Starting phenix.real_space_refine on Mon Jul 22 12:26:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/07_2024/7xnv_33327.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/07_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_33327/07_2024/7xnv_33327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/07_2024/7xnv_33327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/07_2024/7xnv_33327.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xnv_33327/07_2024/7xnv_33327.cif" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 10.57, per 1000 atoms: 0.58 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: 6.41 Conformation dependent library (CDL) restraints added in 3.0 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... Secondary structure from input PDB file: 96 helices and 12 sheets defined 74.7% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'G' and resid 3 through 15 removed outlier: 4.227A pdb=" N LEU G 7 " --> pdb=" O GLU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 34 Processing helix chain 'G' and resid 34 through 39 Processing helix chain 'G' and resid 41 through 46 removed outlier: 4.011A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR G 46 " --> pdb=" O GLY G 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 41 through 46' Processing helix chain 'G' and resid 61 through 71 Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 87 through 100 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) removed outlier: 4.272A pdb=" N GLN G 100 " --> pdb=" O TYR G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 221 Processing helix chain 'G' and resid 246 through 276 removed outlier: 3.596A pdb=" N LYS G 250 " --> pdb=" O ARG G 246 " (cutoff:3.500A) 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 3 through 15 removed outlier: 4.256A pdb=" N LEU H 7 " --> pdb=" O GLU H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 34 Processing helix chain 'H' and resid 34 through 39 Processing helix chain 'H' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR H 46 " --> pdb=" O GLY H 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 41 through 46' Processing helix chain 'H' and resid 61 through 71 Processing helix chain 'H' and resid 74 through 87 Processing helix chain 'H' and resid 87 through 100 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 221 Processing helix chain 'H' and resid 246 through 276 removed outlier: 3.599A pdb=" N LYS H 250 " --> pdb=" O ARG H 246 " (cutoff:3.500A) 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 3 through 15 removed outlier: 4.218A pdb=" N LEU I 7 " --> pdb=" O GLU I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 34 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR I 46 " --> pdb=" O GLY I 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 41 through 46' Processing helix chain 'I' and resid 61 through 71 Processing helix chain 'I' and resid 74 through 87 Processing helix chain 'I' and resid 87 through 100 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 221 Processing helix chain 'I' and resid 246 through 276 removed outlier: 3.601A pdb=" N LYS I 250 " --> pdb=" O ARG I 246 " (cutoff:3.500A) 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 3 through 15 removed outlier: 4.228A pdb=" N LEU J 7 " --> pdb=" O GLU J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 34 Processing helix chain 'J' and resid 34 through 39 Processing helix chain 'J' and resid 41 through 46 removed outlier: 4.014A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR J 46 " --> pdb=" O GLY J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 41 through 46' Processing helix chain 'J' and resid 61 through 71 Processing helix chain 'J' and resid 74 through 87 Processing helix chain 'J' and resid 87 through 100 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) removed outlier: 3.673A pdb=" N GLN J 100 " --> pdb=" O TYR J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 221 Processing helix chain 'J' and resid 246 through 276 removed outlier: 3.605A pdb=" N LYS J 250 " --> pdb=" O ARG J 246 " (cutoff:3.500A) 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 3 through 15 removed outlier: 4.255A pdb=" N LEU K 7 " --> pdb=" O GLU K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 34 Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 41 through 46 removed outlier: 4.020A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TYR K 46 " --> pdb=" O GLY K 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 41 through 46' Processing helix chain 'K' and resid 61 through 71 Processing helix chain 'K' and resid 74 through 87 Processing helix chain 'K' and resid 87 through 100 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) removed outlier: 3.608A pdb=" N GLN K 100 " --> pdb=" O TYR K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 221 Processing helix chain 'K' and resid 246 through 276 removed outlier: 3.602A pdb=" N LYS K 250 " --> pdb=" O ARG K 246 " (cutoff:3.500A) 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 3 through 15 removed