Starting phenix.real_space_refine on Tue Apr 16 05:22:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xkt_33270/04_2024/7xkt_33270_trim.pdb" } resolution = 2.2 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= 0.155 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: 5 Type Number sf(0) Gaussians S 156 5.16 5 C 12444 2.51 5 N 2544 2.21 5 O 3336 1.98 5 H 16008 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 210": "OE1" <-> "OE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 210": "OE1" <-> "OE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 210": "OE1" <-> "OE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E GLU 210": "OE1" <-> "OE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 210": "OE1" <-> "OE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "L PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 210": "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: 34488 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "B" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "C" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "D" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "E" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "F" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "G" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "H" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "I" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "J" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "K" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "L" Number of atoms: 2664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 2664 Classifications: {'peptide': 166} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 159} Chain breaks: 1 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "F" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "H" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "J" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "L" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 173 Unusual residues: {'LHG': 1, 'MC3': 6, 'Y01': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 222 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 199 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'MC3:plan-2': 6, 'MC3:plan-1': 6} Unresolved non-hydrogen planarities: 42 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "I" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "J" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "K" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Chain: "L" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 37 Classifications: {'water': 37} Link IDs: {None: 36} Time building chain proxies: 14.80, per 1000 atoms: 0.43 Number of scatterers: 34488 At special positions: 0 Unit cell: (97.875, 100.575, 147.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 156 16.00 O 3336 8.00 N 2544 7.00 C 12444 6.00 H 16008 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 242 " distance=2.04 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 236 " distance=2.04 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 242 " distance=2.04 Simple disulfide: pdb=" SG CYS B 62 " - pdb=" SG CYS B 236 " distance=2.04 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS C 242 " distance=2.04 Simple disulfide: pdb=" SG CYS C 62 " - pdb=" SG CYS C 236 " distance=2.04 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 242 " distance=2.04 Simple disulfide: pdb=" SG CYS D 62 " - pdb=" SG CYS D 236 " distance=2.04 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 231 " distance=2.04 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 242 " distance=2.04 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 236 " distance=2.04 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 231 " distance=2.04 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 242 " distance=2.04 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 236 " distance=2.04 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 231 " distance=2.04 Simple disulfide: pdb=" SG CYS G 55 " - pdb=" SG CYS G 242 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 236 " distance=2.04 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 231 " distance=2.04 Simple disulfide: pdb=" SG CYS H 55 " - pdb=" SG CYS H 242 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 236 " distance=2.04 Simple disulfide: pdb=" SG CYS H 66 " - pdb=" SG CYS H 231 " distance=2.04 Simple disulfide: pdb=" SG CYS I 55 " - pdb=" SG CYS I 242 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 236 " distance=2.04 Simple disulfide: pdb=" SG CYS I 66 " - pdb=" SG CYS I 231 " distance=2.04 Simple disulfide: pdb=" SG CYS J 55 " - pdb=" SG CYS J 242 " distance=2.04 Simple disulfide: pdb=" SG CYS J 62 " - pdb=" SG CYS J 236 " distance=2.04 Simple disulfide: pdb=" SG CYS J 66 " - pdb=" SG CYS J 231 " distance=2.04 Simple disulfide: pdb=" SG CYS K 55 " - pdb=" SG CYS K 242 " distance=2.04 Simple disulfide: pdb=" SG CYS K 62 " - pdb=" SG CYS K 236 " distance=2.04 Simple disulfide: pdb=" SG CYS K 66 " - pdb=" SG CYS K 231 " distance=2.04 Simple disulfide: pdb=" SG CYS L 55 " - pdb=" SG CYS L 242 " distance=2.04 Simple disulfide: pdb=" SG CYS L 62 " - pdb=" SG CYS L 236 " distance=2.04 