Starting phenix.real_space_refine on Sun Feb 18 03:03:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/02_2024/7vnm_32042_updated.pdb" } resolution = 2.86 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= 0.008 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 9 5.49 5 Mg 30 5.21 5 S 82 5.16 5 C 14484 2.51 5 N 2897 2.21 5 O 3085 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 6": "OE1" <-> "OE2" Residue "L ARG 109": "NH1" <-> "NH2" Residue "L ARG 217": "NH1" <-> "NH2" Residue "L ARG 231": "NH1" <-> "NH2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "M GLU 95": "OE1" <-> "OE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M PHE 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 232": "OE1" <-> "OE2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "M GLU 246": "OE1" <-> "OE2" Residue "M ARG 253": "NH1" <-> "NH2" Residue "M GLU 263": "OE1" <-> "OE2" Residue "H PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H ARG 118": "NH1" <-> "NH2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "H ARG 177": "NH1" <-> "NH2" Residue "H GLU 180": "OE1" <-> "OE2" Residue "H GLU 230": "OE1" <-> "OE2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "K TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 14": "NH1" <-> "NH2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "O TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S GLU 45": "OE1" <-> "OE2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 53": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "C GLU 15": "OE1" <-> "OE2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 53": "NH1" <-> "NH2" Residue "X GLU 59": "OE1" <-> "OE2" Residue "1 ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20588 Number of models: 1 Model: "" Number of chains: 55 Chain: "L" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2232 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2431 Classifications: {'peptide': 305} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 292} Chain: "H" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1875 Classifications: {'peptide': 247} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 223} Chain: "A" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "B" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "G" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "V" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 327 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "W" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "C" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 316 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "7" Number of atoms: 392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 392 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "8" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "9" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "0" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "X" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 406 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "2" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 270 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 1, 'TRANS': 30} Chain: "L" Number of atoms: 327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 327 Unusual residues: {'BCL': 2, 'BPH': 2, 'PC1': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 320 Unusual residues: {'BCL': 2, 'CDL': 1, 'FE2': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 118 Unusual residues: {'PC1': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 44 Chain: "A" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 251 Unusual residues: {'BCL': 2, 'PC1': 2, 'SPO': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 31 Chain: "D" Number of atoms: 192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 192 Unusual residues: {'BCL': 1, 'SPO': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 216 Unusual residues: {'BCL': 2, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 174 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 105 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SPO:plan-4': 1} Unresolved non-hydrogen planarities: 3 Chain: "9" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 169 Unusual residues: {'BCL': 2, 'SPO': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "0" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 84 Unusual residues: {'SPO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 18 Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'BCL:plan_0002': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 11.20, per 1000 atoms: 0.54 Number of scatterers: 20588 At special positions: 0 Unit cell: (133.388, 125.103, 126.