Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 18:53:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2023/7xnv_33327_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 156 5.16 5 C 12618 2.51 5 N 2712 2.21 5 O 2892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 3": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G GLU 271": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H GLU 271": "OE1" <-> "OE2" Residue "I TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I GLU 271": "OE1" <-> "OE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J GLU 271": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K GLU 271": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L GLU 271": "OE1" <-> "OE2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 34": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 47": "OD1" <-> "OD2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "B ARG 24": "NH1" <-> "NH2" Residue "B ARG 34": "NH1" <-> "NH2" Residue "B TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B GLU 249": "OE1" <-> "OE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C ARG 34": "NH1" <-> "NH2" Residue "C TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 69": "NH1" <-> "NH2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 34": "NH1" <-> "NH2" Residue "D TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 246": "NH1" <-> "NH2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E ARG 34": "NH1" <-> "NH2" Residue "E TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E ARG 77": "NH1" <-> "NH2" Residue "E PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "E ARG 246": "NH1" <-> "NH2" Residue "E GLU 249": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "F ARG 24": "NH1" <-> "NH2" Residue "F ARG 34": "NH1" <-> "NH2" Residue "F TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 69": "NH1" <-> "NH2" Residue "F ARG 77": "NH1" <-> "NH2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 246": "NH1" <-> "NH2" Residue "F GLU 249": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18378 Number of models: 1 Model: "" Number of chains: 24 Chain: "G" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "H" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "I" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "J" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "K" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "L" Number of atoms: 1458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1458 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 174} Chain breaks: 1 Chain: "A" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "B" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "C" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "E" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "F" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1349 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 160} Chain breaks: 1 Chain: "G" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "H" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "I" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "J" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "K" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "L" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 144 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 362 Unresolved non-hydrogen angles: 461 Unresolved non-hydrogen dihedrals: 208 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'MC3:plan-2': 11, 'MC3:plan-1': 11} Unresolved non-hydrogen planarities: 68 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'MC3': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 328 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'MC3:plan-2': 8, 'MC3:plan-1': 8} Unresolved non-hydrogen planarities: 48 Time building chain proxies: 9.70, per 1000 atoms: 0.53 Number of scatterers: 18378 At special positions: 0 Unit cell: (104.622, 115.15, 144.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 156 16.00 O 2892 8.00 N 2712 7.00 C 12618 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.03 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.03 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.03 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.03 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.03 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.03 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.03 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.03 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.03 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.03 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.03 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.03 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.03 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.03 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.03 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.03 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.03 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.78 Conformation dependent library (CDL) restraints added in 2.5 seconds 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 90 helices and 12 sheets defined 67.0% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'G' and resid 4 through 14 Processing helix chain 'G' and resid 21 through 33 