Simple disulfide: pdb=" SG CYS L 66 " - pdb=" SG CYS L 231 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 24.88 Conformation dependent library (CDL) restraints added in 3.1 seconds 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3744 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 76.0% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 removed outlier: 3.689A pdb=" N GLY A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE A 25 " --> pdb=" O MET A 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL A 45 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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: 4.100A pdb=" N ARG B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE B 25 " --> pdb=" O MET B 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B 41 " --> pdb=" O ILE B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL B 45 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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: 4.100A pdb=" N ARG C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 41 " --> pdb=" O ILE C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL C 45 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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: 4.100A pdb=" N ARG D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE D 25 " --> pdb=" O MET D 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL D 41 " --> pdb=" O ILE D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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: 4.100A pdb=" N ARG E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE E 25 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL E 41 " --> pdb=" O ILE E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL E 45 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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: 4.099A pdb=" N ARG F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE F 25 " --> pdb=" O MET F 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL F 41 " --> pdb=" O ILE F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL F 45 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 3.798A 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 101 removed outlier: 3.509A 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 helix chain 'G' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL G 41 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL G 45 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'G' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU G 91 " --> pdb=" O CYS G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 222 Processing helix chain 'G' and resid 246 through 276 Processing helix chain 'H' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG H 24 " --> pdb=" O THR H 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE H 25 " --> pdb=" O MET H 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL H 41 " --> pdb=" O ILE H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'H' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU H 91 " --> pdb=" O CYS H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 222 Processing helix chain 'H' and resid 246 through 276 Processing helix chain 'I' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG I 24 " --> pdb=" O THR I 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE I 25 " --> pdb=" O MET I 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 41 " --> pdb=" O ILE I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL I 45 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'I' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU I 91 " --> pdb=" O CYS I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 222 Processing helix chain 'I' and resid 246 through 276 Processing helix chain 'J' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE J 25 " --> pdb=" O MET J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL J 41 " --> pdb=" O ILE J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL J 45 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU J 91 " --> pdb=" O CYS J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 222 Processing helix chain 'J' and resid 246 through 276 Processing helix chain 'K' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG K 24 " --> pdb=" O THR K 20 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE K 25 " --> pdb=" O MET K 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL K 41 " --> pdb=" O ILE K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL K 45 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU K 91 " --> pdb=" O CYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 222 Processing helix chain 'K' and resid 246 through 276 Processing helix chain 'L' and resid 20 through 41 removed outlier: 4.100A pdb=" N ARG L 24 " --> pdb=" O THR L 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ILE L 25 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL L 41 " --> pdb=" O ILE L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 46 removed outlier: 3.707A pdb=" N VAL L 45 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.798A 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 86 Processing helix chain 'L' and resid 87 through 101 removed outlier: 3.509A pdb=" N LEU L 91 " --> pdb=" O CYS L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 222 Processing helix chain 'L' and resid 246 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA4, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'E' and resid 54 through 55 Processing sheet with id=AA6, first strand: chain 'F' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'G' and resid 54 through 55 Processing sheet with id=AA8, first strand: chain 'H' and resid 54 through 55 Processing sheet with id=AA9, first strand: chain 'I' and resid 54 through 55 Processing sheet with id=AB1, first strand: chain 'J' and resid 54 through 55 Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 1176 hydrogen bonds defined for protein. 