Starting phenix.real_space_refine on Sun Mar 24 22:40:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jlw_22382/03_2024/7jlw_22382_trim_updated.pdb" } resolution = 2.5 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= 0.013 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: 6 Type Number sf(0) Gaussians P 24 5.49 5 S 120 5.16 5 C 14664 2.51 5 N 3132 2.21 5 O 3624 1.98 5 H 18720 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 48": "OE1" <-> "OE2" Residue "I ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 48": "OE1" <-> "OE2" Residue "J ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 76": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 106": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40284 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "B" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "D" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "E" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "F" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "G" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "H" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "I" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "J" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "K" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "L" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "K" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 9} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 16.95, per 1000 atoms: 0.42 Number of scatterers: 40284 At special positions: 0 Unit cell: (96.701, 96.701, 161.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 24 15.00 O 3624 8.00 N 3132 7.00 C 14664 6.00 H 18720 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.95 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.95 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.94 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.95 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.94 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.94 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.94 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.95 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.94 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.95 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.04 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.95 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " distance=2.94 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 Time building additional restraints: 29.24 Conformation dependent library (CDL) restraints added in 4.0 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 96 helices and 12 sheets defined 69.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 removed outlier: 4.031A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 32 Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 41 through 44 No H-bonds generated for 'chain 'A' and resid 41 through 44' Processing helix chain 'A' and resid 61 through 69 Processing helix chain 'A' and resid 74 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 180 removed outlier: 3.980A pdb=" N ARG A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 235 Processing helix chain 'B' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 34 through 39 Processing helix chain 'B' and resid 41 through 44 No H-bonds generated for 'chain 'B' and resid 41 through 44' Processing helix chain 'B' and resid 61 through 69 Processing helix chain 'B' and resid 74 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 235 Processing helix chain 'C' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 41 through 44 No H-bonds generated for 'chain 'C' and resid 41 through 44' Processing helix chain 'C' and resid 61 through 69 Processing helix chain 'C' and resid 74 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG C 156 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 235 Processing helix chain 'D' and resid 5 through 16 removed outlier: 4.031A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 32 Processing helix chain 'D' and resid 34 through 39 Processing helix chain 'D' and resid 41 through 44 No H-bonds generated for 'chain 'D' and resid 41 through 44' Processing helix chain 'D' and resid 61 through 69 Processing helix chain 'D' and resid 74 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 180 removed outlier: 3.980A pdb=" N ARG D 156 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 235 Processing helix chain 'E' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 32 Processing helix chain 'E' and resid 34 through 39 Processing helix chain 'E' and resid 41 through 44 No H-bonds generated for 'chain 'E' and resid 41 through 44' Processing helix chain 'E' and resid 61 through 69 Processing helix chain 'E' and resid 74 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 235 Processing helix chain 'F' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 32 Processing helix chain 'F' and resid 34 through 39 Processing helix chain 'F' and resid 41 through 44 No H-bonds generated for 'chain 'F' and resid 41 through 44' Processing helix chain 'F' and resid 61 through 69 Processing helix chain 'F' and resid 74 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 235 Processing helix chain 'G' and resid 5 through 16 removed outlier: 4.031A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 32 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 44 No H-bonds generated for 'chain 'G' and resid 41 through 44' Processing helix chain 'G' and resid 61 through 69 Processing helix chain 'G' and resid 