Starting phenix.real_space_refine (version: dev) on Thu Feb 23 02:32:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k3b_22655/02_2023/7k3b_22655.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.007 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 Process input model Symmetric amino acids flipped Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B GLU 69": "OE1" <-> "OE2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "C TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 280": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D GLU 67": "OE1" <-> "OE2" Residue "D GLU 69": "OE1" <-> "OE2" Residue "D ARG 124": "NH1" <-> "NH2" Residue "E TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 280": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F GLU 67": "OE1" <-> "OE2" Residue "F GLU 69": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "G ARG 17": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 98": "NH1" <-> "NH2" Residue "I ARG 17": "NH1" <-> "NH2" Residue "I PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 166": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 19038 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "D" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "E" Number of atoms: 2375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2375 Classifications: {'peptide': 307} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 287} Chain: "F" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 650 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "G" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "H" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "I" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "J" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 Chain: "K" Number of atoms: 1502 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 202, 1501 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 1 Conformer: "A" Number of residues, atoms: 202, 1500 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1528 Chain: "L" Number of atoms: 1608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1608 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 11, 'TRANS': 200} Chain breaks: 1 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 chiralities: 2 Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 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 chiralities: 2 Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 5 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 12.66, per 1000 atoms: 0.66 Number of scatterers: 19038 At special positions: 0 Unit cell: (184.87, 186.2, 127.68, 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 81 16.00 O 3864 8.00 N 3192 7.00 C 11901 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.02 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.02 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 76 " distance=2.02 Simple disulfide: pdb=" SG CYS C 97 " - pdb=" SG CYS C 139 " distance=2.02 Simple disulfide: pdb=" SG CYS C 281 " - pdb=" SG CYS C 305 " distance=2.02 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 277 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 76 " distance=2.03 Simple disulfide: pdb=" SG CYS E 97 " - pdb=" SG CYS E 139 " distance=2.02 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 305 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 90 " distance=2.04 Simple disulfide: pdb=" SG CYS G 139 " - pdb=" SG CYS G 199 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 90 " distance=2.04 Simple disulfide: pdb=" SG CYS I 139 " - pdb=" SG CYS I 199 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 150 " - pdb=" SG CYS J 206 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.04 Simple disulfide: pdb=" SG CYS K 139 " - pdb=" SG CYS K 199 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 150 " - pdb=" SG CYS L 206 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN O 5 " - " MAN O 6 " " MAN R 5 " - " MAN R 6 " " MAN U 5 " - " MAN U 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 8 " " MAN O 4 " - " MAN O 7 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 8 " " MAN R 4 " - " MAN R 7 " " BMA T 3 " - " MAN T 4 " " BMA U 3 " - " MAN U 8 " " MAN U 4 " - " MAN U 7 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA O 3 " - " MAN O 4 " " MAN O 4 " - " MAN O 5 " " BMA Q 3 " - " MAN Q 5 " " BMA R 3 " - " MAN R 4 " " MAN R 4 " - " MAN R 5 " " BMA T 3 " - " MAN T 5 " " BMA U 3 " - " MAN U 4 " " MAN U 4 " - " MAN U 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " NAG-ASN " NAG A 401 " - " ASN A 22 " " NAG A 402 " - " ASN A 81 " " NAG C 401 " - " ASN C 22 " " NAG C 402 " - " ASN C 81 " " NAG E 401 " - " ASN E 22 " " NAG E 402 " - " ASN E 81 " " NAG M 1 " - " ASN A 38 " " NAG N 1 " - " ASN A 165 " " NAG O 1 " - " ASN A 285 " " NAG P 1 " - " ASN C 38 " " NAG Q 1 " - " ASN C 165 " " NAG R 1 " - " ASN C 285 " " NAG S 1 " - " ASN E 38 " " NAG T 1 " - " ASN E 165 " " NAG U 1 " - " ASN E 285 " Time building additional restraints: 8.23 Conformation dependent library (CDL) restraints added in 3.1 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4404 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 63 sheets defined 16.8% alpha, 32.