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 82 16.00 P 9 15.00 Mg 30 11.99 O 3085 8.00 N 2897 7.00 C 14484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=29, symmetry=0 Number of additional bonds: simple=29, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.61 Conformation dependent library (CDL) restraints added in 3.7 seconds 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3930 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 5 sheets defined 65.2% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.645A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.066A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 Processing helix chain 'L' and resid 259 through 267 removed outlier: 3.949A pdb=" N GLN L 264 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP L 265 " --> pdb=" O ASP L 261 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N TRP L 266 " --> pdb=" O TRP L 262 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 272 No H-bonds generated for 'chain 'L' and resid 270 through 272' Processing helix chain 'M' and resid 26 through 28 No H-bonds generated for 'chain 'M' and resid 26 through 28' Processing helix chain 'M' and resid 37 through 42 removed outlier: 4.037A pdb=" N PHE M 42 " --> pdb=" O LEU M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 88 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.835A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 225 Processing helix chain 'M' and resid 227 through 229 No H-bonds generated for 'chain 'M' and resid 227 through 229' Processing helix chain 'M' and resid 234 through 239 removed outlier: 3.514A pdb=" N ALA M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 256 Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.677A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 37 removed outlier: 4.311A pdb=" N ARG H 37 " --> pdb=" O THR H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 69 No H-bonds generated for 'chain 'H' and resid 67 through 69' Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.521A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 4.004A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 10 Processing helix chain 'A' and resid 13 through 37 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'B' and resid 14 through 45 Processing helix chain 'D' and resid 4 through 10 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 14 through 45 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 14 through 45 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 43 through 50 Processing helix chain 'J' and resid 14 through 45 Processing helix chain 'K' and resid 4 through 10 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 14 through 45 Processing helix chain 'O' and resid 4 through 9 Processing helix chain 'O' and resid 13 through 37 Processing helix chain 'O' and resid 43 through 50 Processing helix chain 'P' and resid 14 through 45 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 50 Processing helix chain 'R' and resid 14 through 45 Processing helix chain 'S' and resid 4 through 9 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 14 through 45 Processing helix chain 'U' and resid 4 through 10 Processing helix chain 'U' and resid 13 through 37 Processing helix chain 'U' and resid 43 through 51 Processing helix chain 'V' and resid 14 through 45 Processing helix chain 'W' and resid 4 through 9 Processing helix chain 'W' and resid 13 through 37 Processing helix chain 'W' and resid 43 through 51 Processing helix chain 'C' and resid 14 through 45 Processing helix chain '7' and resid 4 through 9 Processing helix chain '7' and resid 13 through 37 Processing helix chain '8' and resid 14 through 45 Processing helix chain '9' and resid 4 through 9 Processing helix chain '9' and resid 13 through 37 Processing helix chain '9' and resid 43 through 50 Processing helix chain '0' and resid 14 through 45 Processing helix chain 'X' and resid 17 through 53 Processing helix chain '1' and resid 13 through 37 Processing helix chain '1' and resid 43 through 50 Processing helix chain '2' and resid 19 through 45 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 4.321A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.435A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.751A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.621A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 1053 hydrogen bonds defined for protein. 