Starting phenix.real_space_refine on Wed Apr 10 03:19:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2024/7xnv_33327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2024/7xnv_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_2024/7xnv_33327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2024/7xnv_33327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2024/7xnv_33327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/04_2024/7xnv_33327_updated.pdb" } resolution = 3.4 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= 0.002 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-dev-5288/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: 318 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: 318 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: 318 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: 318 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: 318 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: 318 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: 224 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: 224 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: 224 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: 224 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: 224 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: 224 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: 9.59, per 1000 atoms: 0.52 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: 6.74 Conformation dependent library (CDL) restraints added in 2.7 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: 2.76 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: 5.13 Time building geometry restraints manager: 7.41 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: 3.570 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: 13.840 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 46.340 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.120 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.740 ------------------------------------------------------------------------------- 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 % Allowed : 11.25 % Favored : 87.85 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 79 HIS 0.004 0.001 HIS I 75 PHE 0.019 0.001 PHE C 198 TYR 0.018 0.002 TYR H 96 ARG 0.023 0.001 ARG C 77 *********************** 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 : 1.910 Fit side-chains REVERT: I 69 ARG cc_start: 0.7919 (tpt170) cc_final: 0.7702 (tpt90) REVERT: I 204 VAL cc_start: 0.9039 (t) cc_final: 0.8819 (m) REVERT: I 207 ASN cc_start: 0.8432 (m-40) cc_final: 0.8109 (m110) REVERT: L 204 VAL cc_start: 0.9029 (t) cc_final: 0.8816 (m) REVERT: A 69 ARG cc_start: 0.7874 (tpt170) cc_final: 0.7651 (ttm-80) REVERT: B 69 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7649 (ttm-80) REVERT: B 77 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8141 (mpt180) REVERT: B 232 ASN cc_start: 0.9042 (p0) cc_final: 0.8831 (p0) REVERT: B 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6692 (mp) REVERT: C 69 ARG cc_start: 0.7838 (tpt170) cc_final: 0.7635 (ttm-80) REVERT: C 275 LEU cc_start: 0.6725 (mp) cc_final: 0.6502 (mp) REVERT: D 77 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8209 (mpt180) REVERT: E 69 ARG cc_start: 0.7861 (tpt170) cc_final: 0.7631 (ttm-80) REVERT: E 232 ASN cc_start: 0.9045 (p0) cc_final: 0.8839 (p0) REVERT: E 239 GLU cc_start: 0.8360 (tt0) cc_final: 0.8120 (tt0) REVERT: E 275 LEU cc_start: 0.6905 (mp) cc_final: 0.6689 (mp) REVERT: F 275 LEU cc_start: 0.6756 (mp) cc_final: 0.6503 (mp) outliers start: 17 outliers final: 13 residues processed: 399 average time/residue: 0.3143 time to fit residues: 186.9592 Evaluate side-chains 344 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 329 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 253 PHE Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 253 PHE Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 77 ARG 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: 1.9990 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: 0.8980 chunk 119 optimal weight: 4.9990 chunk 185 optimal weight: 0.0470 overall best weight: 0.9680 ------------------------------------------------------------------------------- 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 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: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.0865 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= 0.177 Angle : 0.473 5.679 24780 Z= 0.247 Chirality : 0.041 0.133 2730 Planarity : 0.003 