74 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG G 156 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 235 Processing helix chain 'H' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 32 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 44 No H-bonds generated for 'chain 'H' and resid 41 through 44' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 74 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 180 removed outlier: 3.980A pdb=" N ARG H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 235 Processing helix chain 'I' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 32 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 44 No H-bonds generated for 'chain 'I' and resid 41 through 44' Processing helix chain 'I' and resid 61 through 69 Processing helix chain 'I' and resid 74 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG I 156 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR I 157 " --> pdb=" O THR I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 235 Processing helix chain 'J' and resid 5 through 16 removed outlier: 4.031A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 32 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 44 No H-bonds generated for 'chain 'J' and resid 41 through 44' Processing helix chain 'J' and resid 61 through 69 Processing helix chain 'J' and resid 74 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 180 removed outlier: 3.980A pdb=" N ARG J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR J 157 " --> pdb=" O THR J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 235 Processing helix chain 'K' and resid 5 through 16 removed outlier: 4.031A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 32 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 44 No H-bonds generated for 'chain 'K' and resid 41 through 44' Processing helix chain 'K' and resid 61 through 69 Processing helix chain 'K' and resid 74 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG K 156 " --> pdb=" O GLY K 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 235 Processing helix chain 'L' and resid 5 through 16 removed outlier: 4.032A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 32 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 44 No H-bonds generated for 'chain 'L' and resid 41 through 44' Processing helix chain 'L' and resid 61 through 69 Processing helix chain 'L' and resid 74 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 180 removed outlier: 3.979A pdb=" N ARG L 156 " --> pdb=" O GLY L 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR L 157 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 235 Processing sheet with id= A, first strand: chain 'A' and resid 187 through 190 Processing sheet with id= B, first strand: chain 'B' and resid 187 through 190 Processing sheet with id= C, first strand: chain 'C' and resid 187 through 190 Processing sheet with id= D, first strand: chain 'D' and resid 187 through 190 Processing sheet with id= E, first strand: chain 'E' and resid 187 through 190 Processing sheet with id= F, first strand: chain 'F' and resid 187 through 190 Processing sheet with id= G, first strand: chain 'G' and resid 187 through 190 Processing sheet with id= H, first strand: chain 'H' and resid 187 through 190 Processing sheet with id= I, first strand: chain 'I' and resid 187 through 190 Processing sheet with id= J, first strand: chain 'J' and resid 187 through 190 Processing sheet with id= K, first strand: chain 'K' and resid 187 through 190 Processing sheet with id= L, first strand: chain 'L' and resid 187 through 190 1212 hydrogen bonds defined for protein. 3600 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: 15.21 Time building geometry restraints manager: 30.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 18708 1.03 - 1.23: 327 1.23 - 1.43: 8409 1.43 - 1.63: 12840 1.63 - 1.82: 204 Bond restraints: 40488 Sorted by residual: bond pdb=" ND2 ASN E 63 " pdb="HD21 ASN E 63 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 63 " pdb="HD21 ASN B 63 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN J 63 " pdb="HD21 ASN J 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN G 63 " pdb="HD21 ASN G 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 63 " pdb="HD21 ASN A 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 40483 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.68: 1230 106.68 - 113.58: 44694 113.58 - 120.49: 14577 120.49 - 127.40: 10366 127.40 - 134.30: 317 Bond angle restraints: 71184 Sorted by residual: angle pdb=" O3P MC3 B 506 " pdb=" P MC3 B 506 " pdb=" O4P MC3 B 506 " ideal model delta sigma weight residual 93.26 107.57 -14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 E 506 " pdb=" P MC3 E 506 " pdb=" O4P MC3 E 506 " ideal model delta sigma weight residual 93.26 107.57 -14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 G 501 " pdb=" P MC3 G 501 " pdb=" O4P MC3 G 501 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 F 506 " pdb=" P MC3 F 506 " pdb=" O4P MC3 F 506 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 I 506 " pdb=" P MC3 I 506 " pdb=" O4P MC3 I 506 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 ... (remaining 71179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 18990 27.51 - 55.01: 750 55.01 - 82.52: 192 82.52 - 110.03: 0 110.03 - 137.53: 24 Dihedral angle restraints: 19956 sinusoidal: 11352 harmonic: 8604 Sorted by residual: dihedral pdb=" N MC3 C 507 " pdb=" C4 MC3 C 507 " pdb=" C5 MC3 C 507 " pdb=" O4P MC3 C 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" N MC3 L 