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL A 78 " --> pdb=" O HIS A 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN A 80 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 187 through 195 Processing helix chain 'B' and resid 75 through 125 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 73 through 80 removed outlier: 5.244A pdb=" N VAL C 78 " --> pdb=" O HIS C 75 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 80 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 116 Processing helix chain 'C' and resid 187 through 195 Processing helix chain 'D' and resid 75 through 125 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 73 through 80 removed outlier: 5.245A pdb=" N VAL E 78 " --> pdb=" O HIS E 75 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 80 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 116 Processing helix chain 'E' and resid 187 through 195 Processing helix chain 'F' and resid 75 through 125 Processing helix chain 'G' and resid 81 through 85 Processing helix chain 'G' and resid 126 through 133 Processing helix chain 'G' and resid 187 through 192 removed outlier: 3.669A pdb=" N GLU G 192 " --> pdb=" O LYS G 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 110 Processing helix chain 'H' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY H 200 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR H 201 " --> pdb=" O SER H 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 85 removed outlier: 3.557A pdb=" N GLU I 85 " --> pdb=" O ALA I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 132 Processing helix chain 'I' and resid 188 through 192 removed outlier: 3.689A pdb=" N GLU I 192 " --> pdb=" O LYS I 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 192' Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 62 through 65 Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.513A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 110 Processing helix chain 'J' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY J 200 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR J 201 " --> pdb=" O SER J 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 85 Processing helix chain 'K' and resid 126 through 132 removed outlier: 3.763A pdb=" N LEU K 130 " --> pdb=" O SER K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 194 Processing helix chain 'L' and resid 28 through 32 Processing helix chain 'L' and resid 62 through 65 Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.514A pdb=" N ASP L 90 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 110 Processing helix chain 'L' and resid 195 through 202 removed outlier: 4.539A pdb=" N GLY L 200 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N THR L 201 " --> pdb=" O SER L 197 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA3, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.697A pdb=" N ILE A 51 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS A 277 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN A 53 " --> pdb=" O CYS A 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 58 through 61 Processing sheet with id=AA6, first strand: chain 'A' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE A 179 " --> pdb=" O GLY A 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY A 256 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 100 through 101 removed outlier: 7.710A pdb=" N ILE A 179 " --> pdb=" O PRO A 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 130 through 131 Processing sheet with id=AA9, first strand: chain 'A' and resid 136 through 141 removed outlier: 7.668A pdb=" N ALA A 138 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY A 144 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 164 through 169 Processing sheet with id=AB2, first strand: chain 'A' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS A 281 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 303 through 304 removed outlier: 3.578A pdb=" N LYS B 62 " --> pdb=" O GLY A 303 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 24 through 26 Processing sheet with id=AB5, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE C 51 " --> pdb=" O ASP C 275 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N CYS C 277 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN C 53 " --> pdb=" O CYS C 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 58 through 61 Processing sheet with id=AB9, first strand: chain 'C' and resid 100 through 101 removed outlier: 5.044A pdb=" N ILE C 179 " --> pdb=" O GLY C 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY C 256 " --> pdb=" O ILE C 179 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE C 179 " --> pdb=" O PRO C 254 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 130 through 131 Processing sheet with id=AC3, first strand: chain 'C' and resid 136 through 141 removed outlier: 7.669A pdb=" N ALA C 138 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 10.658A pdb=" N GLY C 144 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 164 through 169 Processing sheet with id=AC5, first strand: chain 'C' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS C 281 " --> pdb=" O ILE C 288 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 303 through 304 removed outlier: 3.517A pdb=" N LYS D 62 " --> pdb=" O GLY C 303 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 24 through 26 Processing sheet with id=AC8, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AC9, first strand: chain 'E' and resid 43 through 44 Processing sheet with id=AD1, first strand: chain 'E' and resid 51 through 54 removed outlier: 5.698A pdb=" N ILE E 51 " --> pdb=" O ASP E 275 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS E 277 