0.022 2904 Dihedral : 13.810 59.997 3525 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.69 % Favored : 99.02 % Rotamer: Outliers : 3.66 % Allowed : 12.63 % Favored : 83.70 % 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: 1.66 (0.18), residues: 2040 helix: 1.99 (0.13), residues: 1380 sheet: -0.09 (0.36), residues: 204 loop : -1.11 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 277 HIS 0.004 0.001 HIS B 99 PHE 0.007 0.001 PHE A 53 TYR 0.009 0.001 TYR H 96 ARG 0.002 0.000 ARG D 69 *********************** 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 416 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 347 time to evaluate : 1.889 Fit side-chains REVERT: I 69 ARG cc_start: 0.7932 (tpt170) cc_final: 0.7706 (tpt90) REVERT: L 204 VAL cc_start: 0.9052 (t) cc_final: 0.8836 (m) REVERT: L 237 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8238 (mm) REVERT: A 69 ARG cc_start: 0.7867 (tpt170) cc_final: 0.7617 (ttm-80) REVERT: A 230 GLU cc_start: 0.7790 (mp0) cc_final: 0.7570 (mp0) REVERT: B 69 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7606 (ttm-80) REVERT: B 230 GLU cc_start: 0.7748 (mp0) cc_final: 0.7527 (mp0) REVERT: B 238 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8026 (mtmt) REVERT: B 275 LEU cc_start: 0.6847 (mp) cc_final: 0.6635 (mp) REVERT: C 69 ARG cc_start: 0.7872 (tpt170) cc_final: 0.7612 (ttm-80) REVERT: C 238 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7921 (mtmt) REVERT: C 275 LEU cc_start: 0.6744 (mp) cc_final: 0.6524 (mp) REVERT: D 238 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8093 (mtmt) REVERT: E 69 ARG cc_start: 0.7824 (tpt170) cc_final: 0.7592 (ttm-80) REVERT: E 230 GLU cc_start: 0.7766 (mp0) cc_final: 0.7533 (mp0) REVERT: E 232 ASN cc_start: 0.9032 (p0) cc_final: 0.8827 (p0) REVERT: E 238 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.8018 (mtmt) REVERT: F 230 GLU cc_start: 0.7756 (mp0) cc_final: 0.7507 (mp0) REVERT: F 275 LEU cc_start: 0.6797 (mp) cc_final: 0.6584 (mp) outliers start: 69 outliers final: 34 residues processed: 383 average time/residue: 0.3280 time to fit residues: 185.9769 Evaluate side-chains 366 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 327 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 238 LYS Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 238 LYS Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 271 GLU 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: 2.9990 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 chunk 185 optimal weight: 0.6980 chunk 200 optimal weight: 0.9980 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 0.0980 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 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: 0.8380 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18678 Z= 0.214 Angle : 0.469 6.357 24780 Z= 0.242 Chirality : 0.041 0.131 2730 Planarity : 0.003 0.026 2904 Dihedral : 12.615 59.924 3495 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.69 % Favored : 99.02 % Rotamer: Outliers : 2.87 % Allowed : 13.48 % Favored : 83.65 % 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: 2.10 (0.18), residues: 2040 helix: 2.26 (0.14), residues: 1380 sheet: -0.01 (0.37), residues: 204 loop : -0.65 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 79 HIS 0.003 0.001 HIS L 18 PHE 0.010 0.001 PHE A 81 TYR 0.008 0.001 TYR A 67 ARG 0.002 0.000 ARG D 69 *********************** 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 386 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 332 time to evaluate : 1.921 Fit side-chains REVERT: G 52 MET cc_start: 0.9131 (mmt) cc_final: 0.8781 (mmt) REVERT: H 52 MET cc_start: 0.9116 (mmt) cc_final: 0.8751 (mmt) REVERT: I 69 ARG cc_start: 0.7978 (tpt170) cc_final: 0.7699 (tpt90) REVERT: I 204 VAL cc_start: 0.9067 (t) cc_final: 0.8834 (m) REVERT: I 232 ASN cc_start: 0.7982 (p0) cc_final: 0.7549 (t0) REVERT: J 52 MET cc_start: 0.9152 (mmt) cc_final: 0.8815 (mmt) REVERT: K 52 MET cc_start: 0.9117 (mmt) cc_final: 0.8746 (mmt) REVERT: L 204 VAL cc_start: 0.9061 (t) cc_final: 0.8840 (m) REVERT: L 237 ILE cc_start: 0.8811 (OUTLIER) cc_final: 0.8606 (mm) REVERT: A 69 ARG cc_start: 0.7950 (tpt170) cc_final: 0.7612 (ttm-80) REVERT: A 77 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8171 (mpp-170) REVERT: B 63 ASN cc_start: 0.8992 (m-40) cc_final: 0.8788 (m-40) REVERT: B 69 ARG cc_start: 0.7946 (tpt170) cc_final: 0.7577 (ttm-80) REVERT: C 69 ARG cc_start: 0.7889 (tpt170) cc_final: 0.7566 (ttm-80) REVERT: D 238 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8227 (mtmt) REVERT: E 69 ARG cc_start: 0.7897 (tpt170) cc_final: 0.7610 (ttm-80) REVERT: E 238 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: F 275 LEU cc_start: 0.6763 (mp) cc_final: 0.6552 (mp) outliers start: 54 outliers final: 40 residues processed: 362 average time/residue: 0.3053 time to fit residues: 169.5545 Evaluate side-chains 361 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 317 time to evaluate : 2.