3027 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: 5.51 Time building geometry restraints manager: 9.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.34: 5337 1.34 - 1.55: 15433 1.55 - 1.76: 342 1.76 - 1.96: 159 1.96 - 2.17: 120 Bond restraints: 21391 Sorted by residual: bond pdb=" C12 SPO P 102 " pdb=" C14 SPO P 102 " ideal model delta sigma weight residual 1.359 1.581 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" C32 SPO F 103 " pdb=" C33 SPO F 103 " ideal model delta sigma weight residual 1.336 1.547 -0.211 2.00e-02 2.50e+03 1.11e+02 bond pdb=" C12 SPO I 103 " pdb=" C14 SPO I 103 " ideal model delta sigma weight residual 1.359 1.567 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 SPO Q 102 " pdb=" C14 SPO Q 102 " ideal model delta sigma weight residual 1.359 1.567 -0.208 2.00e-02 2.50e+03 1.08e+02 bond pdb=" C12 SPO R 103 " pdb=" C14 SPO R 103 " ideal model delta sigma weight residual 1.359 1.566 -0.207 2.00e-02 2.50e+03 1.07e+02 ... (remaining 21386 not shown) Histogram of bond angle deviations from ideal: 84.63 - 100.26: 132 100.26 - 115.90: 14125 115.90 - 131.54: 14822 131.54 - 147.17: 257 147.17 - 162.81: 61 Bond angle restraints: 29397 Sorted by residual: angle pdb=" C11 SPO 0 102 " pdb=" C10 SPO 0 102 " pdb=" C9 SPO 0 102 " ideal model delta sigma weight residual 123.01 148.92 -25.91 3.00e+00 1.11e-01 7.46e+01 angle pdb=" C8 SPO 0 102 " pdb=" C7 SPO 0 102 " pdb=" C9 SPO 0 102 " ideal model delta sigma weight residual 123.96 103.09 20.87 3.00e+00 1.11e-01 4.84e+01 angle pdb=" C36 SPO U 103 " pdb=" C37 SPO U 103 " pdb=" C38 SPO U 103 " ideal model delta sigma weight residual 128.11 107.25 20.86 3.00e+00 1.11e-01 4.84e+01 angle pdb=" C17 SPO E 102 " pdb=" C19 SPO E 102 " pdb=" C20 SPO E 102 " ideal model delta sigma weight residual 127.83 108.14 19.69 3.00e+00 1.11e-01 4.31e+01 angle pdb=" C13 SPO P 102 " pdb=" C12 SPO P 102 " pdb=" C14 SPO P 102 " ideal model delta sigma weight residual 123.54 104.39 19.15 3.00e+00 1.11e-01 4.08e+01 ... (remaining 29392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 11039 35.84 - 71.68: 389 71.68 - 107.53: 43 107.53 - 143.37: 4 143.37 - 179.21: 1 Dihedral angle restraints: 11476 sinusoidal: 5364 harmonic: 6112 Sorted by residual: dihedral pdb=" C1 BCL L 305 " pdb=" C2 BCL L 305 " pdb=" C3 BCL L 305 " pdb=" C5 BCL L 305 " ideal model delta sinusoidal sigma weight residual 180.00 0.79 179.21 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C6 U10 L 304 " pdb=" C7 U10 L 304 " pdb=" C8 U10 L 304 " pdb=" C9 U10 L 304 " ideal model delta sinusoidal sigma weight residual 101.51 -133.19 -125.30 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" C3M U10 M 404 " pdb=" C3 U10 M 404 " pdb=" O3 U10 M 404 " pdb=" C4 U10 M 404 " ideal model delta sinusoidal sigma weight residual 244.38 127.50 116.87 1 2.00e+01 2.50e-03 3.48e+01 ... (remaining 11473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2189 0.046 - 0.093: 589 0.093 - 0.139: 88 0.139 - 0.185: 9 0.185 - 0.232: 3 Chirality restraints: 2878 Sorted by residual: chirality pdb=" C2C BPH L 306 " pdb=" C1C BPH L 306 " pdb=" C3C BPH L 306 " pdb=" CMC BPH L 306 " both_signs ideal model delta sigma weight residual False -2.81 -2.58 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" C2C BPH L 302 " pdb=" C1C BPH L 302 " pdb=" C3C BPH L 302 " pdb=" CMC BPH L 302 " both_signs ideal model delta sigma weight residual False -2.81 -2.60 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" C3C BPH L 302 " pdb=" C2C BPH L 302 " pdb=" C4C BPH L 302 " pdb=" CAC BPH L 302 " both_signs ideal model delta sigma weight residual False 2.83 2.65 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 2875 not shown) Planarity restraints: 