outlier: 4.215A pdb=" N LEU L 7 " --> pdb=" O GLU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 34 Processing helix chain 'L' and resid 34 through 39 Processing helix chain 'L' and resid 41 through 46 removed outlier: 4.019A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR L 46 " --> pdb=" O GLY L 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 41 through 46' Processing helix chain 'L' and resid 61 through 71 Processing helix chain 'L' and resid 74 through 87 Processing helix chain 'L' and resid 87 through 100 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 221 Processing helix chain 'L' and resid 246 through 276 removed outlier: 3.603A pdb=" N LYS L 250 " --> pdb=" O ARG L 246 " (cutoff:3.500A) 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 41 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 41 through 46 removed outlier: 3.728A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 46 " --> pdb=" O GLY A 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 41 through 46' Processing helix chain 'A' and resid 61 through 71 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.635A pdb=" N LEU A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 222 Processing helix chain 'A' and resid 246 through 276 Processing helix chain 'B' and resid 20 through 41 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 41 through 46 removed outlier: 3.770A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR B 46 " --> pdb=" O GLY B 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 41 through 46' Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 87 through 100 removed outlier: 3.577A pdb=" N LEU B 91 " --> pdb=" O CYS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 222 Processing helix chain 'B' and resid 246 through 276 Processing helix chain 'C' and resid 20 through 41 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 41 through 46 removed outlier: 3.769A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TYR C 46 " --> pdb=" O GLY C 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 41 through 46' Processing helix chain 'C' and resid 61 through 71 Processing helix chain 'C' and resid 74 through 86 Processing helix chain 'C' and resid 87 through 100 removed outlier: 3.616A pdb=" N LEU C 91 " --> pdb=" O CYS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 222 Processing helix chain 'C' and resid 246 through 276 Processing helix chain 'D' and resid 20 through 41 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 41 through 46 removed outlier: 3.765A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 41 through 46' Processing helix chain 'D' and resid 61 through 71 Processing helix chain 'D' and resid 74 through 86 Processing helix chain 'D' and resid 87 through 100 removed outlier: 3.633A pdb=" N LEU D 91 " --> pdb=" O CYS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 222 Processing helix chain 'D' and resid 246 through 276 Processing helix chain 'E' and resid 20 through 41 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 41 through 46 removed outlier: 3.773A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR E 46 " --> pdb=" O GLY E 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 41 through 46' Processing helix chain 'E' and resid 61 through 71 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'E' and resid 87 through 100 removed outlier: 3.574A pdb=" N LEU E 91 " --> pdb=" O CYS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 222 Processing helix chain 'E' and resid 246 through 276 Processing helix chain 'F' and resid 20 through 41 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 41 through 46 removed outlier: 3.740A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR F 46 " --> pdb=" O GLY F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 61 through 71 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'F' and resid 87 through 100 removed outlier: 3.621A pdb=" N LEU F 91 " --> pdb=" O CYS F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 222 Processing helix chain 'F' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'L' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'F' and resid 54 through 55 1153 hydrogen bonds defined for protein. 3387 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: 5.03 Time building geometry restraints manager: 7.05 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: 2299 2.75 - 3.29: 16225 3.29 - 3.83: 29467 3.83 - 4.36: 33943 4.36 - 4.90: 61975 Nonbonded interactions: 143909 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 143904 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: 5.440 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: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.410 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.610 ------------------------------------------------------------------------------- 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= 0.320 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 : 2.045 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: 