Processing helix chain 'G' and resid 35 through 38 No H-bonds generated for 'chain 'G' and resid 35 through 38' Processing helix chain 'G' and resid 42 through 45 No H-bonds generated for 'chain 'G' and resid 42 through 45' Processing helix chain 'G' and resid 62 through 70 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 88 through 99 removed outlier: 4.211A pdb=" N PHE G 93 " --> pdb=" O PRO G 89 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL G 98 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 220 Processing helix chain 'G' and resid 247 through 275 removed outlier: 3.593A pdb=" N THR G 251 " --> pdb=" O PRO G 247 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 14 Processing helix chain 'H' and resid 21 through 33 Processing helix chain 'H' and resid 35 through 38 No H-bonds generated for 'chain 'H' and resid 35 through 38' Processing helix chain 'H' and resid 42 through 45 No H-bonds generated for 'chain 'H' and resid 42 through 45' Processing helix chain 'H' and resid 62 through 70 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 88 through 99 removed outlier: 4.242A pdb=" N PHE H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL H 98 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 220 Processing helix chain 'H' and resid 247 through 275 removed outlier: 3.578A pdb=" N THR H 251 " --> pdb=" O PRO H 247 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 14 Processing helix chain 'I' and resid 21 through 33 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 45 No H-bonds generated for 'chain 'I' and resid 42 through 45' Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 88 through 99 removed outlier: 4.237A pdb=" N PHE I 93 " --> pdb=" O PRO I 89 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL I 98 " --> pdb=" O ILE I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 220 Processing helix chain 'I' and resid 247 through 275 removed outlier: 3.584A pdb=" N THR I 251 " --> pdb=" O PRO I 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE I 253 " --> pdb=" O GLU I 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 14 Processing helix chain 'J' and resid 21 through 33 Processing helix chain 'J' and resid 35 through 38 No H-bonds generated for 'chain 'J' and resid 35 through 38' Processing helix chain 'J' and resid 42 through 45 No H-bonds generated for 'chain 'J' and resid 42 through 45' Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 88 through 99 removed outlier: 4.208A pdb=" N PHE J 93 " --> pdb=" O PRO J 89 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N THR J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL J 98 " --> pdb=" O ILE J 94 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS J 99 " --> pdb=" O THR J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 220 Processing helix chain 'J' and resid 247 through 275 removed outlier: 3.592A pdb=" N THR J 251 " --> pdb=" O PRO J 247 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 14 Processing helix chain 'K' and resid 21 through 33 Processing helix chain 'K' and resid 35 through 38 No H-bonds generated for 'chain 'K' and resid 35 through 38' Processing helix chain 'K' and resid 42 through 45 No H-bonds generated for 'chain 'K' and resid 42 through 45' Processing helix chain 'K' and resid 62 through 70 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 88 through 99 removed outlier: 4.207A pdb=" N PHE K 93 " --> pdb=" O PRO K 89 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL K 98 " --> pdb=" O ILE K 94 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS K 99 " --> pdb=" O THR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 220 Processing helix chain 'K' and resid 247 through 275 removed outlier: 3.576A pdb=" N THR K 251 " --> pdb=" O PRO K 247 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE K 253 " --> pdb=" O GLU K 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 14 Processing helix chain 'L' and resid 21 through 33 Processing helix chain 'L' and resid 35 through 38 No H-bonds generated for 'chain 'L' and resid 35 through 38' Processing helix chain 'L' and resid 42 through 45 No H-bonds generated for 'chain 'L' and resid 42 through 45' Processing helix chain 'L' and resid 62 through 70 Processing helix chain 'L' and resid 75 through 86 Processing helix chain 'L' and resid 88 through 99 removed outlier: 4.192A pdb=" N PHE L 93 " --> pdb=" O PRO L 89 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 220 Processing helix chain 'L' and resid 247 through 275 removed outlier: 3.585A pdb=" N THR L 251 " --> pdb=" O PRO L 247 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE L 253 " --> pdb=" O GLU L 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 40 removed outlier: 4.105A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 45 No H-bonds generated for 'chain 'A' and resid 42 through 45' Processing helix chain 'A' and resid 62 through 70 Processing helix chain 'A' and resid 75 through 99 removed outlier: 3.598A pdb=" N CYS A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR A 88 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Proline residue: A 89 - end of helix Processing helix chain 'A' and resid 195 through 221 Processing helix chain 'A' and resid 247 through 275 Processing helix chain 'B' and resid 20 through 40 removed outlier: 