3587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 SPO 0 101 " -0.419 2.00e-02 2.50e+03 3.76e-01 1.76e+03 pdb=" C12 SPO 0 101 " 0.435 2.00e-02 2.50e+03 pdb=" C13 SPO 0 101 " -0.080 2.00e-02 2.50e+03 pdb=" C14 SPO 0 101 " 0.439 2.00e-02 2.50e+03 pdb=" C15 SPO 0 101 " -0.375 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C36 SPO U 103 " 0.319 2.00e-02 2.50e+03 3.27e-01 1.33e+03 pdb=" C37 SPO U 103 " -0.600 2.00e-02 2.50e+03 pdb=" C38 SPO U 103 " 0.257 2.00e-02 2.50e+03 pdb=" C39 SPO U 103 " 0.064 2.00e-02 2.50e+03 pdb=" C40 SPO U 103 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C36 SPO E 102 " -0.284 2.00e-02 2.50e+03 3.14e-01 1.23e+03 pdb=" C37 SPO E 102 " 0.570 2.00e-02 2.50e+03 pdb=" C38 SPO E 102 " -0.291 2.00e-02 2.50e+03 pdb=" C39 SPO E 102 " -0.024 2.00e-02 2.50e+03 pdb=" C40 SPO E 102 " 0.028 2.00e-02 2.50e+03 ... (remaining 3584 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 242 2.66 - 3.22: 17590 3.22 - 3.78: 33080 3.78 - 4.34: 48393 4.34 - 4.90: 76580 Nonbonded interactions: 175885 Sorted by model distance: nonbonded pdb=" OE1 GLN Q 20 " pdb=" OH TYR R 24 " model vdw 2.100 2.440 nonbonded pdb=" OG1 THR 9 38 " pdb=" O SER 9 40 " model vdw 2.148 2.440 nonbonded pdb=" OG1 THR O 38 " pdb=" O SER O 40 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR K 38 " pdb=" O SER K 40 " model vdw 2.188 2.440 nonbonded pdb=" O ALA 1 28 " pdb=" ND1 HIS 1 32 " model vdw 2.199 2.520 ... (remaining 175880 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 '0' and resid 10 through 49) selection = (chain '8' and resid 10 through 49) selection = (chain 'B' and resid 10 through 49) selection = (chain 'E' and resid 10 through 49) selection = (chain 'G' and resid 10 through 49) selection = (chain 'J' and resid 10 through 49) selection = (chain 'N' and resid 10 through 49) selection = (chain 'P' and resid 10 through 49) selection = (chain 'R' and resid 10 through 49) selection = (chain 'T' and resid 10 through 49) selection = chain 'V' } ncs_group { reference = chain '7' selection = (chain 'W' and (resid 1 through 46 or (resid 101 and (name NB or name ND or name \ C1 or name C10 or name C11 or name C12 or name C13 or name C14 or name C15 or n \ ame C1A or name C1B or name C1C or name C1D or name C2 or name C2A or name C2B o \ r name C2C or name C2D or name C3 or name C3A or name C3B or name C3C or name C3 \ D or name C4 or name C4A or name C4B or name C4C or name C4D or name C5 or name \ C6 or name C7 or name C8 or name C9 or name CAA or name CAB or name CAC or name \ CAD or name CBA or name CBB or name CBC or name CBD or name CED or name CGA or n \ ame CGD or name CHA or name CHB or name CHC or name CHD or name CMA or name CMB \ or name CMC or name CMD or name NA or name NC or name O1A or name O1D or name O2 \ A or name O2D or name OBB or name OBD or name MG )))) } ncs_group { reference = (chain '9' and resid 1 through 54) selection = (chain 'A' and resid 1 through 54) selection = (chain 'D' and resid 1 through 54) selection = (chain 'F' and resid 1 through 54) selection = (chain 'I' and resid 1 through 54) selection = (chain 'K' and resid 1 through 54) selection = (chain 'O' and resid 1 through 54) selection = (chain 'Q' and resid 1 through 54) selection = (chain 'S' and resid 1 through 54) selection = (chain 'U' and resid 1 through 54) } 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: 1.820 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: 7.310 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 54.720 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.170 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:11.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.021 0.222 21391 Z= 1.030 Angle : 1.929 25.914 29397 Z= 0.682 Chirality : 0.042 0.232 2878 Planarity : 0.047 0.376 3587 Dihedral : 16.865 179.212 7546 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.34 % Allowed : 2.44 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.54 (0.18), residues: 2052 helix: 2.62 (0.13), residues: 1312 sheet: -0.67 (0.81), residues: 34 loop : 0.01 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 271 HIS 0.011 0.001 HIS L 168 PHE 0.017 0.002 PHE H 20 TYR 0.012 0.002 TYR H 243 ARG 0.004 0.001 ARG D 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 2.256 Fit side-chains revert: symmetry clash