0.3133 time to fit residues: 187.1586 Evaluate side-chains 344 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 329 time to evaluate : 2.203 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 50 GLN H 50 GLN I 50 GLN J 50 GLN K 50 GLN L 50 GLN 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 99 HIS ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 GLN D 82 GLN D 99 HIS ** 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1000 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= 0.202 Angle : 0.519 5.565 24780 Z= 0.279 Chirality : 0.042 0.135 2730 Planarity : 0.003 0.024 2904 Dihedral : 13.882 59.982 3525 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.98 % Favored : 98.73 % Rotamer: Outliers : 3.72 % Allowed : 13.00 % Favored : 83.28 % 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: 1.84 (0.18), residues: 2040 helix: 2.09 (0.13), residues: 1380 sheet: 0.41 (0.38), residues: 174 loop : -1.03 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 277 HIS 0.003 0.001 HIS B 99 PHE 0.010 0.001 PHE A 53 TYR 0.013 0.001 TYR H 96 ARG 0.003 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 415 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 345 time to evaluate : 2.008 Fit side-chains REVERT: H 29 VAL cc_start: 0.8980 (t) cc_final: 0.8780 (t) REVERT: I 69 ARG cc_start: 0.7918 (tpt170) cc_final: 0.7688 (tpt90) REVERT: K 29 VAL cc_start: 0.8980 (t) cc_final: 0.8769 (t) REVERT: L 237 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8286 (mm) REVERT: A 69 ARG cc_start: 0.7877 (tpt170) cc_final: 0.7610 (ttm-80) REVERT: A 230 GLU cc_start: 0.7799 (mp0) cc_final: 0.7563 (mp0) REVERT: B 69 ARG cc_start: 0.7901 (tpt170) cc_final: 0.7610 (ttm-80) REVERT: B 230 GLU cc_start: 0.7748 (mp0) cc_final: 0.7528 (mp0) REVERT: B 238 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.8021 (mtmt) REVERT: B 275 LEU cc_start: 0.6992 (mp) cc_final: 0.6777 (mp) REVERT: C 69 ARG cc_start: 0.7862 (tpt170) cc_final: 0.7596 (ttm-80) REVERT: C 275 LEU cc_start: 0.6844 (mp) cc_final: 0.6623 (mp) REVERT: D 238 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.8142 (mtmt) REVERT: E 69 ARG cc_start: 0.7852 (tpt170) cc_final: 0.7587 (ttm-80) REVERT: E 230 GLU cc_start: 0.7760 (mp0) cc_final: 0.7533 (mp0) REVERT: E 238 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.8028 (mtmt) REVERT: E 275 LEU cc_start: 0.7073 (mp) cc_final: 0.6872 (mp) REVERT: F 230 GLU cc_start: 0.7775 (mp0) cc_final: 0.7518 (mp0) REVERT: F 275 LEU cc_start: 0.6832 (mp) cc_final: 0.6593 (mp) outliers start: 70 outliers final: 35 residues processed: 380 average time/residue: 0.3135 time to fit residues: 176.6483 Evaluate side-chains 362 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 323 time to evaluate : 1.971 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 57 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 185 optimal weight: 0.0050 chunk 200 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 chunk 184 optimal weight: 0.1980 chunk 63 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 overall best weight: 0.8196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 100 GLN A 82 GLN ** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18678 Z= 0.159 Angle : 0.464 5.675 24780 Z= 0.248 Chirality : 0.041 0.135 2730 Planarity : 0.003 0.026 2904 Dihedral : 12.422 59.917 3495 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.29 % Allowed : 0.78 % Favored : 98.92 % Rotamer: Outliers : 2.55 % Allowed : 13.80 % 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: 2.45 (0.18), residues: 2040 helix: 2.45 (0.13), residues: 1380 sheet: 1.26 (0.42), residues: 144 loop : -0.63 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 277 HIS 0.002 0.001 HIS I 75 PHE 0.009 0.001 PHE D 53 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 391 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 343 time to evaluate : 1.951 Fit side-chains REVERT: G 52 MET cc_start: 0.9134 (mmt) cc_final: 0.8761 (mmt) REVERT: H 52 MET cc_start: 0.9143 (mmt) cc_final: 0.8743 (mmt) REVERT: I 29 VAL cc_start: 0.8980 (t) cc_final: 0.8731 (t) REVERT: I 69 ARG cc_start: 0.7963 (tpt170) cc_final: 0.7703 (tpt90) REVERT: J 52 MET cc_start: 0.9150 (mmt) cc_final: 0.8793 (mmt) REVERT: K 52 MET cc_start: 0.9144 (mmt) cc_final: 0.8740 (mmt) REVERT: L 29 VAL cc_start: 0.8976 (t) cc_final: 0.8723 (t) REVERT: L 237 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8561 (mm) REVERT: A 69 ARG cc_start: 0.7905 (tpt170) cc_final: 0.7576 (ttm-80) REVERT: B 63 ASN cc_start: 0.8919 (m-40) cc_final: 0.8712 (m-40) REVERT: B 69 ARG cc_start: 0.7932 (tpt170) cc_final: 0.7564 (ttm-80) REVERT: C 69 ARG cc_start: 0.7878 (tpt170) cc_final: 0.7555 (ttm-80) REVERT: D 238 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8219 (mtmt) REVERT: E 69 ARG cc_start: 0.7883 (tpt170) cc_final: 0.7537 (ttm-80) outliers start: 48 outliers final: 31 residues processed: 359 average time/residue: 0.2884 time to fit residues: 158.9066 Evaluate side-chains 354 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 321 