4.059A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 No H-bonds generated for 'chain 'B' and resid 42 through 45' Processing helix chain 'B' and resid 62 through 70 Processing helix chain 'B' and resid 75 through 99 removed outlier: 3.613A pdb=" N CYS B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Proline residue: B 89 - end of helix Processing helix chain 'B' and resid 195 through 221 Processing helix chain 'B' and resid 247 through 275 Processing helix chain 'C' and resid 20 through 40 removed outlier: 4.214A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 62 through 70 Processing helix chain 'C' and resid 75 through 99 removed outlier: 3.623A pdb=" N CYS C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 88 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Proline residue: C 89 - end of helix Processing helix chain 'C' and resid 195 through 221 Processing helix chain 'C' and resid 247 through 275 Processing helix chain 'D' and resid 20 through 40 removed outlier: 4.114A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 No H-bonds generated for 'chain 'D' and resid 42 through 45' Processing helix chain 'D' and resid 62 through 70 Processing helix chain 'D' and resid 75 through 99 removed outlier: 3.597A pdb=" N CYS D 87 " --> pdb=" O ILE D 83 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Proline residue: D 89 - end of helix Processing helix chain 'D' and resid 195 through 221 Processing helix chain 'D' and resid 247 through 275 Processing helix chain 'E' and resid 20 through 40 removed outlier: 4.108A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 No H-bonds generated for 'chain 'E' and resid 42 through 45' Processing helix chain 'E' and resid 62 through 70 Processing helix chain 'E' and resid 75 through 99 removed outlier: 3.616A pdb=" N CYS E 87 " --> pdb=" O ILE E 83 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR E 88 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Proline residue: E 89 - end of helix Processing helix chain 'E' and resid 195 through 221 Processing helix chain 'E' and resid 247 through 275 Processing helix chain 'F' and resid 20 through 40 removed outlier: 4.300A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 No H-bonds generated for 'chain 'F' and resid 42 through 45' Processing helix chain 'F' and resid 62 through 70 Processing helix chain 'F' and resid 75 through 99 removed outlier: 3.624A pdb=" N CYS F 87 " --> pdb=" O ILE F 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Proline residue: F 89 - end of helix Processing helix chain 'F' and resid 195 through 221 Processing helix chain 'F' and resid 247 through 275 Processing sheet with id= A, first strand: chain 'G' and resid 228 through 231 Processing sheet with id= B, first strand: chain 'H' and resid 228 through 231 Processing sheet with id= C, first strand: chain 'I' and resid 228 through 231 Processing sheet with id= D, first strand: chain 'J' and resid 228 through 231 Processing sheet with id= E, first strand: chain 'K' and resid 228 through 231 Processing sheet with id= F, first strand: chain 'L' and resid 228 through 231 Processing sheet with id= G, first strand: chain 'A' and resid 228 through 231 Processing sheet with id= H, first strand: chain 'B' and resid 228 through 231 Processing sheet with id= I, first strand: chain 'C' and resid 228 through 231 Processing sheet with id= J, first strand: chain 'D' and resid 228 through 231 Processing sheet with id= K, first strand: chain 'E' and resid 228 through 231 Processing sheet with id= L, first strand: chain 'F' and resid 228 through 231 1006 hydrogen bonds defined for protein. 2982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.60 Time building geometry restraints manager: 7.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5181 1.34 - 1.46: 4404 1.46 - 1.58: 8889 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 18678 Sorted by residual: bond pdb=" CB LEU F 26 " pdb=" CG LEU F 26 " ideal model delta sigma weight residual 1.530 1.560 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C11 MC3 D 407 " pdb=" C12 MC3 D 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.80e+00 bond pdb=" C11 MC3 E 407 " pdb=" C12 MC3 E 407 " ideal model delta sigma weight residual 1.502 1.529 -0.027 2.00e-02 2.50e+03 1.76e+00 bond pdb=" C11 MC3 F 407 " pdb=" C12 MC3 F 407 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.75e+00 bond pdb=" C11 MC3 B 404 " pdb=" C12 MC3 B 404 " ideal model delta sigma weight residual 1.502 1.528 -0.026 2.00e-02 2.50e+03 1.74e+00 ... (remaining 18673 not shown) Histogram of bond angle deviations from ideal: 100.32 - 107.05: 412 107.05 - 113.78: 10943 113.78 - 120.51: 7191 120.51 - 127.23: 6074 127.23 - 133.96: 160 Bond angle restraints: 24780 Sorted by residual: angle pdb=" C CYS C 236 " pdb=" N ILE C 237 " pdb=" CA ILE C 237 " ideal model delta sigma weight residual 121.80 125.72 -3.92 1.40e+00 5.10e-01 7.86e+00 angle pdb=" C CYS A 236 " pdb=" N ILE A 237 " pdb=" CA ILE A 237 " ideal model delta sigma weight residual 121.80 125.59 -3.79 1.40e+00 5.10e-01 7.33e+00 angle pdb=" N ILE L 237 " pdb=" CA ILE L 237 " pdb=" C ILE L 237 " ideal model delta sigma weight residual 109.80 106.31 3.49 1.33e+00 5.65e-01 6.87e+00 angle pdb=" C LEU F 58 " pdb=" N GLN F 59 " pdb=" CA GLN F 59 " ideal model delta sigma weight residual 121.61 125.14 -3.53 1.39e+00 