3456 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: 12.41 Time building geometry restraints manager: 25.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.03: 15972 1.03 - 1.23: 1013 1.23 - 1.44: 6583 1.44 - 1.64: 10548 1.64 - 1.85: 300 Bond restraints: 34416 Sorted by residual: bond pdb=" CAI Y01 E 405 " pdb=" CAZ Y01 E 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 L 405 " pdb=" CAZ Y01 L 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 C 405 " pdb=" CAZ Y01 C 405 " ideal model delta sigma weight residual 1.332 1.034 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" CAI Y01 J 405 " pdb=" CAZ Y01 J 405 " ideal model delta sigma weight residual 1.332 1.035 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" CAI Y01 A 405 " pdb=" CAZ Y01 A 405 " ideal model delta sigma weight residual 1.332 1.035 0.297 2.00e-02 2.50e+03 2.21e+02 ... (remaining 34411 not shown) Histogram of bond angle deviations from ideal: 96.98 - 104.44: 480 104.44 - 111.90: 35396 111.90 - 119.37: 10773 119.37 - 126.83: 13911 126.83 - 134.29: 220 Bond angle restraints: 60780 Sorted by residual: angle pdb=" CAM Y01 L 406 " pdb=" CAY Y01 L 406 " pdb=" OAW Y01 L 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 I 406 " pdb=" CAY Y01 I 406 " pdb=" OAW Y01 I 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 C 406 " pdb=" CAY Y01 C 406 " pdb=" OAW Y01 C 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 K 406 " pdb=" CAY Y01 K 406 " pdb=" OAW Y01 K 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 angle pdb=" CAM Y01 B 406 " pdb=" CAY Y01 B 406 " pdb=" OAW Y01 B 406 " ideal model delta sigma weight residual 111.19 123.59 -12.40 3.00e+00 1.11e-01 1.71e+01 ... (remaining 60775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 15048 21.99 - 43.97: 2165 43.97 - 65.96: 715 65.96 - 87.94: 96 87.94 - 109.93: 48 Dihedral angle restraints: 18072 sinusoidal: 10800 harmonic: 7272 Sorted by residual: dihedral pdb=" CAT Y01 I 405 " pdb=" CAR Y01 I 405 " pdb=" CBC Y01 I 405 " pdb=" CAV Y01 I 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.83 109.93 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CAT Y01 C 405 " pdb=" CAR Y01 C 405 " pdb=" CBC Y01 C 405 " pdb=" CAV Y01 C 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.78 109.88 1 3.00e+01 1.11e-03 1.43e+01 dihedral pdb=" CAT Y01 G 405 " pdb=" CAR Y01 G 405 " pdb=" CBC Y01 G 405 " pdb=" CAV Y01 G 405 " ideal model delta sinusoidal sigma weight residual 58.10 -51.76 109.86 1 3.00e+01 1.11e-03 1.43e+01 ... (remaining 18069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1886 0.099 - 0.197: 714 0.197 - 0.295: 124 0.295 - 0.394: 36 0.394 - 0.492: 48 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CBF Y01 D 405 " pdb=" CAS Y01 D 405 " pdb=" CBD Y01 D 405 " pdb=" CBH Y01 D 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CBF Y01 A 405 " pdb=" CAS Y01 A 405 " pdb=" CBD Y01 A 405 " pdb=" CBH Y01 A 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" CBF Y01 G 405 " pdb=" CAS Y01 G 405 " pdb=" CBD Y01 G 405 " pdb=" CBH Y01 G 405 " both_signs ideal model delta sigma weight residual False -2.45 -2.94 0.49 2.00e-01 2.50e+01 6.06e+00 ... (remaining 2805 not shown) Planarity restraints: 4716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 238 " -0.033 2.00e-02 2.50e+03 6.36e-02 4.04e+01 pdb=" N GLU E 239 " 0.109 2.00e-02 2.50e+03 pdb=" CA GLU E 239 " -0.028 2.00e-02 2.50e+03 pdb=" H GLU E 239 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 238 " 0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" N GLU G 239 " -0.109 2.00e-02 2.50e+03 pdb=" CA GLU G 239 " 0.028 2.00e-02 2.50e+03 pdb=" H GLU G 239 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 238 " -0.033 2.00e-02 2.50e+03 6.35e-02 4.03e+01 pdb=" N GLU F 239 " 0.109 2.00e-02 2.50e+03 pdb=" CA GLU F 239 " -0.028 2.00e-02 2.50e+03 pdb=" H GLU F 239 " -0.049 2.00e-02 2.50e+03 ... (remaining 4713 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.41: 13842 2.41 - 2.95: 66547 2.95 - 3.50: 83967 3.50 - 4.05: 110286 4.05 - 4.60: 164240 Nonbonded interactions: 438882 Sorted by model distance: nonbonded pdb=" OE1 GLN L 64 " pdb=" H GLN L 64 " model vdw 1.858 1.850 nonbonded pdb=" OE1 GLN I 64 " pdb=" H GLN I 64 " model vdw 1.858 1.850 nonbonded pdb=" OE1 GLN F 64 " pdb=" H GLN F 64 " model vdw 1.858 1.850 nonbonded pdb=" OE1 GLN A 64 " pdb=" H GLN A 64 " model vdw 1.858 1.850 nonbonded pdb=" OE1 GLN G 64 " pdb=" H GLN G 64 " model vdw 1.858 1.850 ... (remaining 438877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 8.420 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: 0.590 Extract box with map and model: 35.100 Check model and map are aligned: 0.480 Set scattering table: 0.320 Process input model: 98.650 Find NCS groups from input model: 1.870 Set up NCS constraints: 0.290 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:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 160.