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN E 53 " --> pdb=" O CYS E 277 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 61 Processing sheet with id=AD3, first strand: chain 'E' and resid 100 through 101 removed outlier: 5.043A pdb=" N ILE E 179 " --> pdb=" O GLY E 256 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLY E 256 " --> pdb=" O ILE E 179 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 100 through 101 removed outlier: 7.709A pdb=" N ILE E 179 " --> pdb=" O PRO E 254 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 130 through 131 Processing sheet with id=AD6, first strand: chain 'E' and resid 136 through 141 removed outlier: 7.670A pdb=" N ALA E 138 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 10.659A pdb=" N GLY E 144 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 164 through 169 Processing sheet with id=AD8, first strand: chain 'E' and resid 281 through 283 removed outlier: 4.082A pdb=" N CYS E 281 " --> pdb=" O ILE E 288 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 303 through 304 removed outlier: 3.646A pdb=" N LYS F 62 " --> pdb=" O GLY E 303 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 10 through 11 removed outlier: 6.294A pdb=" N TRP G 37 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 18 through 22 Processing sheet with id=AE3, first strand: chain 'G' and resid 119 through 123 removed outlier: 3.601A pdb=" N VAL G 138 " --> pdb=" O PHE G 123 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N VAL G 138 " --> pdb=" O LEU G 184 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N LEU G 184 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU G 140 " --> pdb=" O SER G 182 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N SER G 182 " --> pdb=" O LEU G 140 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASN G 142 " --> pdb=" O LEU G 180 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU G 180 " --> pdb=" O ASN G 142 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER G 179 " --> pdb=" O THR G 169 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 149 through 155 removed outlier: 4.291A pdb=" N LYS G 150 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR G 197 " --> pdb=" O PHE G 214 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU H 10 " --> pdb=" O THR H 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR H 186 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL H 191 " --> pdb=" O HIS H 174 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 161 through 164 Processing sheet with id=AF1, first strand: chain 'I' and resid 9 through 12 removed outlier: 6.454A pdb=" N TRP I 37 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 18 through 23 Processing sheet with id=AF3, first strand: chain 'I' and resid 119 through 123 removed outlier: 3.703A pdb=" N VAL I 138 " --> pdb=" O PHE I 123 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TYR I 178 " --> pdb=" O ASN I 143 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'I' and resid 150 through 155 Processing sheet with id=AF5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AF6, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU J 34 " --> pdb=" O TRP J 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU J 10 " --> pdb=" O THR J 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL J 115 " --> pdb=" O ARG J 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'J' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR J 186 " --> pdb=" O ASP J 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL J 191 " --> pdb=" O HIS J 174 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 161 through 164 Processing sheet with id=AG1, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.562A pdb=" N THR K 109 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY K 12 " --> pdb=" O THR K 109 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N TRP K 37 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 17 through 22 Processing sheet with id=AG3, first strand: chain 'K' and resid 119 through 123 removed outlier: 3.531A pdb=" N PHE K 123 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL K 138 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N TYR K 178 " --> pdb=" O ASN K 143 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 158 through 160 removed outlier: 4.438A pdb=" N TRP K 153 " --> pdb=" O GLN K 160 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS K 150 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N CYS K 199 " --> pdb=" O LYS K 212 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS K 212 " --> pdb=" O CYS K 199 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL K 201 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL K 210 " --> pdb=" O VAL K 201 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU L 34 " --> pdb=" O TRP L 50 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.850A pdb=" N GLU L 10 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL L 115 " --> pdb=" O ARG L 98 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'L' and resid 130 through 134 removed outlier: 6.159A pdb=" N TYR L 186 " --> pdb=" O ASP L 154 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL L 191 " --> pdb=" O HIS L 174 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 161 through 164 779 hydrogen bonds defined for protein. 