5.18e-01 6.43e+00 angle pdb=" C LEU E 58 " pdb=" N GLN E 59 " pdb=" CA GLN E 59 " ideal model delta sigma weight residual 121.61 125.13 -3.52 1.39e+00 5.18e-01 6.40e+00 ... (remaining 24775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.81: 9657 16.81 - 33.63: 1147 33.63 - 50.44: 363 50.44 - 67.25: 119 67.25 - 84.07: 24 Dihedral angle restraints: 11310 sinusoidal: 5190 harmonic: 6120 Sorted by residual: dihedral pdb=" CB GLU B 241 " pdb=" CG GLU B 241 " pdb=" CD GLU B 241 " pdb=" OE1 GLU B 241 " ideal model delta sinusoidal sigma weight residual 0.00 84.07 -84.07 1 3.00e+01 1.11e-03 9.56e+00 dihedral pdb=" CB GLU C 241 " pdb=" CG GLU C 241 " pdb=" CD GLU C 241 " pdb=" OE1 GLU C 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.98 -83.98 1 3.00e+01 1.11e-03 9.55e+00 dihedral pdb=" CB GLU F 241 " pdb=" CG GLU F 241 " pdb=" CD GLU F 241 " pdb=" OE1 GLU F 241 " ideal model delta sinusoidal sigma weight residual 0.00 83.91 -83.91 1 3.00e+01 1.11e-03 9.54e+00 ... (remaining 11307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1614 0.035 - 0.069: 752 0.069 - 0.104: 283 0.104 - 0.139: 71 0.139 - 0.174: 10 Chirality restraints: 2730 Sorted by residual: chirality pdb=" CA VAL A 240 " pdb=" N VAL A 240 " pdb=" C VAL A 240 " pdb=" CB VAL A 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CA VAL E 240 " pdb=" N VAL E 240 " pdb=" C VAL E 240 " pdb=" CB VAL E 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.44e-01 chirality pdb=" CA VAL C 240 " pdb=" N VAL C 240 " pdb=" C VAL C 240 " pdb=" CB VAL C 240 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 2727 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 77 " 0.093 9.50e-02 1.11e+02 4.32e-02 2.77e+00 pdb=" NE ARG F 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG F 77 " -0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG F 77 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 77 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 77 " -0.091 9.50e-02 1.11e+02 4.23e-02 2.75e+00 pdb=" NE ARG C 77 " -0.002 2.00e-02 2.50e+03 pdb=" CZ ARG C 77 " 0.024 2.00e-02 2.50e+03 pdb=" NH1 ARG C 77 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG C 77 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 77 " 0.090 9.50e-02 1.11e+02 4.18e-02 2.62e+00 pdb=" NE ARG B 77 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG B 77 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG B 77 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 77 " 0.011 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2305 2.75 - 3.29: 16328 3.29 - 3.83: 29609 3.83 - 4.36: 34219 4.36 - 4.90: 62036 Nonbonded interactions: 144497 Sorted by model distance: nonbonded pdb=" OE1 GLU H 230 " pdb=" NZ LYS E 238 " model vdw 2.213 2.520 nonbonded pdb=" OE1 GLU G 230 " pdb=" NZ LYS D 238 " model vdw 2.213 2.520 nonbonded pdb=" OE1 GLU K 230 " pdb=" NZ LYS B 238 " model vdw 2.218 2.520 nonbonded pdb=" OE1 GLU I 230 " pdb=" NZ LYS F 238 " model vdw 2.227 2.520 nonbonded pdb=" OE1 GLU L 230 " pdb=" NZ LYS C 238 " model vdw 2.237 2.520 ... (remaining 144492 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 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name 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 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'B' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37 or name C38 or name C39 or name C40)) or (resid 403 and (name C11 \ or 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 (resid 404 and (name C13 or name C14 or name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24)) or resid 405 through 407 or (resid 408 and (nam \ e C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C40)))) selection = (chain 'C' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name 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 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'D' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name 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 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'E' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name 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 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'F' and (resid 19 through 100 or resid 196 through 276 or resid 401 or (r \ esid 402 through 403 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or (resid 404 a \ nd (name C33 or name C34 or name 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 405 \ through 407 or (resid 408 and (name C31 or name C32 or name C33 or name C34 or n \ ame C35 or name C36 or name C37 or name C38 or name C39 or name C40)))) selection = (chain 'G' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'H' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'I' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'J' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'K' and (resid 19 through 100 or resid 196 through 276 or resid 403 throu \ gh 405 or (resid 406 and (name C33 or name C34 or name C35 or name C36 or name C \ 37 or name C38 or name C39 or name C40 or name C41 or name C42 or name C43 or na \ me C44)) or resid 407 through 409 or (resid 410 and (name C31 or name C32 or nam \ e C33 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or \ name C40)))) selection = (chain 'L' and (resid 19 through 100 or resid 196 through 276 or resid 403 