507 " pdb=" C4 MC3 L 507 " pdb=" C5 MC3 L 507 " pdb=" O4P MC3 L 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" N MC3 H 507 " pdb=" C4 MC3 H 507 " pdb=" C5 MC3 H 507 " pdb=" O4P MC3 H 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 19953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2769 0.093 - 0.186: 201 0.186 - 0.279: 30 0.279 - 0.371: 12 0.371 - 0.464: 12 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA VAL E 198 " pdb=" N VAL E 198 " pdb=" C VAL E 198 " pdb=" CB VAL E 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA VAL B 198 " pdb=" N VAL B 198 " pdb=" C VAL B 198 " pdb=" CB VAL B 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA VAL F 198 " pdb=" N VAL F 198 " pdb=" C VAL F 198 " pdb=" CB VAL F 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 3021 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 63 " -0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN E 63 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN E 63 " 0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN E 63 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 63 " -0.640 2.00e-02 2.50e+03 pdb="HD22 ASN E 63 " 0.623 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 63 " 0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN G 63 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN G 63 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN G 63 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN G 63 " 0.640 2.00e-02 2.50e+03 pdb="HD22 ASN G 63 " -0.623 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 63 " 0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN I 63 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN I 63 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN I 63 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN I 63 " 0.640 2.00e-02 2.50e+03 pdb="HD22 ASN I 63 " -0.623 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 11008 2.33 - 2.90: 85940 2.90 - 3.47: 103628 3.47 - 4.03: 142361 4.03 - 4.60: 220650 Nonbonded interactions: 563587 Sorted by model distance: nonbonded pdb=" O ILE H 82 " pdb=" HG SER H 86 " model vdw 1.766 1.850 nonbonded pdb=" O ILE I 82 " pdb=" HG SER I 86 " model vdw 1.766 1.850 nonbonded pdb=" O ILE E 82 " pdb=" HG SER E 86 " model vdw 1.766 1.850 nonbonded pdb=" O ILE B 82 " pdb=" HG SER B 86 " model vdw 1.766 1.850 nonbonded pdb=" O ILE G 82 " pdb=" HG SER G 86 " model vdw 1.766 1.850 ... (remaining 563582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 236 or (resid 501 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or (resid 505 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or r \ esid 506 or resid 508 or (resid 509 and (name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42 or name C43 or name C44)) or resid 510 or (resid 511 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'B' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'C' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'D' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'E' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'F' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or (resid 505 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or r \ esid 506 or resid 508 or (resid 509 and (name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42 or name C43 or name C44)) or resid 510 or (resid 511 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'H' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'I' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'J' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'K' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'L' and (resid 2 through 236 or resid 501 or resid 505 or (resid 506 and \ (name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or ( \ resid 508 and (name C15 or name C16 or name C17 or name C18 or name C19 or name \ C20 or name C21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 \ and (name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or na \ me C20 or name C21 or name C22 or name C23 or name C24)) or resid 511)) } 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: 10.890 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: 1.030 Extract box with map and model: 15.580 Check model and map are aligned: 0.590 Set scattering table: 0.330 Process input model: 119.420 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.320 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:13.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.011 0.085 21768 Z= 0.664 Angle : 1.388 14.309 28824 Z= 0.647 Chirality : 0.066 0.464 3024 Planarity : 0.005 0.020 3324 Dihedral : 14.502 137.533 8700 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.14 % Allowed : 4.55 % Favored : 94.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.51 (0.16), residues: 2268 helix: 0.82 (0.12), residues: 1680 sheet: 1.12 (0.44), residues: 132 loop : -1.50 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 193 HIS 0.007 0.001 HIS E 74 PHE 0.029 0.003 PHE E 70 TYR 0.016 0.003 TYR G 66 ARG 0.007 0.001 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 TYR cc_start: 0.8278 (t80) cc_final: 0.8074 (t80) REVERT: E 177 TYR cc_start: 0.8264 (t80) cc_final: 0.8050 (t80) outliers start: 24 outliers final: 18 residues processed: 308 average time/residue: 2.1315 time to fit residues: 773.2680 Evaluate side-chains 255 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 237 time to evaluate : 2.