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain I residue 253 PHE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 237 ILE Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain L residue 253 PHE Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 238 LYS Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 183 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 186 optimal weight: 0.7980 chunk 197 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 176 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1408 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= 0.181 Angle : 0.446 7.407 24780 Z= 0.229 Chirality : 0.040 0.124 2730 Planarity : 0.003 0.025 2904 Dihedral : 11.612 59.787 3490 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 3.08 % Allowed : 15.34 % Favored : 81.58 % 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: 2.30 (0.19), residues: 2040 helix: 2.44 (0.14), residues: 1380 sheet: -0.05 (0.36), residues: 204 loop : -0.59 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 79 HIS 0.002 0.001 HIS L 75 PHE 0.011 0.001 PHE E 81 TYR 0.009 0.001 TYR D 243 ARG 0.003 0.000 ARG E 24 *********************** 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 379 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 321 time to evaluate : 1.976 Fit side-chains REVERT: G 52 MET cc_start: 0.9098 (mmt) cc_final: 0.8804 (mmt) REVERT: I 69 ARG cc_start: 0.7987 (tpt170) cc_final: 0.7709 (tpt90) REVERT: I 204 VAL cc_start: 0.9057 (t) cc_final: 0.8844 (m) REVERT: I 232 ASN cc_start: 0.7957 (p0) cc_final: 0.7573 (t0) REVERT: J 32 ILE cc_start: 0.8493 (mt) cc_final: 0.8292 (mt) REVERT: J 52 MET cc_start: 0.9116 (mmt) cc_final: 0.8837 (mmt) REVERT: K 232 ASN cc_start: 0.8002 (p0) cc_final: 0.7505 (t0) REVERT: A 69 ARG cc_start: 0.7946 (tpt170) cc_final: 0.7559 (ttm-80) REVERT: A 77 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8104 (mpp-170) REVERT: B 69 ARG cc_start: 0.7936 (tpt170) cc_final: 0.7585 (ttm-80) REVERT: C 69 ARG cc_start: 0.7869 (tpt170) cc_final: 0.7512 (ttm-80) REVERT: C 77 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8605 (mpp-170) REVERT: D 233 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7138 (ttt180) REVERT: D 238 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8232 (mtmt) REVERT: E 69 ARG cc_start: 0.7893 (tpt170) cc_final: 0.7569 (ttm-80) REVERT: F 77 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8599 (mpp-170) outliers start: 58 outliers final: 38 residues processed: 356 average time/residue: 0.3012 time to fit residues: 163.0409 Evaluate side-chains 354 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 311 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 164 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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: 0.8411 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18678 Z= 0.294 Angle : 0.506 7.693 24780 Z= 0.258 Chirality : 0.043 0.146 2730 Planarity : 0.003 0.028 2904 Dihedral : 11.472 59.952 3486 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 3.45 % Allowed : 15.29 % Favored : 81.26 % 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: 2.31 (0.14), residues: 1374 sheet: -0.08 (0.36), residues: 204 loop : -0.46 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 79 HIS 0.004 0.001 HIS H 75 PHE 0.013 0.001 PHE F 81 TYR 0.009 0.002 TYR D 243 ARG 0.002 0.001 ARG D 69 *********************** 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 378 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 313 time to evaluate : 1.801 Fit side-chains REVERT: G 52 MET cc_start: 0.9081 (mmt) cc_final: 0.8832 (mmt) REVERT: H 230 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7174 (mm-30) REVERT: I 69 ARG cc_start: 0.7996 (tpt170) cc_final: 0.7697 (tpt90) REVERT: I 204 VAL cc_start: 0.9081 (t) cc_final: 0.8853 (m) REVERT: J 32 ILE cc_start: 0.8526 (mt) cc_final: 0.8324 (mt) REVERT: J 52 MET cc_start: 0.9104 (mmt) cc_final: 0.8869 (mmt) REVERT: J 230 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7336 (mm-30) REVERT: L 230 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7452 (mm-30) REVERT: A 69 ARG