or (r \ esid 404 through 405 and (name C31 or name C32 or name C33 or name C34 or name C \ 35 or name C36 or name C37 or name C38 or name C39 or name C40)) or resid 406 th \ rough 410)) } 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.490 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 44.430 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 18678 Z= 0.316 Angle : 1.072 7.844 24780 Z= 0.462 Chirality : 0.046 0.174 2730 Planarity : 0.005 0.043 2904 Dihedral : 16.869 84.065 7266 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.59 % Allowed : 1.03 % Favored : 98.38 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 0.24 (0.17), residues: 2040 helix: 0.92 (0.13), residues: 1380 sheet: -0.28 (0.36), residues: 204 loop : -1.81 (0.23), residues: 456 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 390 time to evaluate : 1.987 Fit side-chains outliers start: 17 outliers final: 13 residues processed: 399 average time/residue: 0.3106 time to fit residues: 185.0565 Evaluate side-chains 353 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 340 time to evaluate : 1.934 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3459 time to fit residues: 9.0337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 154 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 185 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 GLN H 50 GLN I 50 GLN I 207 ASN J 50 GLN K 50 GLN L 50 GLN ** L 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 ASN B 59 GLN B 82 GLN ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 82 GLN ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 82 GLN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN E 59 GLN E 82 GLN ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 82 GLN ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18678 Z= 0.182 Angle : 0.482 6.685 24780 Z= 0.248 Chirality : 0.041 0.130 2730 Planarity : 0.003 0.022 2904 Dihedral : 13.275 59.984 3486 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.69 % Favored : 99.02 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.18), residues: 2040 helix: 2.16 (0.13), residues: 1344 sheet: -0.11 (0.36), residues: 204 loop : -1.31 (0.24), residues: 492 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 349 time to evaluate : 1.981 Fit side-chains outliers start: 65 outliers final: 30 residues processed: 388 average time/residue: 0.3438 time to fit residues: 194.9302 Evaluate side-chains 355 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 325 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.2208 time to fit residues: 13.5358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 102 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 185 optimal weight: 0.3980 chunk 200 optimal weight: 0.7980 chunk 165 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 18678 Z= 0.167 Angle : 0.451 7.019 24780 Z= 0.230 Chirality : 0.040 0.118 2730 Planarity : 0.003 0.025 2904 Dihedral : 12.133 59.971 3486 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.59 % Favored : 99.12 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.19 (0.18), residues: 2040 helix: 2.51 (0.14), residues: 1344 sheet: -0.10 (0.36), residues: 204 loop : -0.94 (0.25), residues: 492 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 339 time to evaluate : 2.030 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 347 average time/residue: 0.2945 time to fit residues: 156.7570 Evaluate side-chains 320 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 310 time to evaluate : 1.968 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2429 time to fit residues: 6.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 176 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 18678 Z= 0.150 Angle : 0.432 7.221 24780 Z= 0.221 Chirality : 0.039 0.115 2730 Planarity : 0.003 0.024 2904 Dihedral : 11.159 59.270 3486 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.18), residues: 2040 helix: 2.69 (0.14), residues: 1344 sheet: -0.05 (0.36), residues: 204 loop : -0.88 (0.24), residues: 492 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 328 time to evaluate : 1.946 Fit side-chains outliers start: 15 outliers final: 8 residues processed: 335 average time/residue: 0.2796 time to fit residues: 145.5805 Evaluate side-chains 321 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 313 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1657 time to fit residues: 5.2265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 168 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 GLN L 99 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 18678 Z= 0.348 Angle : 0.535 7.253 24780 Z= 0.274 Chirality : 0.045 0.156 2730 Planarity : 0.004 0.034 2904 Dihedral : 11.599 58.505 3486 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.14 (0.18), residues: 2040 helix: 2.41 (0.14), residues: 1338 sheet: -0.12 (0.36), residues: 204 loop : -0.70 (0.25), residues: 498 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 308 time to evaluate : 2.080 Fit side-chains outliers start: 15 outliers final: 5 residues processed: 318 average time/residue: 0.3152 time to fit residues: 151.8882 Evaluate side-chains 302 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 297 time to evaluate : 1.911 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1697 time to fit residues: 