resid 30 through 32' Processing helix chain 'I' and resid 51 through 53 No H-bonds generated for 'chain 'I' and resid 51 through 53' Processing helix chain 'I' and resid 80 through 84 removed outlier: 4.170A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 33 removed outlier: 3.540A pdb=" N ARG J 32 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 93 removed outlier: 3.552A pdb=" N THR J 93 " --> pdb=" O ALA J 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 287 through 291 Processing helix chain 'c' and resid 300 through 310 removed outlier: 3.592A pdb=" N VAL c 304 " --> pdb=" O GLY c 300 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS c 306 " --> pdb=" O THR c 302 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS c 307 " --> pdb=" O ALA c 303 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN c 308 " --> pdb=" O VAL c 304 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL c 309 " --> pdb=" O ALA c 305 " (cutoff:3.500A) Processing helix chain 'c' and resid 313 through 332 removed outlier: 3.888A pdb=" N ASP c 317 " --> pdb=" O GLU c 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET c 318 " --> pdb=" O GLU c 314 " (cutoff:3.500A) Processing helix chain 'c' and resid 335 through 346 Processing helix chain 'c' and resid 347 through 351 Processing helix chain 'c' and resid 352 through 365 Processing helix chain 'c' and resid 401 through 404 Processing helix chain 'c' and resid 405 through 427 removed outlier: 3.510A pdb=" N THR c 418 " --> pdb=" O ASP c 414 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS c 423 " --> pdb=" O GLU c 419 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE c 426 " --> pdb=" O ARG c 422 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 93 removed outlier: 3.659A pdb=" N ILE A 101 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.647A pdb=" N LEU E 74 " --> pdb=" O LEU E 21 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 66 " --> pdb=" O THR E 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.234A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N TYR E 50 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.234A pdb=" N LEU E 11 " --> pdb=" O GLU E 107 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 11 through 13 removed outlier: 6.993A pdb=" N MET F 35 " --> pdb=" O SER F 51 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER F 51 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N TRP F 37 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 20 through 23 removed outlier: 3.576A pdb=" N SER F 80 " --> pdb=" O ASP F 75 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER F 73 " --> pdb=" O TYR F 82 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 394 through 395 Processing sheet with id=AA9, first strand: chain 'B' and resid 67 through 68 Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 93 removed outlier: 3.520A pdb=" N ILE B 101 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.593A pdb=" N ALA G 19 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR G 73 " --> pdb=" O SER G 66 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER G 66 " --> pdb=" O THR G 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.182A pdb=" N LEU G 11 " --> pdb=" O GLU G 107 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N TYR G 50 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.182A pdb=" N LEU G 11 " --> pdb=" O GLU G 107 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 13 removed outlier: 3.547A pdb=" N ALA H 94 " --> pdb=" O VAL H 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 36 " --> pdb=" O ALA H 99 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N MET H 35 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N SER H 51 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N TRP H 37 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 21 through 23 removed outlier: 3.579A pdb=" N SER H 80 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER H 73 " --> pdb=" O TYR H 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 285 through 286 removed outlier: 4.065A pdb=" N LYS b 297 " --> pdb=" O LEU b 286 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 394 through 395 Processing sheet with id=AB9, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AC1, first strand: chain 'C' and resid 90 through 93 Processing sheet with id=AC2, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.566A