1944 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: 6.24 Time building geometry restraints manager: 8.79 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: 6038 1.34 - 1.46: 4512 1.46 - 1.58: 8770 1.58 - 1.70: 0 1.70 - 1.82: 114 Bond restraints: 19434 Sorted by residual: bond pdb=" CA CYS C 139 " pdb=" CB CYS C 139 " ideal model delta sigma weight residual 1.531 1.484 0.047 3.28e-02 9.30e+02 2.04e+00 bond pdb=" CA CYS A 139 " pdb=" CB CYS A 139 " ideal model delta sigma weight residual 1.531 1.484 0.047 3.28e-02 9.30e+02 2.03e+00 bond pdb=" CA CYS E 139 " pdb=" CB CYS E 139 " ideal model delta sigma weight residual 1.531 1.484 0.046 3.28e-02 9.30e+02 2.00e+00 bond pdb=" C GLN H 23 " pdb=" N VAL H 24 " ideal model delta sigma weight residual 1.329 1.301 0.028 2.08e-02 2.31e+03 1.84e+00 bond pdb=" C GLN L 23 " pdb=" N VAL L 24 " ideal model delta sigma weight residual 1.329 1.302 0.027 2.08e-02 2.31e+03 1.73e+00 ... (remaining 19429 not shown) Histogram of bond angle deviations from ideal: 99.03 - 106.03: 488 106.03 - 113.03: 11204 113.03 - 120.03: 5981 120.03 - 127.03: 8501 127.03 - 134.03: 244 Bond angle restraints: 26418 Sorted by residual: angle pdb=" C HIS G 194 " pdb=" N LYS G 195 " pdb=" CA LYS G 195 " ideal model delta sigma weight residual 121.54 127.81 -6.27 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C GLY B 50 " pdb=" N LYS B 51 " pdb=" CA LYS B 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.82e+00 angle pdb=" C GLY F 50 " pdb=" N LYS F 51 " pdb=" CA LYS F 51 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.81e+00 angle pdb=" C GLY D 50 " pdb=" N LYS D 51 " pdb=" CA LYS D 51 " ideal model delta sigma weight residual 121.54 126.87 -5.33 1.91e+00 2.74e-01 7.79e+00 angle pdb=" C GLY K 52 " pdb=" N ASN K 53 " pdb=" CA ASN K 53 " ideal model delta sigma weight residual 121.54 126.47 -4.93 1.91e+00 2.74e-01 6.65e+00 ... (remaining 26413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 10686 17.31 - 34.62: 845 34.62 - 51.93: 126 51.93 - 69.23: 30 69.23 - 86.54: 16 Dihedral angle restraints: 11703 sinusoidal: 4833 harmonic: 6870 Sorted by residual: dihedral pdb=" CB CYS I 139 " pdb=" SG CYS I 139 " pdb=" SG CYS I 199 " pdb=" CB CYS I 199 " ideal model delta sinusoidal sigma weight residual 93.00 37.38 55.62 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS G 139 " pdb=" SG CYS G 139 " pdb=" SG CYS G 199 " pdb=" CB CYS G 199 " ideal model delta sinusoidal sigma weight residual 93.00 40.51 52.49 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA GLN I 81 " pdb=" C GLN I 81 " pdb=" N ALA I 82 " pdb=" CA ALA I 82 " ideal model delta harmonic sigma weight residual -180.00 -157.10 -22.90 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 11700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2691 0.069 - 0.137: 438 0.137 - 0.206: 12 0.206 - 0.274: 9 0.274 - 0.343: 3 Chirality restraints: 3153 Sorted by residual: chirality pdb=" C1 NAG E 401 " pdb=" ND2 ASN E 22 " pdb=" C2 NAG E 401 " pdb=" O5 NAG E 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C1 NAG A 401 " pdb=" ND2 ASN A 22 " pdb=" C2 NAG A 401 " pdb=" O5 NAG A 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1 NAG C 401 " pdb=" ND2 ASN C 22 " pdb=" C2 NAG C 401 " pdb=" O5 NAG C 401 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 3150 not shown) Planarity restraints: 3324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 194 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO J 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO J 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO J 195 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 194 " -0.025 5.00e-02 4.00e+02 3.83e-02 2.34e+00 pdb=" N PRO H 195 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO H 195 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO H 195 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 194 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO L 195 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO L 195 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO L 195 " 0.021 5.00e-02 4.00e+02 ... (remaining 3321 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 867 2.70 - 3.25: 18430 3.25 - 3.80: 31238 3.80 - 4.35: 38786 4.35 - 4.90: 67752 Nonbonded interactions: 157073 Sorted by model distance: nonbonded pdb=" OE1 GLN G 129 " pdb=" OG SER G 136 " model vdw 2.155 2.440 nonbonded pdb=" ND2 ASN K 163 " pdb=" O THR K 185 " model vdw 2.183 2.520 nonbonded pdb=" O SER K 92 " pdb=" OG SER K 100 " model vdw 2.184 2.440 nonbonded pdb=" O SER I 92 " pdb=" OG SER I 100 " model vdw 2.200 2.440 nonbonded pdb=" O SER G 92 " pdb=" OG SER G 100 " model vdw 2.202 2.440 ... (remaining 157068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'I' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) selection = (chain 'K' and (resid 2 through 113 or resid 115 through 169 or resid 171 throug \ h 217)) } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'P' selection = chain 'S' } ncs_group { reference = chain 'N' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'O' selection = chain 'R' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 11901 2.51 5 N 3192 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 7.260 Check model and map are aligned: 0.270 Process input model: 51.960 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.170 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 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 : 0.008 0.047 19434 Z= 0.494 Angle : 0.676 6.820 26418 Z= 0.375 Chirality : 0.048 0.343 3153 Planarity : 0.004 0.038 3309 Dihedral : 12.658 86.542 7227 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.19 (0.18), residues: 2352 helix: 2.41 (0.30), residues: 282 sheet: -0.34 (0.18), residues: 771 loop : -0.51 (0.18), residues: 1299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 424 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 424 average time/residue: 0.3477 time to fit residues: 214.0268 Evaluate side-chains 273 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 2.