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 : 0.029 0.298 18408 Z= 1.746 Angle : 1.848 12.521 24696 Z= 0.837 Chirality : 0.117 0.492 2808 Planarity : 0.008 0.051 2820 Dihedral : 20.882 109.928 8412 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.33 % Allowed : 14.67 % Favored : 84.00 % 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: 1.53 (0.17), residues: 1944 helix: 1.92 (0.13), residues: 1320 sheet: 0.26 (0.36), residues: 144 loop : -1.32 (0.23), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP F 79 HIS 0.007 0.003 HIS H 274 PHE 0.035 0.005 PHE L 53 TYR 0.030 0.006 TYR F 67 ARG 0.003 0.000 ARG J 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 2.564 Fit side-chains outliers start: 24 outliers final: 0 residues processed: 252 average time/residue: 2.6991 time to fit residues: 763.0783 Evaluate side-chains 196 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.6980 chunk 145 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 GLN B 100 GLN C 100 GLN D 100 GLN E 100 GLN F 100 GLN G 100 GLN H 100 GLN I 100 GLN J 100 GLN K 100 GLN L 100 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18408 Z= 0.226 Angle : 0.788 8.060 24696 Z= 0.385 Chirality : 0.046 0.182 2808 Planarity : 0.005 0.029 2820 Dihedral : 16.874 67.249 4848 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.67 % Allowed : 16.11 % Favored : 83.22 % 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: 2.88 (0.18), residues: 1944 helix: 2.77 (0.13), residues: 1356 sheet: 1.45 (0.39), residues: 120 loop : -0.69 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.003 0.001 HIS L 274 PHE 0.013 0.001 PHE E 53 TYR 0.013 0.002 TYR K 67 ARG 0.002 0.001 ARG K 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 188 time to evaluate : 2.945 Fit side-chains outliers start: 12 outliers final: 0 residues processed: 200 average time/residue: 2.9114 time to fit residues: 648.6422 Evaluate side-chains 172 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 172 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 155 optimal weight: 3.9990 chunk 173 optimal weight: 0.0000 chunk 59 optimal weight: 3.9990 chunk 140 optimal weight: 0.4980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18408 Z= 0.234 Angle : 0.719 8.028 24696 Z= 0.359 Chirality : 0.044 0.143 2808 Planarity : 0.004 0.024 2820 Dihedral : 14.158 56.888 4848 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.44 % Allowed : 15.22 % Favored : 83.33 % 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: 3.16 (0.18), residues: 1944 helix: 3.12 (0.13), residues: 1356 sheet: 1.95 (0.42), residues: 120 loop : -1.23 (0.23), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP H 79 HIS 0.004 0.001 HIS C 274 PHE 0.022 0.002 PHE H 53 TYR 0.018 0.003 TYR H 243 ARG 0.002 0.001 ARG J 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 148 time to evaluate : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4042 (tt) REVERT: C 198 PHE cc_start: 0.6011 (OUTLIER) cc_final: 0.4929 (m-10) REVERT: D 195 ILE cc_start: 0.4468 (OUTLIER) cc_final: 0.4026 (tt) REVERT: F 198 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4926 (m-10) REVERT: G 195 ILE cc_start: 0.4483 (OUTLIER) cc_final: 0.4041 (tt) REVERT: I 198 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.4927 (m-10) REVERT: L 198 PHE cc_start: 0.6009 (OUTLIER) cc_final: 0.5026 (m-80) outliers start: 26 outliers final: 0 residues processed: 172 average time/residue: 3.2250 time to fit residues: 613.2864 Evaluate side-chains 151 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain D residue 195 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain G residue 195 ILE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 0.6980 chunk 131 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 175 optimal weight: 4.9990 chunk 185 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18408 Z= 0.181 Angle : 0.607 4.791 24696 Z= 0.311 Chirality : 0.041 0.149 2808 Planarity : 0.004 0.025 2820 Dihedral : 13.251 59.980 4848 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.83 % Allowed : 15.67 % Favored : 82.50 % 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: 3.47 (0.18), residues: 1944 helix: 3.39 (0.13), residues: 1356 sheet: 1.89 (0.41), residues: 120 loop : -1.18 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 79 HIS 0.003 0.001 HIS I 274 PHE 0.014 0.001 PHE H 53 TYR 0.013 0.002 TYR J 67 ARG 0.001 0.000 ARG H 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 198 PHE cc_start: 0.5907 (OUTLIER) cc_final: 0.4837 (m-10) REVERT: F 198 PHE cc_start: 0.5905 (OUTLIER) cc_final: 0.4835 (m-10) REVERT: I 198 PHE cc_start: 0.5906 (OUTLIER) cc_final: 0.4836 (m-10) REVERT: L 198 PHE cc_start: 0.5920 (OUTLIER) cc_final: 0.4853 (m-10) outliers start: 33 outliers final: 0 residues processed: 175 average time/residue: 3.2603 time to fit residues: 630.3908 Evaluate side-chains 145 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 2.