cc_start: 0.7984 (tpt170) cc_final: 0.7533 (ttm-80) REVERT: A 77 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8063 (mpp-170) REVERT: A 233 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7192 (ttt180) REVERT: B 69 ARG cc_start: 0.7969 (tpt170) cc_final: 0.7531 (ttm-80) REVERT: B 233 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7272 (ttt180) REVERT: C 69 ARG cc_start: 0.7910 (tpt170) cc_final: 0.7495 (ttm-80) REVERT: C 77 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8522 (mpp-170) REVERT: D 22 ILE cc_start: 0.6198 (OUTLIER) cc_final: 0.5981 (mp) REVERT: D 77 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8113 (mpp-170) REVERT: D 233 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7223 (ttt180) REVERT: D 238 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8354 (mtmt) REVERT: E 69 ARG cc_start: 0.7935 (tpt170) cc_final: 0.7514 (ttm-80) REVERT: E 233 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7297 (ttt180) REVERT: E 238 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8246 (mtmt) REVERT: F 77 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8573 (mpp-170) outliers start: 65 outliers final: 42 residues processed: 350 average time/residue: 0.3212 time to fit residues: 167.9344 Evaluate side-chains 357 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 304 time to evaluate : 2.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 94 ILE Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 238 LYS Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 271 GLU 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: 0.9990 chunk 38 optimal weight: 0.6980 chunk 115 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 163 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8376 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18678 Z= 0.155 Angle : 0.432 8.019 24780 Z= 0.220 Chirality : 0.039 0.116 2730 Planarity : 0.003 0.026 2904 Dihedral : 10.579 59.604 3486 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.40 % Allowed : 15.82 % Favored : 80.79 % 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: 2.49 (0.14), residues: 1380 sheet: -0.09 (0.35), residues: 204 loop : -0.45 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 4 HIS 0.001 0.000 HIS H 99 PHE 0.010 0.001 PHE E 81 TYR 0.008 0.001 TYR D 243 ARG 0.002 0.000 ARG D 69 *********************** 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 386 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 322 time to evaluate : 1.491 Fit side-chains REVERT: G 52 MET cc_start: 0.9067 (mmt) cc_final: 0.8798 (mmt) REVERT: H 232 ASN cc_start: 0.7840 (p0) cc_final: 0.7509 (t0) REVERT: H 239 GLU cc_start: 0.8018 (tt0) cc_final: 0.7767 (tt0) REVERT: I 69 ARG cc_start: 0.7976 (tpt170) cc_final: 0.7714 (tpt90) REVERT: J 32 ILE cc_start: 0.8503 (mt) cc_final: 0.8298 (mt) REVERT: J 52 MET cc_start: 0.9090 (mmt) cc_final: 0.8839 (mmt) REVERT: J 230 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7323 (mm-30) REVERT: L 230 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 77 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8199 (mpp-170) REVERT: A 233 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7213 (ttt180) REVERT: C 77 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8332 (mpp-170) REVERT: D 22 ILE cc_start: 0.6159 (OUTLIER) cc_final: 0.5952 (mp) REVERT: D 77 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8170 (mpp-170) REVERT: D 233 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7180 (ttt180) REVERT: E 233 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7307 (ttt180) REVERT: E 238 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8258 (mtmt) REVERT: F 77 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8494 (mpp-170) outliers start: 64 outliers final: 39 residues processed: 368 average time/residue: 0.3155 time to fit residues: 173.8371 Evaluate side-chains 360 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 312 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 238 LYS Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 190 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 123 optimal weight: 8.9990 chunk 119 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8409 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18678 Z= 0.266 Angle : 0.487 8.246 24780 Z= 0.249 Chirality : 0.042 0.140 2730 Planarity : 0.003 0.027 2904 Dihedral : 10.712 59.848 3486 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.34 % Allowed : 16.08 % Favored : 80.57 % 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: 2.29 (0.18), residues: 