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.9980 chunk 177 optimal weight: 0.0980 chunk 98 optimal weight: 0.2980 chunk 60 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 94 optimal weight: 0.2980 chunk 183 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 212 optimal weight: 3.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 322 ASN G 53 ASN G 91 GLN H 109 HIS H 165 ASN ** I 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 181 GLN J 209 ASN K 91 GLN ** K 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 19434 Z= 0.187 Angle : 0.598 8.142 26418 Z= 0.304 Chirality : 0.047 0.341 3153 Planarity : 0.004 0.044 3309 Dihedral : 5.269 48.069 2970 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.13 (0.18), residues: 2352 helix: 2.65 (0.30), residues: 282 sheet: -0.40 (0.18), residues: 792 loop : -0.43 (0.18), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 322 time to evaluate : 2.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 336 average time/residue: 0.3098 time to fit residues: 159.4621 Evaluate side-chains 294 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 276 time to evaluate : 2.356 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2001 time to fit residues: 9.0541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 118 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 176 optimal weight: 0.8980 chunk 144 optimal weight: 0.3980 chunk 58 optimal weight: 2.9990 chunk 212 optimal weight: 0.0020 chunk 229 optimal weight: 6.9990 chunk 189 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 overall best weight: 0.4626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN I 171 GLN ** J 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19434 Z= 0.190 Angle : 0.587 10.852 26418 Z= 0.295 Chirality : 0.046 0.333 3153 Planarity : 0.004 0.034 3309 Dihedral : 5.112 49.544 2970 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.17), residues: 2352 helix: 2.96 (0.30), residues: 282 sheet: -0.30 (0.18), residues: 777 loop : -0.47 (0.17), residues: 1293 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 306 time to evaluate : 2.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 312 average time/residue: 0.3102 time to fit residues: 148.0072 Evaluate side-chains 287 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 272 time to evaluate : 2.246 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1824 time to fit residues: 8.0015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9990 chunk 160 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 23 optimal weight: 0.0030 chunk 101 optimal weight: 0.0570 chunk 142 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.7712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 ASN C 197 GLN G 53 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 19434 Z= 0.234 Angle : 0.592 10.217 26418 Z= 0.298 Chirality : 0.046 0.346 3153 Planarity : 0.004 0.035 3309 Dihedral : 5.047 53.005 2970 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.09 (0.17), residues: 2352 helix: 2.99 (0.30), residues: 282 sheet: -0.34 (0.18), residues: 792 loop : -0.52 (0.17), residues: 1278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 282 time to evaluate : 2.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 297 average time/residue: 0.3123 time to fit residues: 141.9211 Evaluate side-chains 284 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 270 time to evaluate : 2.105 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1860 time to fit residues: 7.7885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 188 optimal weight: 6.9990 chunk 128 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 168 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 193 optimal weight: 3.9990 chunk 156 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.0570 chunk 203 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.5102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.039 19434 Z= 0.378 Angle : 0.641 9.348 26418 Z= 0.325 Chirality : 0.048 0.368 3153 Planarity : 0.004 0.036 3309 Dihedral : 5.233 56.145 2970 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.20 (0.17), residues: 2352 helix: 2.77 (0.30), residues: 282 sheet: -0.35 (0.18), residues: 789 loop : -0.61 (0.17), residues: 1281 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 2.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 286 average time/residue: 0.3346 time to fit residues: 149.6148 Evaluate side-chains 280 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 264 time to evaluate : 2.382 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1859 time to fit residues: 8.7036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 76 optimal weight: 0.8980 chunk 203 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 226 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 157 ASN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 19434 Z= 0.350 Angle : 0.626 9.524 26418 Z= 0.318 Chirality : 0.048 0.368 3153 Planarity : 0.004 0.035 3309 Dihedral : 5.210 54.491 2970 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.26 (0.17), residues: 2352 helix: 2.72 (0.30), residues: 282 sheet: -0.37 (0.18), residues: 786 loop : -0.66 (0.17), residues: 1284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 2.