pdb=" N ALA I 19 " --> pdb=" O ILE I 76 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR I 75 " --> pdb=" O SER I 64 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.131A pdb=" N LEU I 11 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL I 34 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR I 50 " --> pdb=" O VAL I 34 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N LYS I 40 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA I 44 " --> pdb=" O LYS I 40 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.131A pdb=" N LEU I 11 " --> pdb=" O GLU I 107 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'J' and resid 7 through 8 removed outlier: 3.905A pdb=" N SER J 22 " --> pdb=" O SER J 8 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER J 73 " --> pdb=" O TYR J 82 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.520A pdb=" N GLY J 11 " --> pdb=" O ILE J 121 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N MET J 35 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER J 51 " --> pdb=" O MET J 35 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TRP J 37 " --> pdb=" O VAL J 49 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'c' and resid 285 through 286 removed outlier: 3.551A pdb=" N LEU c 286 " --> pdb=" O LYS c 297 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS c 297 " --> pdb=" O LEU c 286 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'c' and resid 394 through 395 502 hydrogen bonds defined for protein. 1308 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: 4.49 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4383 1.34 - 1.46: 4032 1.46 - 1.59: 6015 1.59 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 14580 Sorted by residual: bond pdb=" CB CYS C 92 " pdb=" SG CYS C 92 " ideal model delta sigma weight residual 1.808 1.769 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CA TRP b 289 " pdb=" C TRP b 289 " ideal model delta sigma weight residual 1.523 1.502 0.021 1.80e-02 3.09e+03 1.35e+00 bond pdb=" CA VAL c 367 " pdb=" CB VAL c 367 " ideal model delta sigma weight residual 1.547 1.536 0.011 1.10e-02 8.26e+03 9.38e-01 bond pdb=" CG LEU c 393 " pdb=" CD1 LEU c 393 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.70e-01 bond pdb=" C1 NAG N 1 " pdb=" C2 NAG N 1 " ideal model delta sigma weight residual 1.532 1.550 -0.018 2.00e-02 2.50e+03 8.27e-01 ... (remaining 14575 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.16: 187 105.16 - 112.39: 7570 112.39 - 119.62: 4644 119.62 - 126.85: 7109 126.85 - 134.08: 212 Bond angle restraints: 19722 Sorted by residual: angle pdb=" CA TRP b 289 " pdb=" C TRP b 289 " pdb=" N MET b 290 " ideal model delta sigma weight residual 118.27 113.39 4.88 1.59e+00 3.96e-01 9.43e+00 angle pdb=" CB MET b 290 " pdb=" CG MET b 290 " pdb=" SD MET b 290 " ideal model delta sigma weight residual 112.70 103.61 9.09 3.00e+00 1.11e-01 9.17e+00 angle pdb=" CA MET b 290 " pdb=" CB MET b 290 " pdb=" CG MET b 290 " ideal model delta sigma weight residual 114.10 119.81 -5.71 2.00e+00 2.50e-01 8.15e+00 angle pdb=" N ASN A 232 " pdb=" CA ASN A 232 " pdb=" CB ASN A 232 " ideal model delta sigma weight residual 110.45 114.70 -4.25 1.52e+00 4.33e-01 7.83e+00 angle pdb=" CA CYS b 298 " pdb=" CB CYS b 298 " pdb=" SG CYS b 298 " ideal model delta sigma weight residual 114.40 120.47 -6.07 2.30e+00 1.89e-01 6.96e+00 ... (remaining 19717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.04: 8391 22.04 - 44.07: 626 44.07 - 66.11: 107 66.11 - 88.14: 43 88.14 - 110.18: 22 Dihedral angle restraints: 9189 sinusoidal: 4194 harmonic: 4995 Sorted by residual: dihedral pdb=" CB CYS A 92 " pdb=" SG CYS A 92 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -175.77 89.77 1 1.00e+01 1.00e-02 9.56e+01 dihedral pdb=" CB CYS B 92 " pdb=" SG CYS B 92 " pdb=" SG CYS B 239 " pdb=" CB CYS B 239 " ideal model delta sinusoidal sigma weight residual 93.00 43.02 49.98 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA CYS c 298 " pdb=" C CYS c 298 " pdb=" N PHE c 299 " pdb=" CA PHE c 299 " ideal model delta harmonic sigma weight residual -180.00 -153.16 -26.84 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 9186 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2146 0.088 - 0.175: 125 0.175 - 0.263: 3 0.263 - 0.351: 0 0.351 - 0.438: 3 Chirality restraints: 2277 Sorted by residual: chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN C 95 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.81e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 114 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.39e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN A 171 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 2274 not shown) Planarity restraints: 2445 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN a 371 " 0.030 2.00e-02 2.50e+03 2.78e-02 9.68e+00 pdb=" CG ASN a 371 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN a 371 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN a 371 " -0.018 2.00e-02 2.50e+03 pdb=" C1 NAG a 701 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN c 401 " 0.025 2.00e-02 2.50e+03 2.40e-02 7.20e+00 pdb=" CG ASN c 401 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN c 401 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN c 401 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG d 1 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 114 " 0.025 2.00e-02 2.50e+03 2.35e-02 6.91e+00 pdb=" CG ASN B 114 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN B 114 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 114 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.025 2.00e-02 2.50e+03 ... (remaining 2442 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 392 2.70 - 3.25: 13732 3.25 - 3.80: 21699 3.80 - 4.35: 29592 4.35 - 4.90: 49961 Nonbonded interactions: 115376 Sorted by model distance: nonbonded pdb=" OD1 ASN B 171 " pdb=" OG1 THR B 173 " model vdw 2.149 2.440 nonbonded pdb=" N GLN A 183 " pdb=" OE1 GLN A 183 " model vdw 2.234 2.520 nonbonded pdb=" O TYR I 50 " pdb=" OG SER I 54 " model vdw 2.236 2.440 nonbonded pdb=" OD1 ASN A 114 " pdb=" NE2 GLN A 226 " model vdw 2.252 2.520 nonbonded pdb=" OG SER B 93 " pdb=" ND1 HIS B 99 " model vdw 2.258 2.520 ... (remaining 115371 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'P' selection = chain 'V' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 8.380 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 38.960 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14580 Z= 0.212 Angle : 0.599 9.086 19722 Z= 0.309 Chirality : 0.045 0.438 2277 Planarity : 0.004 0.045 2421 Dihedral : 16.832 110.179 5910 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.30 (0.20), residues: 1689 helix: -1.23 (0.26), residues: 357 sheet: -0.82 (0.27), residues: 396 loop : -0.63 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP c 270 HIS 0.004 0.001 HIS B 99 PHE 0.021 0.002 PHE G 72 TYR 0.029 0.001 TYR B 203 ARG 0.010 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 24 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7958 (mmm-85) REVERT: E 108 ILE cc_start: 0.7372 (mp) cc_final: 0.7135 (mp) REVERT: B 253 SER cc_start: 0.8323 (m) cc_final: 0.8049 (t) REVERT: H 88 LEU cc_start: 0.8730 (mt) cc_final: 0.8356 (mt) REVERT: H 95 ILE cc_start: 0.7898 (pt) cc_final: 0.7683 (pt) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2795 time to fit residues: 118.8666 Evaluate side-chains 214 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 214 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 80 optimal weight: 0.2980 chunk 98 optimal weight: 0.0030 chunk 152 optimal weight: 0.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 GLN a 348 ASN b 348 ASN J 36 ASN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14580 Z= 0.177 Angle : 0.603 10.634 19722 Z= 0.310 Chirality : 0.045 0.357 2277 Planarity : 0.004 0.037 2421 Dihedral : 13.051 96.727 2820 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.07 % Allowed : 7.33 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.20), residues: 1689 helix: -0.09 (0.27), residues: 375 sheet: -0.73 (0.25), residues: 429 loop : -0.67 (0.20), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP a 289 HIS 0.004 0.001 HIS b 404 PHE 0.015 0.001 PHE G 72 TYR 0.019 0.001 TYR F 96 ARG 0.006 0.001 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 228 time to evaluate : 1.