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 166 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18408 Z= 0.246 Angle : 0.682 6.135 24696 Z= 0.350 Chirality : 0.043 0.150 2808 Planarity : 0.004 0.027 2820 Dihedral : 13.852 59.587 4848 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.22 % Allowed : 16.61 % Favored : 82.17 % 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: 3.38 (0.18), residues: 1944 helix: 3.27 (0.13), residues: 1356 sheet: 1.92 (0.42), residues: 120 loop : -1.07 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 79 HIS 0.002 0.001 HIS C 274 PHE 0.019 0.002 PHE J 53 TYR 0.017 0.003 TYR A 67 ARG 0.002 0.000 ARG B 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 148 time to evaluate : 2.767 Fit side-chains REVERT: A 198 PHE cc_start: 0.5976 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: B 239 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7608 (tt0) REVERT: C 198 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5133 (m-80) REVERT: D 198 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5078 (m-80) REVERT: E 239 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7604 (tt0) REVERT: F 198 PHE cc_start: 0.6091 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: G 198 PHE cc_start: 0.5977 (OUTLIER) cc_final: 0.5076 (m-80) REVERT: I 198 PHE cc_start: 0.6090 (OUTLIER) cc_final: 0.5132 (m-80) REVERT: J 198 PHE cc_start: 0.5978 (OUTLIER) cc_final: 0.5077 (m-80) REVERT: L 198 PHE cc_start: 0.6093 (OUTLIER) cc_final: 0.5134 (m-80) outliers start: 22 outliers final: 8 residues processed: 168 average time/residue: 3.3177 time to fit residues: 614.4609 Evaluate side-chains 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 148 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain I residue 83 ILE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain J residue 198 PHE Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain L residue 83 ILE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 185 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 18408 Z= 0.159 Angle : 0.561 4.482 24696 Z= 0.291 Chirality : 0.040 0.149 2808 Planarity : 0.003 0.020 2820 Dihedral : 12.840 59.815 4848 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.83 % Allowed : 17.00 % Favored : 82.17 % 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: 3.85 (0.18), residues: 1944 helix: 3.67 (0.13), residues: 1356 sheet: 2.18 (0.40), residues: 120 loop : -1.08 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 79 HIS 0.002 0.001 HIS G 274 PHE 0.013 0.001 PHE B 53 TYR 0.011 0.002 TYR A 67 ARG 0.001 0.000 ARG I 233 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 152 time to evaluate : 2.574 Fit side-chains REVERT: C 198 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.4816 (m-10) REVERT: F 198 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4818 (m-10) REVERT: I 198 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.4816 (m-10) REVERT: L 198 PHE cc_start: 0.5868 (OUTLIER) cc_final: 0.4801 (m-10) outliers start: 15 outliers final: 0 residues processed: 164 average time/residue: 3.4452 time to fit residues: 620.8359 Evaluate side-chains 152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 2.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain F residue 198 PHE Chi-restraints excluded: chain I residue 198 PHE Chi-restraints excluded: chain L residue 198 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 156 optimal weight: 0.0570 chunk 103 optimal weight: 0.6980 chunk 185 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18408 Z= 0.173 Angle : 0.577 4.642 24696 Z= 0.299 Chirality : 0.041 0.149 2808 Planarity : 0.003 0.024 2820 Dihedral : 12.820 59.893 4848 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.67 % Allowed : 16.89 % Favored : 82.44 % 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: 3.92 (0.18), residues: 1944 helix: 3.72 (0.12), residues: 1356 sheet: 2.07 (0.41), residues: 120 loop : -0.98 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 79 HIS 0.002 0.000 HIS K 274 PHE 0.015 0.001 PHE J 53 TYR 0.012 0.002 TYR H 243 ARG 0.001 0.000 ARG I 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 160 time to evaluate : 2.611 Fit side-chains REVERT: A 198 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4748 (m-10) REVERT: D 198 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4749 (m-10) REVERT: G 198 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4749 (m-10) REVERT: J 198 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.4756 (m-10) outliers start: 12 outliers final: 0 residues processed: 168 average time/residue: 3.3892 time to fit residues: 628.0110 Evaluate side-chains 152 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 2.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 145 optimal weight: 0.6980 chunk 168 optimal weight: 8.