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 284 average time/residue: 0.3031 time to fit residues: 134.0085 Evaluate side-chains 265 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 2.285 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1707 time to fit residues: 6.0060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 218 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 190 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 141 optimal weight: 0.0870 chunk 137 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN G 36 HIS G 53 ASN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 19434 Z= 0.224 Angle : 0.592 9.119 26418 Z= 0.300 Chirality : 0.046 0.359 3153 Planarity : 0.004 0.041 3309 Dihedral : 5.030 55.635 2970 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.17 (0.17), residues: 2352 helix: 2.88 (0.30), residues: 282 sheet: -0.28 (0.18), residues: 774 loop : -0.64 (0.17), residues: 1296 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 273 time to evaluate : 2.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 281 average time/residue: 0.3055 time to fit residues: 134.1534 Evaluate side-chains 261 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 253 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1911 time to fit residues: 5.9410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 205 optimal weight: 0.2980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 19434 Z= 0.326 Angle : 0.625 9.906 26418 Z= 0.318 Chirality : 0.048 0.375 3153 Planarity : 0.004 0.035 3309 Dihedral : 5.095 59.536 2970 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.28 (0.17), residues: 2352 helix: 2.78 (0.30), residues: 282 sheet: -0.33 (0.19), residues: 756 loop : -0.73 (0.17), residues: 1314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 259 time to evaluate : 2.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 10 residues processed: 264 average time/residue: 0.2949 time to fit residues: 121.7169 Evaluate side-chains 261 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 251 time to evaluate : 2.247 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1741 time to fit residues: 6.2302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 0.6980 chunk 197 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 189 optimal weight: 7.9990 chunk 198 optimal weight: 0.7980 chunk 209 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19434 Z= 0.276 Angle : 0.607 10.007 26418 Z= 0.309 Chirality : 0.047 0.362 3153 Planarity : 0.004 0.034 3309 Dihedral : 5.014 58.540 2970 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.22 (0.17), residues: 2352 helix: 2.82 (0.30), residues: 282 sheet: -0.21 (0.19), residues: 741 loop : -0.75 (0.17), residues: 1329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 262 time to evaluate : 2.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 265 average time/residue: 0.3039 time to fit residues: 125.8244 Evaluate side-chains 253 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 250 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1722 time to fit residues: 4.0783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 222 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 105 optimal weight: 0.0470 chunk 154 optimal weight: 2.9990 chunk 233 optimal weight: 4.9990 chunk 214 optimal weight: 5.9990 chunk 185 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 19434 Z= 0.190 Angle : 0.588 10.098 26418 Z= 0.299 Chirality : 0.046 0.344 3153 Planarity : 0.004 0.033 3309 Dihedral : 4.870 58.934 2970 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 0.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.17), residues: 2352 helix: 2.94 (0.30), residues: 282 sheet: -0.13 (0.19), residues: 762 loop : -0.69 (0.17), residues: 1308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 273 average time/residue: 0.2907 time to fit residues: 124.9408 Evaluate side-chains 254 residues out of total 2085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 2.217 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 197 optimal weight: 0.0570 chunk 56 optimal weight: 0.0370 chunk 171 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 51 optimal weight: 0.4980 chunk 185 optimal weight: 0.4980 chunk 77 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 91 GLN ** I 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 165 ASN ** 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 = 0.3642 r_free = 0.3642 target = 0.128490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085629 restraints weight = 33725.037| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.43 r_work: 0.2794 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 19434 Z= 0.209 Angle : 0.590 9.646 26418 Z= 0.299 Chirality : 0.046 0.337 3153 Planarity : 0.004 0.033 3309 Dihedral : 4.796 59.246 2970 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -0.08 (0.17), residues: 2352 helix: 2.96 (0.30), residues: 282 sheet: -0.08 (0.19), residues: 762 loop : -0.69 (0.17), residues: 1308 =============================================================================== Job complete usr+sys time: 4267.61 seconds wall clock time: 78 minutes 33.14 seconds (4713.14 seconds total)