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 6 ILE Chi-restraints excluded: chain G residue 238 LYS Chi-restraints excluded: chain I residue 238 LYS 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 237 ILE 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 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 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 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: 4.9990 chunk 139 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 124 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 176 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8357 moved from start: 0.1608 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= 0.180 Angle : 0.467 5.925 24780 Z= 0.247 Chirality : 0.041 0.137 2730 Planarity : 0.003 0.029 2904 Dihedral : 11.381 59.986 3486 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.92 % Allowed : 15.13 % Favored : 81.95 % 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: 2.51 (0.18), residues: 2040 helix: 2.55 (0.13), residues: 1380 sheet: 0.45 (0.39), residues: 174 loop : -0.53 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 277 HIS 0.003 0.001 HIS I 75 PHE 0.011 0.001 PHE F 81 TYR 0.009 0.001 TYR E 67 ARG 0.003 0.000 ARG D 69 *********************** 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 375 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 320 time to evaluate : 1.826 Fit side-chains REVERT: G 52 MET cc_start: 0.9091 (mmt) cc_final: 0.8846 (mmt) REVERT: H 232 ASN cc_start: 0.8001 (p0) cc_final: 0.7471 (t0) REVERT: I 69 ARG cc_start: 0.7975 (tpt170) cc_final: 0.7697 (tpt90) REVERT: I 204 VAL cc_start: 0.9049 (t) cc_final: 0.8837 (m) REVERT: I 232 ASN cc_start: 0.7949 (p0) cc_final: 0.7585 (t0) REVERT: J 52 MET cc_start: 0.9116 (mmt) cc_final: 0.8879 (mmt) REVERT: L 232 ASN cc_start: 0.8001 (p0) cc_final: 0.7589 (t0) REVERT: L 237 ILE cc_start: 0.8891 (OUTLIER) cc_final: 0.8687 (mm) REVERT: C 69 ARG cc_start: 0.7873 (tpt170) cc_final: 0.7654 (ttm-80) REVERT: D 238 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8252 (mtmt) REVERT: E 238 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8232 (mtmt) outliers start: 55 outliers final: 40 residues processed: 349 average time/residue: 0.2794 time to fit residues: 150.2067 Evaluate side-chains 353 residues out of total 1884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 310 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 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 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 44 THR 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.8159 > 50: distance: 38 - 59: 3.315 distance: 42 - 71: 21.953 distance: 49 - 85: 37.411 distance: 55 - 59: 4.344 distance: 56 - 92: 20.518 distance: 59 - 60: 5.356 distance: 60 - 61: 9.663 distance: 60 - 63: 10.941 distance: 61 - 62: 9.780 distance: 61 - 71: 8.199 distance: 62 - 103: 14.834 distance: 63 - 64: 10.490 distance: 64 - 65: 5.456 distance: 65 - 67: 7.293 distance: 66 - 68: 5.771 distance: 67 - 69: 4.015 distance: 68 - 69: 5.066 distance: 71 - 72: 11.679 distance: 72 - 73: 13.713 distance: 72 - 75: 18.147 distance: 73 - 74: 28.203 distance: 73 - 85: 36.077 distance: 74 - 112: 18.167 distance: 76 - 77: 8.170 distance: 76 - 78: 4.779 distance: 77 - 79: 4.036 distance: 78 - 80: 4.491 distance: 78 - 81: 3.252 distance: 79 - 80: 3.708 distance: 80 - 82: 4.413 distance: 81 - 83: 3.695 distance: 83 - 84: 4.548 distance: 85 - 86: 45.887 distance: 86 - 87: 10.979 distance: 86 - 89: 23.176 distance: 87 - 88: 8.972 distance: 87 - 92: 16.560 distance: 88 - 120: 21.268 distance: 89 - 90: 7.231 distance: 89 - 91: 23.910 distance: 92 - 93: 9.028 distance: 93 - 94: 13.686 distance: 93 - 96: 10.157 distance: 94 - 95: 7.191 distance: 94 - 103: 3.750 distance: 95 - 128: 6.468 distance: 96 - 97: 9.291 distance: 97 - 98: 7.482 distance: 97 - 99: 5.209 distance: 98 - 100: 6.687 distance: 99 - 101: 3.402 distance: 100 - 102: 9.561 distance: 103 - 104: 4.518 distance: 104 - 105: 6.545 distance: 104 - 107: 8.110 distance: 105 - 106: 4.840 distance: 105 - 112: 6.088 distance: 106 - 136: 6.959 distance: 107 - 108: 5.956 distance: 108 - 109: 6.069 distance: 109 - 110: 6.100 distance: 109 - 111: 6.542 distance: 112 - 113: 7.000 distance: 113 - 114: 5.300 distance: 113 - 116: 4.068 distance: 114 - 115: 7.763 distance: 116 - 118: 7.341 distance: 117 - 119: 3.837 distance: 122 - 128: 10.023 distance: 124 - 125: 9.220 distance: 124 - 126: 6.788 distance: 125 - 127: 17.793 distance: 128 - 129: 5.454 distance: 129 - 130: 9.028 distance: 129 - 132: 5.038 distance: 130 - 131: 8.480 distance: 130 - 136: 9.509 distance: 132 - 133: 4.190 distance: 133 - 134: 5.095 distance: 134 - 135: 9.384 distance: 136 - 137: 9.777 distance: 137 - 138: 13.026 distance: 137 - 140: 12.561 distance: 138 - 139: 11.578 distance: 138 - 143: 12.859 distance: 140 - 141: 16.564 distance: 140 - 142: 10.521 distance: 143 - 144: 14.532 distance: 144 - 145: 3.689 distance: 144 - 147: 17.248 distance: 145 - 146: 9.147 distance: 147 - 148: 16.097