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 253 SER cc_start: 0.8121 (m) cc_final: 0.7919 (t) REVERT: H 88 LEU cc_start: 0.8788 (mt) cc_final: 0.8341 (mt) REVERT: H 95 ILE cc_start: 0.8207 (pt) cc_final: 0.7984 (pt) outliers start: 16 outliers final: 8 residues processed: 236 average time/residue: 0.2283 time to fit residues: 82.8495 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 212 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain J residue 29 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 359 ASN c 396 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14580 Z= 0.287 Angle : 0.610 12.520 19722 Z= 0.310 Chirality : 0.046 0.400 2277 Planarity : 0.004 0.030 2421 Dihedral : 11.265 96.359 2820 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.20 % Allowed : 9.20 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1689 helix: 0.28 (0.27), residues: 384 sheet: -0.70 (0.25), residues: 432 loop : -0.73 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP a 270 HIS 0.005 0.001 HIS A 146 PHE 0.019 0.002 PHE C 259 TYR 0.020 0.002 TYR I 50 ARG 0.007 0.000 ARG J 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 207 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 322 ILE cc_start: 0.8733 (mm) cc_final: 0.8495 (mm) REVERT: B 131 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7711 (mmtt) REVERT: H 88 LEU cc_start: 0.8852 (mt) cc_final: 0.8581 (mt) REVERT: H 111 MET cc_start: 0.8520 (mtt) cc_final: 0.8264 (mmt) outliers start: 33 outliers final: 18 residues processed: 225 average time/residue: 0.2349 time to fit residues: 81.8020 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 201 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 274 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 80 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14580 Z= 0.181 Angle : 0.547 6.753 19722 Z= 0.281 Chirality : 0.044 0.389 2277 Planarity : 0.003 0.032 2421 Dihedral : 10.034 94.135 2820 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.20 % Allowed : 10.47 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1689 helix: 0.57 (0.27), residues: 384 sheet: -0.70 (0.25), residues: 432 loop : -0.69 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP b 270 HIS 0.003 0.001 HIS b 404 PHE 0.012 0.001 PHE G 72 TYR 0.018 0.001 TYR I 50 ARG 0.004 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 206 time to evaluate : 1.614 Fit side-chains revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4312 (OUTLIER) cc_final: 0.3200 (mm-30) REVERT: a 292 LEU cc_start: 0.8769 (tp) cc_final: 0.8544 (tp) REVERT: a 322 ILE cc_start: 0.8702 (mm) cc_final: 0.8468 (mm) REVERT: H 88 LEU cc_start: 0.8823 (mt) cc_final: 0.8315 (mt) REVERT: H 111 MET cc_start: 0.8477 (mtt) cc_final: 0.8192 (mtt) outliers start: 33 outliers final: 20 residues processed: 221 average time/residue: 0.2301 time to fit residues: 78.1531 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 314 GLU Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 85 MET Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 411 GLN C 73 GLN J 36 ASN ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 14580 Z= 0.526 Angle : 0.722 10.598 19722 Z= 0.364 Chirality : 0.050 0.480 2277 Planarity : 0.004 0.033 2421 Dihedral : 10.113 90.686 2820 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.67 % Allowed : 11.27 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1689 helix: 0.25 (0.26), residues: 369 sheet: -0.81 (0.25), residues: 468 loop : -0.83 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP c 270 HIS 0.007 0.002 HIS E 39 PHE 0.015 0.002 PHE c 405 TYR 0.016 0.002 TYR G 50 ARG 0.005 0.001 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: a 292 LEU cc_start: 0.8887 (tp) cc_final: 0.8678 (tp) REVERT: a 322 ILE cc_start: 0.8819 (mm) cc_final: 0.8618 (mm) REVERT: H 88 LEU cc_start: 0.8860 (mt) cc_final: 0.8603 (mt) REVERT: H 111 MET cc_start: 0.8615 (mtt) cc_final: 0.8381 (mtt) REVERT: b 299 PHE cc_start: 0.8982 (OUTLIER) cc_final: 0.8406 (m-80) outliers start: 40 outliers final: 24 residues processed: 224 average time/residue: 0.2475 time to fit residues: 85.6434 Evaluate side-chains 216 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 287 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 73 GLN Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN a 411 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14580 Z= 0.220 Angle : 0.582 7.854 19722 Z= 0.296 Chirality : 0.045 0.448 2277 Planarity : 0.003 0.030 2421 Dihedral : 9.391 86.944 2820 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.13 % Allowed : 12.87 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1689 helix: 0.40 (0.26), residues: 387 sheet: -0.76 (0.25), residues: 444 loop : -0.72 (0.21), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP b 270 HIS 0.003 0.001 HIS A 238 PHE 0.013 0.001 PHE G 72 TYR 0.017 0.001 TYR I 50 ARG 0.003 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4392 (OUTLIER) cc_final: 0.3221 (mm-30) REVERT: a 322 ILE cc_start: 0.8771 (mm) cc_final: 0.8512 (mm) REVERT: H 88 LEU cc_start: 0.8791 (mt) cc_final: 0.8535 (mt) REVERT: b 299 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8476 (m-80) REVERT: J 111 MET cc_start: 0.8322 (mtt) cc_final: 0.7986 (mtt) REVERT: c 372 TYR cc_start: 0.8030 (m-80) cc_final: 0.7828 (m-80) outliers start: 32 outliers final: 22 residues processed: 217 average time/residue: 0.2686 time to fit residues: 88.5111 Evaluate side-chains 220 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 274 ASP Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN a 411 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14580 Z= 0.216 Angle : 0.575 7.587 19722 Z= 0.291 Chirality : 0.044 0.440 2277 Planarity : 0.003 0.029 2421 Dihedral : 9.001 83.356 2820 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.20 % Allowed : 13.47 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1689 helix: 0.54 (0.27), residues: 387 sheet: -0.66 (0.25), residues: 438 loop : -0.67 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP b 270 HIS 0.003 0.001 HIS C 99 PHE 0.011 0.001 PHE G 72 TYR 0.017 0.001 TYR B 72 ARG 0.004 0.000 ARG F 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4394 (OUTLIER) cc_final: 0.3239 (mm-30) REVERT: a 322 ILE cc_start: 0.8761 (mm) cc_final: 0.8546 (mm) REVERT: B 131 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7889 (mmtt) REVERT: B 164 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8587 (p0) REVERT: H 88 LEU cc_start: 0.8786 (mt) cc_final: 0.8534 (mt) REVERT: b 299 PHE cc_start: 0.8764 (OUTLIER) cc_final: 0.8388 (m-80) REVERT: J 111 MET cc_start: 0.8304 (mtt) cc_final: 0.8070 (mtt) outliers start: 33 outliers final: 23 residues processed: 217 average time/residue: 0.2376 time to fit residues: 79.5783 Evaluate side-chains 222 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 7.9990 chunk 102 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN a 396 ASN a 411 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 308 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14580 Z= 0.327 Angle : 0.622 9.069 19722 Z= 0.313 Chirality : 0.046 0.479 2277 Planarity : 0.003 0.029 2421 Dihedral : 8.895 79.570 2820 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.20 % Allowed : 13.87 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.20), residues: 1689 helix: 0.67 (0.27), residues: 369 sheet: -0.70 (0.25), residues: 456 loop : -0.67 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP b 270 HIS 0.005 0.001 HIS B 99 PHE 0.012 0.002 PHE G 72 TYR 0.015 0.002 TYR B 72 ARG 0.003 0.000 ARG I 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4498 (OUTLIER) cc_final: 0.3310 (mm-30) REVERT: a 322 ILE cc_start: 0.8815 (mm) cc_final: 0.8596 (mm) REVERT: B 131 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7968 (mmtt) REVERT: B 164 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8627 (p0) REVERT: H 88 LEU cc_start: 0.8812 (mt) cc_final: 0.8563 (mt) REVERT: H 111 MET cc_start: 0.8418 (mmt) cc_final: 0.8004 (mmt) REVERT: b 299 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8376 (m-80) outliers start: 33 outliers final: 27 residues processed: 215 average time/residue: 0.2315 time to fit residues: 76.3911 Evaluate side-chains 225 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 194 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 107 GLN Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 394 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain b residue 309 VAL Chi-restraints excluded: chain b residue 394 VAL Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 107 GLN Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Chi-restraints excluded: chain c residue 373 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.0060 chunk 150 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 136 optimal weight: 0.0870 chunk 142 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 overall best weight: 0.5374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14580 Z= 0.157 Angle : 0.561 7.919 19722 Z= 0.284 Chirality : 0.044 0.458 2277 Planarity : 0.003 0.030 2421 Dihedral : 8.340 75.851 2820 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.67 % Allowed : 14.53 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1689 helix: 0.74 (0.27), residues: 387 sheet: -0.64 (0.25), residues: 438 loop : -0.60 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP b 270 HIS 0.003 0.001 HIS C 99 PHE 0.011 0.001 PHE G 72 TYR 0.017 0.001 TYR I 50 ARG 0.003 0.000 ARG J 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 205 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4403 (OUTLIER) cc_final: 0.3310 (mm-30) REVERT: a 322 ILE cc_start: 0.8749 (mm) cc_final: 0.8535 (mm) REVERT: B 131 LYS cc_start: 0.8284 (mmtt) cc_final: 0.8040 (mmtt) REVERT: B 164 ASN cc_start: 0.9042 (OUTLIER) cc_final: 0.8558 (p0) REVERT: H 88 LEU cc_start: 0.8761 (mt) cc_final: 0.8514 (mt) REVERT: H 111 MET cc_start: 0.8441 (mmt) cc_final: 0.7996 (mmt) REVERT: b 299 PHE cc_start: 0.8607 (OUTLIER) cc_final: 0.8194 (m-80) REVERT: J 82 TYR cc_start: 0.7573 (m-10) cc_final: 0.7373 (m-10) outliers start: 25 outliers final: 16 residues processed: 216 average time/residue: 0.2335 time to fit residues: 76.7313 Evaluate side-chains 215 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 196 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 chunk 81 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 411 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 308 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14580 Z= 0.412 Angle : 0.678 10.370 19722 Z= 0.340 Chirality : 0.048 0.532 2277 Planarity : 0.004 0.028 2421 Dihedral : 8.550 70.355 2820 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.73 % Allowed : 14.47 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1689 helix: 0.57 (0.27), residues: 369 sheet: -0.72 (0.25), residues: 456 loop : -0.71 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP b 270 HIS 0.005 0.001 HIS E 39 PHE 0.015 0.002 PHE c 405 TYR 0.014 0.002 TYR A 241 ARG 0.004 0.000 ARG A 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3378 Ramachandran restraints generated. 1689 Oldfield, 0 Emsley, 1689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 196 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: E 107 GLU cc_start: 0.4676 (OUTLIER) cc_final: 0.3473 (mm-30) REVERT: B 131 LYS cc_start: 0.8250 (mmtt) cc_final: 0.8046 (mmtt) REVERT: B 164 ASN cc_start: 0.9125 (OUTLIER) cc_final: 0.8644 (p0) REVERT: H 88 LEU cc_start: 0.8834 (mt) cc_final: 0.8588 (mt) REVERT: H 111 MET cc_start: 0.8541 (mmt) cc_final: 0.8121 (mmt) REVERT: b 299 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8289 (m-80) REVERT: C 258 LYS cc_start: 0.8050 (pttm) cc_final: 0.7724 (ptmm) outliers start: 26 outliers final: 21 residues processed: 209 average time/residue: 0.2414 time to fit residues: 77.4724 Evaluate side-chains 217 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain E residue 30 ILE Chi-restraints excluded: chain E residue 107 GLU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain a residue 309 VAL Chi-restraints excluded: chain a residue 411 GLN Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 107 GLN Chi-restraints excluded: chain b residue 299 PHE Chi-restraints excluded: chain C residue 115 ASP Chi-restraints excluded: chain C residue 131 LYS Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 108 ILE Chi-restraints excluded: chain J residue 29 THR Chi-restraints excluded: chain J residue 121 ILE Chi-restraints excluded: chain c residue 274 ASP Chi-restraints excluded: chain c residue 299 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 411 GLN ** G 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.080648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.064461 restraints weight = 36315.343| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.09 r_work: 0.2956 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14580 Z= 0.226 Angle : 0.603 8.564 19722 Z= 0.304 Chirality : 0.045 0.534 2277 Planarity : 0.003 0.028 2421 Dihedral : 8.180 67.455 2820 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.87 % Allowed : 14.67 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1689 helix: 0.81 (0.27), residues: 369 sheet: -0.71 (0.25), residues: 459 loop : -0.59 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 270 HIS 0.003 0.001 HIS A 146 PHE 0.013 0.001 PHE G 72 TYR 0.016 0.001 TYR A 72 ARG 0.003 0.000 ARG J 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.27 seconds wall clock time: 55 minutes 27.89 seconds (3327.89 seconds total)