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18408 Z= 0.194 Angle : 0.598 4.242 24696 Z= 0.311 Chirality : 0.041 0.150 2808 Planarity : 0.004 0.025 2820 Dihedral : 13.090 59.240 4848 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.61 % Allowed : 17.28 % Favored : 82.11 % 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: 3.85 (0.18), residues: 1944 helix: 3.67 (0.12), residues: 1356 sheet: 1.98 (0.41), residues: 120 loop : -1.01 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 79 HIS 0.001 0.000 HIS E 274 PHE 0.016 0.002 PHE J 53 TYR 0.014 0.002 TYR G 67 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 2.788 Fit side-chains REVERT: A 198 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.4968 (m-10) REVERT: B 239 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7618 (tt0) REVERT: D 198 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.4753 (m-10) REVERT: E 239 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: G 198 PHE cc_start: 0.5936 (OUTLIER) cc_final: 0.4967 (m-10) REVERT: J 198 PHE cc_start: 0.5942 (OUTLIER) cc_final: 0.4971 (m-10) outliers start: 11 outliers final: 0 residues processed: 164 average time/residue: 3.4426 time to fit residues: 621.2292 Evaluate side-chains 162 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 156 time to evaluate : 2.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 172 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18408 Z= 0.196 Angle : 0.604 4.191 24696 Z= 0.315 Chirality : 0.041 0.149 2808 Planarity : 0.004 0.028 2820 Dihedral : 13.293 59.595 4848 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.89 % Allowed : 16.94 % Favored : 82.17 % 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: 3.82 (0.18), residues: 1944 helix: 3.66 (0.12), residues: 1356 sheet: 1.96 (0.41), residues: 120 loop : -1.07 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 79 HIS 0.001 0.000 HIS K 274 PHE 0.016 0.002 PHE J 53 TYR 0.014 0.002 TYR D 67 ARG 0.002 0.000 ARG J 246 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 2.648 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.4946 (m-10) REVERT: B 239 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: D 198 PHE cc_start: 0.5967 (OUTLIER) cc_final: 0.4945 (m-10) REVERT: E 239 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: G 198 PHE cc_start: 0.5966 (OUTLIER) cc_final: 0.4945 (m-10) REVERT: J 198 PHE cc_start: 0.5972 (OUTLIER) cc_final: 0.4950 (m-10) outliers start: 16 outliers final: 4 residues processed: 168 average time/residue: 3.3531 time to fit residues: 620.9986 Evaluate side-chains 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 0.4980 chunk 120 optimal weight: 7.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18408 Z= 0.185 Angle : 0.592 4.249 24696 Z= 0.309 Chirality : 0.041 0.150 2808 Planarity : 0.004 0.026 2820 Dihedral : 13.195 59.791 4848 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.56 % Allowed : 17.28 % Favored : 82.17 % 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: 3.91 (0.18), residues: 1944 helix: 3.73 (0.12), residues: 1356 sheet: 1.99 (0.41), residues: 120 loop : -1.01 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP J 79 HIS 0.001 0.000 HIS E 274 PHE 0.015 0.001 PHE E 53 TYR 0.014 0.002 TYR J 67 ARG 0.001 0.000 ARG I 246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3888 Ramachandran restraints generated. 1944 Oldfield, 0 Emsley, 1944 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 198 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.4918 (m-10) REVERT: B 239 GLU cc_start: 0.7836 (OUTLIER) cc_final: 0.7593 (tt0) REVERT: D 198 PHE cc_start: 0.5941 (OUTLIER) cc_final: 0.4919 (m-10) REVERT: E 239 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: G 198 PHE cc_start: 0.5940 (OUTLIER) cc_final: 0.4919 (m-10) REVERT: J 198 PHE cc_start: 0.5945 (OUTLIER) cc_final: 0.4922 (m-10) outliers start: 10 outliers final: 4 residues processed: 164 average time/residue: 3.4213 time to fit residues: 617.1706 Evaluate side-chains 166 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 2.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain B residue 239 GLU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain E residue 239 GLU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 198 PHE Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 198 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 42 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 63 optimal weight: 0.4980 chunk 156 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.177947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123155 restraints weight = 42426.547| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.32 r_work: 0.3347 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18408 Z= 0.144 Angle : 0.535 4.012 24696 Z= 0.279 Chirality : 0.040 0.153 2808 Planarity : 0.003 0.021 2820 Dihedral : 12.456 59.893 4848 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.56 % Allowed : 17.28 % Favored : 82.17 % 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: 4.27 (0.18), residues: 1944 helix: 3.97 (0.12), residues: 1356 sheet: 2.50 (0.42), residues: 120 loop : -0.94 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP K 79 HIS 0.001 0.001 HIS E 75 PHE 0.010 0.001 PHE E 53 TYR 0.011 0.001 TYR L 67 ARG 0.001 0.000 ARG K 233 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11623.49 seconds wall clock time: 227 minutes 15.63 seconds (13635.63 seconds total)