2040 helix: 2.38 (0.14), residues: 1380 sheet: -0.18 (0.35), residues: 204 loop : -0.35 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 79 HIS 0.003 0.001 HIS K 75 PHE 0.010 0.001 PHE B 81 TYR 0.009 0.002 TYR D 243 ARG 0.002 0.000 ARG D 246 *********************** 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 371 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 308 time to evaluate : 1.748 Fit side-chains REVERT: G 52 MET cc_start: 0.9071 (mmt) cc_final: 0.8811 (mmt) REVERT: G 230 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7246 (mm-30) REVERT: G 239 GLU cc_start: 0.7985 (tt0) cc_final: 0.7548 (tt0) REVERT: I 69 ARG cc_start: 0.7981 (tpt170) cc_final: 0.7671 (tpt90) REVERT: I 230 GLU cc_start: 0.7596 (tp30) cc_final: 0.7360 (mm-30) REVERT: J 32 ILE cc_start: 0.8524 (mt) cc_final: 0.8320 (mt) REVERT: J 52 MET cc_start: 0.9101 (mmt) cc_final: 0.8849 (mmt) REVERT: J 230 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7375 (mm-30) REVERT: K 230 GLU cc_start: 0.7624 (mm-30) cc_final: 0.7394 (mm-30) REVERT: L 230 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7129 (mm-30) REVERT: L 239 GLU cc_start: 0.7953 (tt0) cc_final: 0.7634 (tt0) REVERT: A 77 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8066 (mpp-170) REVERT: A 233 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7309 (ttt180) REVERT: B 233 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7432 (ttt180) REVERT: C 77 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8504 (mpp-170) REVERT: C 91 LEU cc_start: 0.8670 (mp) cc_final: 0.8404 (mp) REVERT: D 22 ILE cc_start: 0.6171 (OUTLIER) cc_final: 0.5943 (mp) REVERT: D 77 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8117 (mpp-170) REVERT: D 233 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7232 (ttt180) REVERT: E 77 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.6825 (mpp-170) REVERT: E 233 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7443 (ttt180) REVERT: F 77 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8547 (mpp-170) outliers start: 63 outliers final: 45 residues processed: 353 average time/residue: 0.3137 time to fit residues: 164.1626 Evaluate side-chains 353 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 298 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 99 HIS Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 233 ARG Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 121 optimal weight: 0.0030 chunk 78 optimal weight: 0.8980 chunk 117 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 overall best weight: 0.6790 ------------------------------------------------------------------------------- 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: 0.8377 moved from start: 0.1821 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= 0.135 Angle : 0.427 8.113 24780 Z= 0.220 Chirality : 0.039 0.117 2730 Planarity : 0.003 0.025 2904 Dihedral : 10.156 59.563 3486 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 3.03 % Allowed : 16.93 % Favored : 80.04 % 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: 2.54 (0.14), residues: 1380 sheet: -0.12 (0.35), residues: 204 loop : -0.40 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 4 HIS 0.011 0.000 HIS H 99 PHE 0.010 0.001 PHE C 33 TYR 0.009 0.001 TYR D 243 ARG 0.001 0.000 ARG D 69 *********************** 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 368 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 311 time to evaluate : 1.999 Fit side-chains REVERT: G 52 MET cc_start: 0.9061 (mmt) cc_final: 0.8831 (mmt) REVERT: H 232 ASN cc_start: 0.7873 (p0) cc_final: 0.7575 (t0) REVERT: I 69 ARG cc_start: 0.7953 (tpt170) cc_final: 0.7704 (tpt90) REVERT: I 230 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7063 (mp0) REVERT: J 52 MET cc_start: 0.9084 (mmt) cc_final: 0.8872 (mmt) REVERT: J 230 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7374 (mm-30) REVERT: K 232 ASN cc_start: 0.7865 (p0) cc_final: 0.7620 (t0) REVERT: K 239 GLU cc_start: 0.8056 (tt0) cc_final: 0.7824 (tt0) REVERT: L 230 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7077 (mm-30) REVERT: L 239 GLU cc_start: 0.7930 (tt0) cc_final: 0.7582 (tt0) REVERT: A 77 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8218 (mpp-170) REVERT: A 233 ARG cc_start: 0.7713 (OUTLIER) cc_final: 0.7246 (ttt180) REVERT: B 233 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7372 (ttt180) REVERT: C 77 ARG cc_start: 0.8982 (OUTLIER) cc_final: 0.8336 (mpp-170) REVERT: D 22 ILE cc_start: 0.6154 (OUTLIER) cc_final: 0.5937 (mp) REVERT: D 77 