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 178 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS C 176 HIS E 176 HIS F 176 HIS H 176 HIS I 176 HIS K 176 HIS L 176 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 21768 Z= 0.280 Angle : 0.587 4.524 28824 Z= 0.306 Chirality : 0.042 0.139 3024 Planarity : 0.004 0.051 3324 Dihedral : 13.899 127.941 4452 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.37 % Allowed : 9.61 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.17), residues: 2268 helix: 2.15 (0.12), residues: 1680 sheet: 0.77 (0.38), residues: 204 loop : -1.90 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 193 HIS 0.006 0.001 HIS L 176 PHE 0.019 0.002 PHE J 202 TYR 0.016 0.003 TYR I 66 ARG 0.004 0.001 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 257 time to evaluate : 2.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7133 (mt-10) REVERT: E 42 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7132 (mt-10) outliers start: 29 outliers final: 16 residues processed: 274 average time/residue: 2.8213 time to fit residues: 880.3065 Evaluate side-chains 264 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 246 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain I residue 231 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 115 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 224 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS E 176 HIS H 176 HIS K 176 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21768 Z= 0.240 Angle : 0.515 4.173 28824 Z= 0.273 Chirality : 0.041 0.127 3024 Planarity : 0.003 0.028 3324 Dihedral : 13.562 123.207 4440 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.23 % Allowed : 8.76 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.17), residues: 2268 helix: 2.59 (0.12), residues: 1680 sheet: 0.28 (0.35), residues: 204 loop : -1.74 (0.25), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 193 HIS 0.005 0.001 HIS B 176 PHE 0.022 0.002 PHE L 202 TYR 0.013 0.002 TYR I 66 ARG 0.003 0.000 ARG A 156 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 2.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 216 MET cc_start: 0.8361 (mmm) cc_final: 0.8033 (mmt) REVERT: K 37 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8305 (mt) REVERT: L 216 MET cc_start: 0.8362 (mmm) cc_final: 0.8038 (mmt) outliers start: 47 outliers final: 17 residues processed: 246 average time/residue: 2.8198 time to fit residues: 787.6944 Evaluate side-chains 222 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 204 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 21768 Z= 0.339 Angle : 0.568 4.585 28824 Z= 0.302 Chirality : 0.043 0.136 3024 Planarity : 0.004 0.035 3324 Dihedral : 14.422 126.349 4440 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.41 % Allowed : 9.19 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.17), residues: 2268 helix: 2.38 (0.12), residues: 1680 sheet: 0.10 (0.34), residues: 204 loop : -1.66 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 193 HIS 0.005 0.001 HIS G 161 PHE 0.025 0.003 PHE B 202 TYR 0.017 0.003 TYR B 66 ARG 0.003 0.001 ARG A 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 205 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: D 77 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8187 (tt) REVERT: E 42 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7229 (mt-10) REVERT: H 42 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.7262 (mt-10) REVERT: J 77 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8209 (tt) REVERT: K 42 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7247 (mt-10) outliers start: 51 outliers final: 22 residues processed: 241 average time/residue: 2.9115 time to fit residues: 797.6121 Evaluate side-chains 221 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 3.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 183 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 188 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 112 optimal weight: 2.9990 chunk 197 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21768 Z= 0.164 Angle : 0.456 3.986 28824 Z= 0.239 Chirality : 0.038 0.115 3024 Planarity : 0.003 0.023 3324 Dihedral : 13.163 118.157 4440 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 2.51 % Allowed : 9.23 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.17), residues: 2268 helix: 2.77 (0.12), residues: 1680 sheet: 0.09 (0.34), residues: 204 loop : -1.71 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 193 HIS 0.003 0.001 HIS J 161 PHE 0.017 0.002 PHE L 202 TYR 0.012 0.002 TYR I 66 ARG 0.005 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 196 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: D 68 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: D 77 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8147 (tt) REVERT: J 77 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8152 (tt) REVERT: K 37 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8229 (mt) REVERT: K 42 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7165 (mt-10) outliers start: 53 outliers final: 14 residues processed: 230 average time/residue: 2.7872 time to fit residues: 727.9498 Evaluate side-chains 213 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 193 time to evaluate : 2.