4.3407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 66 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 163 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 18678 Z= 0.198 Angle : 0.451 6.958 24780 Z= 0.231 Chirality : 0.040 0.126 2730 Planarity : 0.003 0.025 2904 Dihedral : 10.793 59.006 3486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.33 (0.18), residues: 2040 helix: 2.56 (0.14), residues: 1344 sheet: -0.14 (0.36), residues: 204 loop : -0.64 (0.25), residues: 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 316 time to evaluate : 2.094 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 331 average time/residue: 0.2944 time to fit residues: 150.3343 Evaluate side-chains 316 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 307 time to evaluate : 1.927 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1590 time to fit residues: 5.5304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 18678 Z= 0.292 Angle : 0.498 6.695 24780 Z= 0.256 Chirality : 0.043 0.145 2730 Planarity : 0.003 0.029 2904 Dihedral : 10.937 59.159 3486 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.22 (0.18), residues: 2040 helix: 2.46 (0.14), residues: 1344 sheet: -0.24 (0.36), residues: 204 loop : -0.57 (0.25), residues: 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 321 time to evaluate : 2.062 Fit side-chains outliers start: 15 outliers final: 12 residues processed: 324 average time/residue: 0.2980 time to fit residues: 148.2181 Evaluate side-chains 323 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 311 time to evaluate : 2.094 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1689 time to fit residues: 6.5466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.5980 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 133 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 HIS ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 18678 Z= 0.179 Angle : 0.440 6.335 24780 Z= 0.227 Chirality : 0.040 0.121 2730 Planarity : 0.003 0.026 2904 Dihedral : 10.311 59.991 3486 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer Outliers : 0.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.18), residues: 2040 helix: 2.62 (0.14), residues: 1344 sheet: -0.22 (0.35), residues: 204 loop : -0.57 (0.25), residues: 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 326 time to evaluate : 2.060 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 329 average time/residue: 0.2950 time to fit residues: 148.4089 Evaluate side-chains 328 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 322 time to evaluate : 1.834 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1614 time to fit residues: 4.2789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 10.0000 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 18678 Z= 0.263 Angle : 0.481 6.266 24780 Z= 0.247 Chirality : 0.042 0.137 2730 Planarity : 0.003 0.029 2904 Dihedral : 10.508 59.740 3486 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.28 (0.18), residues: 2040 helix: 2.52 (0.14), residues: 1344 sheet: -0.32 (0.35), residues: 204 loop : -0.54 (0.25), residues: 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 312 time to evaluate : 1.829 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 313 average time/residue: 0.3016 time to fit residues: 144.1872 Evaluate side-chains 312 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 309 time to evaluate : 1.963 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1641 time to fit residues: 3.4718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 chunk 203 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 18678 Z= 0.283 Angle : 0.493 6.254 24780 Z= 0.253 Chirality : 0.042 0.144 2730 Planarity : 0.003 0.030 2904 Dihedral : 10.687 59.990 3486 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.22 (0.18), residues: 2040 helix: 2.48 (0.14), residues: 1338 sheet: -0.33 (0.35), residues: 204 loop : -0.57 (0.25), residues: 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4080 Ramachandran restraints generated. 2040 Oldfield, 0 Emsley, 2040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 311 time to evaluate : 2.068 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 311 average time/residue: 0.3079 time to fit residues: 146.1214 Evaluate side-chains 307 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2110 time to fit residues: 3.0441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 172 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 166 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 0.1980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.142389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.110356 restraints weight = 20245.156| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.23 r_work: 0.2703 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 18678 Z= 0.167 Angle : 0.432 6.876 24780 Z= 0.223 Chirality : 0.039 0.118 2730 Planarity : 0.003 0.027 2904 Dihedral : 9.981 59.152 3486 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 2.46 (0.18), residues: 2040 helix: 2.68 (0.14), residues: 1344 sheet: -0.33 (0.35), residues: 204 loop : -0.51 (0.25), residues: 492 =============================================================================== Job complete usr+sys time: 3693.14 seconds wall clock time: 68 minutes 3.79 seconds (4083.79 seconds total)