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8114 (mpp-170) REVERT: E 77 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.6776 (mpp-170) REVERT: E 233 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7365 (ttt180) REVERT: F 77 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8350 (mpp-170) outliers start: 57 outliers final: 41 residues processed: 351 average time/residue: 0.3234 time to fit residues: 169.7051 Evaluate side-chains 357 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 306 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 238 LYS Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 238 LYS Chi-restraints excluded: chain K residue 238 LYS Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 21 MET Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 94 ILE Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 94 ILE Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 188 optimal weight: 0.0970 chunk 171 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 110 optimal weight: 0.6980 chunk 79 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 120 optimal weight: 0.2980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 HIS 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** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1953 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= 0.119 Angle : 0.407 7.555 24780 Z= 0.210 Chirality : 0.038 0.115 2730 Planarity : 0.002 0.025 2904 Dihedral : 9.370 59.700 3486 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.60 % Allowed : 17.36 % Favored : 80.04 % 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: 2.64 (0.18), residues: 2040 helix: 2.69 (0.14), residues: 1380 sheet: -0.04 (0.36), residues: 204 loop : -0.38 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 79 HIS 0.001 0.000 HIS E 99 PHE 0.010 0.001 PHE D 33 TYR 0.012 0.001 TYR K 229 ARG 0.001 0.000 ARG D 69 *********************** 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 368 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 319 time to evaluate : 2.085 Fit side-chains REVERT: G 230 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7453 (mm-30) REVERT: G 232 ASN cc_start: 0.7822 (p0) cc_final: 0.7470 (t0) REVERT: H 29 VAL cc_start: 0.9003 (t) cc_final: 0.8792 (t) REVERT: H 52 MET cc_start: 0.9058 (mmt) cc_final: 0.8778 (mmt) REVERT: H 232 ASN cc_start: 0.7838 (p0) cc_final: 0.7608 (t0) REVERT: I 69 ARG cc_start: 0.7951 (tpt170) cc_final: 0.7694 (tpt90) REVERT: I 230 GLU cc_start: 0.7159 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: I 232 ASN cc_start: 0.7806 (p0) cc_final: 0.7568 (t0) REVERT: J 230 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7344 (mm-30) REVERT: J 232 ASN cc_start: 0.7826 (p0) cc_final: 0.7471 (t0) REVERT: K 29 VAL cc_start: 0.9011 (t) cc_final: 0.8788 (t) REVERT: K 52 MET cc_start: 0.9052 (mmt) cc_final: 0.8773 (mmt) REVERT: K 232 ASN cc_start: 0.7851 (p0) cc_final: 0.7631 (t0) REVERT: L 230 GLU cc_start: 0.7691 (mm-30) cc_final: 0.6977 (mm-30) REVERT: L 239 GLU cc_start: 0.7938 (tt0) cc_final: 0.7606 (tt0) REVERT: A 77 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8187 (mpp-170) REVERT: A 233 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7222 (ttt180) REVERT: B 233 ARG cc_start: 0.7733 (OUTLIER) cc_final: 0.7323 (ttt180) REVERT: C 77 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8316 (mpp-170) REVERT: D 22 ILE cc_start: 0.6136 (OUTLIER) cc_final: 0.5914 (mp) REVERT: D 77 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8153 (mpp-170) REVERT: E 77 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.6745 (mpp-170) REVERT: E 233 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7338 (ttt180) REVERT: F 77 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8316 (mpp-170) outliers start: 49 outliers final: 30 residues processed: 354 average time/residue: 0.3243 time to fit residues: 169.9163 Evaluate side-chains 352 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 312 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 6 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 230 GLU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 22 ILE Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 82 GLN Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 271 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 204 random chunks: chunk 193 optimal weight: 0.7980 chunk 118 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 134 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 187 optimal weight: 0.0010 chunk 161 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 