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 54 optimal weight: 0.0270 chunk 220 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21768 Z= 0.245 Angle : 0.501 4.197 28824 Z= 0.264 Chirality : 0.040 0.123 3024 Planarity : 0.003 0.022 3324 Dihedral : 13.353 116.540 4440 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 1.85 % Allowed : 9.19 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.18), residues: 2268 helix: 2.66 (0.12), residues: 1680 sheet: 0.08 (0.34), residues: 204 loop : -1.65 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 193 HIS 0.005 0.001 HIS B 98 PHE 0.022 0.002 PHE K 202 TYR 0.014 0.002 TYR I 66 ARG 0.004 0.000 ARG H 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 203 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7509 (tp30) REVERT: B 42 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: B 68 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7606 (tp30) REVERT: D 68 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: D 77 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8176 (tt) REVERT: E 68 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: F 68 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: H 68 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7587 (tp30) REVERT: I 68 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: J 77 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8203 (tt) REVERT: K 37 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8266 (mt) REVERT: K 42 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7219 (mt-10) REVERT: K 68 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7586 (tp30) REVERT: L 68 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7756 (tp30) outliers start: 39 outliers final: 14 residues processed: 232 average time/residue: 2.6935 time to fit residues: 711.6659 Evaluate side-chains 226 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 198 time to evaluate : 2.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 219 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21768 Z= 0.213 Angle : 0.476 4.081 28824 Z= 0.251 Chirality : 0.039 0.116 3024 Planarity : 0.003 0.019 3324 Dihedral : 12.884 111.181 4440 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.08 % Allowed : 9.66 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.18), residues: 2268 helix: 2.72 (0.12), residues: 1680 sheet: 0.13 (0.34), residues: 204 loop : -1.64 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 193 HIS 0.006 0.001 HIS C 98 PHE 0.021 0.002 PHE I 202 TYR 0.014 0.002 TYR B 66 ARG 0.002 0.000 ARG F 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 202 time to evaluate : 3.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7419 (tp30) REVERT: A 77 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (tt) REVERT: B 42 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7199 (mt-10) REVERT: B 68 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7528 (tp30) REVERT: D 68 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7480 (tp30) REVERT: D 77 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8198 (tt) REVERT: E 68 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: F 68 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7701 (tp30) REVERT: G 77 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8182 (tt) REVERT: H 68 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7513 (tp30) REVERT: I 68 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7714 (tp30) REVERT: J 77 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8189 (tt) REVERT: K 37 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8252 (mt) REVERT: K 42 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7191 (mt-10) REVERT: K 68 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7503 (tp30) REVERT: L 68 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7674 (tp30) outliers start: 44 outliers final: 14 residues processed: 235 average time/residue: 2.7429 time to fit residues: 733.9611 Evaluate side-chains 229 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21768 Z= 0.248 Angle : 0.500 4.135 28824 Z= 0.263 Chirality : 0.040 0.122 3024 Planarity : 0.003 0.020 3324 Dihedral : 12.891 108.462 4440 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 1.94 % Allowed : 9.99 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.17), residues: 2268 helix: 2.65 (0.12), residues: 1680 sheet: 0.11 (0.34), residues: 204 loop : -1.57 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 193 HIS 0.004 0.001 HIS D 161 PHE 0.022 0.002 PHE B 202 TYR 0.015 0.002 TYR I 66 ARG 0.002 0.000 ARG F 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 3.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: A 77 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8202 (tt) REVERT: B 42 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7222 (mt-10) REVERT: B 68 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7592 (tp30) REVERT: D 68 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7561 (tp30) REVERT: D 77 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8193 (tt) REVERT: E 68 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: F 68 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7749 (tp30) REVERT: G 68 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7489 (tp30) REVERT: G 77 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8189 (tt) REVERT: H 42 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7247 (mt-10) REVERT: H 68 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: I 68 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: J 68 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7429 (tp30) REVERT: J 77 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8219 (tt) REVERT: K 37 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8276 (mt) REVERT: K 42 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7218 (mt-10) REVERT: K 68 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: L 68 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7745 (tp30) outliers start: 41 outliers final: 14 residues processed: 239 average time/residue: 2.6756 time to fit residues: 730.2770 Evaluate side-chains 233 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 3.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 68 GLU Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 68 GLU Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 68 GLU Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 199 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 204 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 89 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21768 Z= 0.156 Angle : 0.449 3.964 28824 Z= 0.234 Chirality : 0.038 0.113 3024 Planarity : 0.003 0.017 3324 Dihedral : 12.108 97.631 4440 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.85 % Allowed : 10.13 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.18), residues: 2268 helix: 2.93 (0.12), residues: 1680 sheet: 0.15 (0.34), residues: 204 loop : -1.64 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.003 0.001 HIS J 161 PHE 0.017 0.002 PHE I 202 TYR 0.011 0.002 TYR I 66 ARG 0.002 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 208 time to evaluate : 3.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 42 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: B 68 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: D 68 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: D 77 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8168 (tt) REVERT: E 68 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7421 (tp30) REVERT: G 68 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7506 (tp30) REVERT: G 77 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8177 (tt) REVERT: H 42 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7178 (mt-10) REVERT: H 68 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: J 68 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7360 (tp30) REVERT: J 77 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8168 (tt) REVERT: K 37 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8234 (mt) REVERT: K 42 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7126 (mt-10) REVERT: K 68 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7434 (tp30) outliers start: 39 outliers final: 14 residues processed: 243 average time/residue: 2.6091 time to fit residues: 725.8567 Evaluate side-chains 235 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 206 time to evaluate : 2.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 chunk 209 optimal weight: 0.8980 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 143 optimal weight: 20.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21768 Z= 0.179 Angle : 0.458 4.052 28824 Z= 0.239 Chirality : 0.038 0.113 3024 Planarity : 0.003 0.017 3324 Dihedral : 11.984 96.988 4440 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.61 % Allowed : 10.65 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.97 (0.17), residues: 2268 helix: 2.92 (0.12), residues: 1680 sheet: 0.15 (0.34), residues: 204 loop : -1.63 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 193 HIS 0.004 0.001 HIS J 161 PHE 0.020 0.002 PHE F 202 TYR 0.013 0.002 TYR I 66 ARG 0.001 0.000 ARG K 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 215 time to evaluate : 3.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8175 (tt) REVERT: B 42 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: B 68 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7532 (tp30) REVERT: D 68 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7441 (tp30) REVERT: D 77 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8186 (tt) REVERT: E 68 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: G 68 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: G 77 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8179 (tt) REVERT: H 42 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: H 68 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: J 68 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: J 77 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8192 (tt) REVERT: K 37 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8232 (mt) REVERT: K 42 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7122 (mt-10) REVERT: K 68 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7511 (tp30) outliers start: 34 outliers final: 14 residues processed: 245 average time/residue: 2.5548 time to fit residues: 717.4245 Evaluate side-chains 240 residues out of total 2112 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 68 GLU Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 192 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.166035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114876 restraints weight = 51156.265| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.18 r_work: 0.2963 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21768 Z= 0.220 Angle : 0.476 4.109 28824 Z= 0.250 Chirality : 0.039 0.117 3024 Planarity : 0.003 0.018 3324 Dihedral : 12.024 96.982 4440 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.80 % Allowed : 10.51 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.17), residues: 2268 helix: 2.80 (0.12), residues: 1680 sheet: 0.15 (0.34), residues: 204 loop : -1.58 (0.26), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 193 HIS 0.004 0.001 HIS G 161 PHE 0.021 0.002 PHE H 202 TYR 0.014 0.002 TYR I 66 ARG 0.002 0.000 ARG F 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13075.83 seconds wall clock time: 229 minutes 26.38 seconds (13766.38 seconds total)