HIS 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 18678 Z= 0.302 Angle : 0.506 7.810 24780 Z= 0.259 Chirality : 0.043 0.153 2730 Planarity : 0.003 0.026 2904 Dihedral : 10.275 59.744 3486 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 2.55 % Allowed : 17.41 % Favored : 80.04 % 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: 2.35 (0.18), residues: 2040 helix: 2.47 (0.14), residues: 1374 sheet: -0.24 (0.35), residues: 204 loop : -0.40 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 79 HIS 0.003 0.001 HIS K 75 PHE 0.012 0.001 PHE B 81 TYR 0.012 0.002 TYR F 243 ARG 0.003 0.000 ARG I 69 ********************** 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 351 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 2.008 Fit side-chains revert: symmetry clash REVERT: G 52 MET cc_start: 0.9064 (mmt) cc_final: 0.8802 (mmt) REVERT: G 230 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7298 (mm-30) REVERT: G 239 GLU cc_start: 0.8021 (tt0) cc_final: 0.7666 (tt0) REVERT: H 232 ASN cc_start: 0.7920 (p0) cc_final: 0.7569 (t0) REVERT: I 69 ARG cc_start: 0.7988 (tpt170) cc_final: 0.7679 (tpt90) REVERT: I 232 ASN cc_start: 0.7838 (p0) cc_final: 0.7585 (t0) REVERT: J 52 MET cc_start: 0.9095 (mmt) cc_final: 0.8838 (mmt) REVERT: J 230 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7360 (mm-30) REVERT: K 232 ASN cc_start: 0.7857 (p0) cc_final: 0.7636 (t0) REVERT: L 230 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7039 (mm-30) REVERT: L 239 GLU cc_start: 0.8032 (tt0) cc_final: 0.7737 (tt0) REVERT: A 77 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8091 (mpp-170) REVERT: A 233 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7354 (ttt180) REVERT: B 233 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7437 (ttt180) REVERT: C 77 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8361 (mpp-170) REVERT: C 91 LEU cc_start: 0.8622 (mp) cc_final: 0.8372 (mp) REVERT: D 77 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8108 (mpp-170) REVERT: E 233 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7438 (ttt180) REVERT: F 77 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8359 (mpp-170) REVERT: F 91 LEU cc_start: 0.8623 (mp) cc_final: 0.8369 (mp) outliers start: 48 outliers final: 34 residues processed: 337 average time/residue: 0.3156 time to fit residues: 159.7780 Evaluate side-chains 339 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 298 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 253 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 238 LYS Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 253 PHE Chi-restraints excluded: chain K residue 44 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 238 LYS Chi-restraints excluded: chain A residue 77 ARG Chi-restraints excluded: chain A residue 94 ILE Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 22 ILE Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 82 GLN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 233 ARG Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain E residue 41 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 77 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 233 ARG Chi-restraints excluded: chain E residue 271 GLU Chi-restraints excluded: chain F residue 41 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 77 ARG Chi-restraints excluded: chain F residue 271 GLU 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: 0.9980 chunk 149 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.0980 chunk 162 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 142 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.142611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.110212 restraints weight = 20207.722| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.18 r_work: 0.2770 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18678 Z= 0.151 Angle : 0.431 7.587 24780 Z= 0.221 Chirality : 0.039 0.123 2730 Planarity : 0.003 0.025 2904 Dihedral : 9.629 59.659 3486 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.34 % Allowed : 17.36 % Favored : 80.31 % 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: 2.55 (0.18), residues: 2040 helix: 2.61 (0.14), residues: 1380 sheet: -0.19 (0.35), residues: 204 loop : -0.32 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP K 4 HIS 0.002 0.000 HIS K 75 PHE 0.010 0.001 PHE B 81 TYR 0.008 0.001 TYR F 243 ARG 0.001 0.000 ARG D 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3957.25 seconds wall clock time: 77 minutes 21.74 seconds (4641.74 seconds total)