REVERT: H 35 ASN cc_start: 0.8005 (m110) cc_final: 0.7262 (m110) REVERT: B 19 GLU cc_start: 0.7811 (tt0) cc_final: 0.7557 (tt0) REVERT: J 40 LEU cc_start: 0.8958 (tp) cc_final: 0.8535 (mt) REVERT: K 10 ILE cc_start: 0.8376 (pt) cc_final: 0.8111 (pt) REVERT: R 25 MET cc_start: 0.8350 (mmt) cc_final: 0.7866 (mmm) REVERT: V 24 TYR cc_start: 0.8082 (t80) cc_final: 0.7816 (t80) REVERT: 8 26 SER cc_start: 0.7821 (m) cc_final: 0.7523 (m) REVERT: 8 40 LEU cc_start: 0.7555 (tp) cc_final: 0.7324 (tt) outliers start: 6 outliers final: 1 residues processed: 289 average time/residue: 1.2126 time to fit residues: 400.2903 Evaluate side-chains 242 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 2.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN O 42 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 21391 Z= 0.379 Angle : 0.895 17.825 29397 Z= 0.362 Chirality : 0.044 0.184 2878 Planarity : 0.005 0.055 3587 Dihedral : 16.762 179.508 3820 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.27 % Allowed : 6.63 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.03 (0.18), residues: 2052 helix: 2.05 (0.13), residues: 1369 sheet: -0.73 (0.82), residues: 34 loop : -0.01 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 263 HIS 0.013 0.002 HIS M 182 PHE 0.019 0.002 PHE I 11 TYR 0.014 0.002 TYR R 9 ARG 0.005 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 260 time to evaluate : 2.284 Fit side-chains REVERT: L 168 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7749 (p-80) REVERT: L 207 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.5614 (mpt90) REVERT: M 52 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.6844 (tm) REVERT: M 60 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7792 (mt) REVERT: H 1 MET cc_start: 0.8058 (tpt) cc_final: 0.7580 (tpt) REVERT: H 154 ARG cc_start: 0.7585 (OUTLIER) cc_final: 0.6247 (ttm-80) REVERT: H 202 ARG cc_start: 0.7970 (ptp90) cc_final: 0.6798 (ptp90) REVERT: B 19 GLU cc_start: 0.7878 (tt0) cc_final: 0.7590 (tt0) REVERT: K 10 ILE cc_start: 0.8517 (pt) cc_final: 0.8297 (pt) REVERT: R 22 SER cc_start: 0.8196 (t) cc_final: 0.7840 (p) REVERT: R 25 MET cc_start: 0.8346 (mmm) cc_final: 0.8100 (mmm) REVERT: R 26 SER cc_start: 0.8790 (m) cc_final: 0.8471 (m) REVERT: 7 30 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7758 (ttt) REVERT: 8 40 LEU cc_start: 0.7598 (tp) cc_final: 0.7382 (tt) REVERT: X 27 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.6877 (mtp) outliers start: 40 outliers final: 20 residues processed: 277 average time/residue: 1.2693 time to fit residues: 401.6973 Evaluate side-chains 267 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 240 time to evaluate : 2.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 168 HIS Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain X residue 27 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 8.9990 chunk 56 optimal weight: 0.0870 chunk 151 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 0.6980 chunk 162 optimal weight: 0.0970 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 GLN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21391 Z= 0.156 Angle : 0.652 13.625 29397 Z= 0.267 Chirality : 0.036 0.130 2878 Planarity : 0.004 0.036 3587 Dihedral : 15.677 179.172 3820 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 2.04 % Allowed : 9.18 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.66 (0.18), residues: 2052 helix: 2.58 (0.13), residues: 1368 sheet: -0.46 (0.86), residues: 34 loop : 0.12 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.008 0.001 HIS M 182 PHE 0.013 0.001 PHE H 64 TYR 0.011 0.001 TYR K 41 ARG 0.003 0.000 ARG D 15 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 260 time to evaluate : 2.247 Fit side-chains REVERT: L 207 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.5692 (mpt90) REVERT: M 52 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.6911 (tm) REVERT: A 1 MET cc_start: 0.5608 (OUTLIER) cc_final: 0.4194 (tmt) REVERT: A 52 ASN cc_start: 0.7587 (m110) cc_final: 0.7344 (m110) REVERT: B 19 GLU cc_start: 0.7760 (tt0) cc_final: 0.7459 (tt0) REVERT: K 10 ILE cc_start: 0.8402 (pt) cc_final: 0.8144 (pt) REVERT: Q 1 MET cc_start: 0.1669 (mtt) cc_final: -0.1545 (pp-130) REVERT: R 26 SER cc_start: 0.8803 (m) cc_final: 0.8474 (m) REVERT: 9 1 MET cc_start: 0.6311 (mpt) cc_final: 0.6002 (mmt) REVERT: X 27 MET cc_start: 0.7490 (mmt) cc_final: 0.6894 (mtp) outliers start: 36 outliers final: 14 residues processed: 279 average time/residue: 1.2262 time to fit residues: 391.7585 Evaluate side-chains 255 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 238 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 2 residue 23 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 5.9990 chunk 136 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 193 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21391 Z= 0.266 Angle : 0.749 13.925 29397 Z= 0.306 Chirality : 0.040 0.155 2878 Planarity : 0.004 0.042 3587 Dihedral : 15.740 179.458 3820 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.83 % Allowed : 10.09 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.50 (0.18), residues: 2052 helix: 2.42 (0.13), residues: 1372 sheet: -0.55 (0.85), residues: 34 loop : 0.15 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 157 HIS 0.011 0.002 HIS L 153 PHE 0.015 0.002 PHE H 20 TYR 0.013 0.002 TYR K 41 ARG 0.005 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 1.944 Fit side-chains REVERT: L 207 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.5704 (mpt90) REVERT: M 52 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.6855 (tm) REVERT: M 60 LEU cc_start: 0.8387 (tt) cc_final: 0.7832 (mt) REVERT: M 263 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: A 1 MET cc_start: 0.5578 (OUTLIER) cc_final: 0.4186 (tmt) REVERT: B 19 GLU cc_start: 0.7822 (tt0) cc_final: 0.7560 (tt0) REVERT: K 10 ILE cc_start: 0.8471 (pt) cc_final: 0.8208 (pt) REVERT: O 1 MET cc_start: 0.5223 (OUTLIER) cc_final: 0.4085 (mmm) REVERT: O 3 LYS cc_start: 0.8279 (tppp) cc_final: 0.8024 (tppp) REVERT: R 26 SER cc_start: 0.8795 (m) cc_final: 0.8475 (m) REVERT: R 40 LEU cc_start: 0.9058 (tp) cc_final: 0.8685 (tt) REVERT: U 1 MET cc_start: 0.4026 (mpm) cc_final: 0.3725 (mpm) REVERT: U 9 MET cc_start: 0.5492 (mmt) cc_final: 0.5138 (mmm) REVERT: 8 22 SER cc_start: 0.7855 (m) cc_final: 0.7562 (p) REVERT: 9 1 MET cc_start: 0.6244 (mpt) cc_final: 0.6004 (mmt) REVERT: X 27 MET cc_start: 0.7825 (OUTLIER) cc_final: 0.6989 (mtp) REVERT: 2 25 MET cc_start: 0.2570 (OUTLIER) cc_final: 0.1598 (tmm) outliers start: 50 outliers final: 28 residues processed: 265 average time/residue: 1.2064 time to fit residues: 365.3730 Evaluate side-chains 270 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 2.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain U residue 52 ASN Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain X residue 27 MET Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 173 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 199 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 21391 Z= 0.260 Angle : 0.729 13.538 29397 Z= 0.300 Chirality : 0.039 0.156 2878 Planarity : 0.004 0.042 3587 Dihedral : 15.515 179.377 3820 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.51 % Allowed : 10.32 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.50 (0.18), residues: 2052 helix: 2.40 (0.13), residues: 1377 sheet: -0.52 (0.85), residues: 34 loop : 0.18 (0.26), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 157 HIS 0.011 0.002 HIS M 182 PHE 0.015 0.002 PHE O 25 TYR 0.015 0.001 TYR V 24 ARG 0.006 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 241 time to evaluate : 2.086 Fit side-chains REVERT: L 207 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.5650 (mpt90) REVERT: M 52 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.6862 (tm) REVERT: M 60 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7845 (mt) REVERT: M 263 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: H 89 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7737 (mtp85) REVERT: H 154 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.6406 (ttm-80) REVERT: A 1 MET cc_start: 0.5559 (OUTLIER) cc_final: 0.4060 (tmt) REVERT: A 52 ASN cc_start: 0.7596 (m110) cc_final: 0.7362 (m110) REVERT: K 10 ILE cc_start: 0.8492 (pt) cc_final: 0.8197 (pt) REVERT: O 1 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4222 (mmm) REVERT: R 26 SER cc_start: 0.8760 (m) cc_final: 0.8490 (m) REVERT: R 40 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8718 (tt) REVERT: S 1 MET cc_start: 0.6353 (OUTLIER) cc_final: 0.5544 (pp-130) REVERT: U 1 MET cc_start: 0.4131 (mpm) cc_final: 0.3847 (mpm) REVERT: U 9 MET cc_start: 0.5398 (mmt) cc_final: 0.5114 (mmm) REVERT: 8 14 ASP cc_start: 0.7878 (OUTLIER) cc_final: 0.7633 (t70) REVERT: 8 22 SER cc_start: 0.7852 (m) cc_final: 0.7588 (p) REVERT: X 27 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6979 (mtp) REVERT: 2 25 MET cc_start: 0.2357 (OUTLIER) cc_final: 0.1484 (tmm) outliers start: 62 outliers final: 29 residues processed: 275 average time/residue: 1.2955 time to fit residues: 406.5196 Evaluate side-chains 277 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 8 residue 14 ASP Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain X residue 27 MET Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 7.9990 chunk 174 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 193 optimal weight: 0.9980 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN W 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 21391 Z= 0.262 Angle : 0.741 13.263 29397 Z= 0.305 Chirality : 0.040 0.154 2878 Planarity : 0.004 0.041 3587 Dihedral : 15.408 179.422 3820 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.46 % Allowed : 10.60 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.50 (0.18), residues: 2052 helix: 2.39 (0.13), residues: 1376 sheet: -0.50 (0.85), residues: 34 loop : 0.20 (0.26), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 157 HIS 0.012 0.002 HIS C 21 PHE 0.015 0.002 PHE O 25 TYR 0.017 0.002 TYR V 24 ARG 0.004 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 241 time to evaluate : 2.115 Fit side-chains REVERT: L 205 GLU cc_start: 0.7620 (mt-10) cc_final: 0.6900 (mt-10) REVERT: L 207 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.5686 (mpt90) REVERT: M 52 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6796 (tm) REVERT: M 60 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7823 (mt) REVERT: M 263 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7844 (tt0) REVERT: H 89 ARG cc_start: 0.8416 (OUTLIER) cc_final: 0.7723 (mtp85) REVERT: A 1 MET cc_start: 0.5530 (OUTLIER) cc_final: 0.3958 (tmt) REVERT: A 12 ASP cc_start: 0.8521 (t70) cc_final: 0.8317 (t0) REVERT: A 52 ASN cc_start: 0.7636 (m110) cc_final: 0.7410 (m110) REVERT: K 10 ILE cc_start: 0.8545 (pt) cc_final: 0.8263 (pt) REVERT: R 26 SER cc_start: 0.8755 (m) cc_final: 0.8483 (m) REVERT: R 40 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8713 (tt) REVERT: S 1 MET cc_start: 0.6387 (OUTLIER) cc_final: 0.5666 (pp-130) REVERT: U 1 MET cc_start: 0.3968 (mpm) cc_final: 0.3693 (mpm) REVERT: 8 22 SER cc_start: 0.7790 (m) cc_final: 0.7560 (p) REVERT: 2 25 MET cc_start: 0.2293 (OUTLIER) cc_final: 0.1377 (ttt) outliers start: 61 outliers final: 29 residues processed: 273 average time/residue: 1.2523 time to fit residues: 389.8216 Evaluate side-chains 273 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 2.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain T residue 44 ILE Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 141 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 120 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21391 Z= 0.298 Angle : 0.773 13.172 29397 Z= 0.317 Chirality : 0.041 0.159 2878 Planarity : 0.005 0.044 3587 Dihedral : 15.583 179.412 3820 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.17 % Allowed : 11.11 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.38 (0.18), residues: 2052 helix: 2.29 (0.13), residues: 1378 sheet: -0.50 (0.85), residues: 34 loop : 0.16 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 271 HIS 0.012 0.002 HIS M 182 PHE 0.017 0.002 PHE O 25 TYR 0.018 0.002 TYR V 24 ARG 0.005 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: L 168 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7548 (p-80) REVERT: L 207 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.5655 (mpt90) REVERT: M 52 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7304 (mt) REVERT: M 60 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7810 (mt) REVERT: M 263 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: H 89 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.7753 (mtp85) REVERT: H 154 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6424 (ttm-80) REVERT: A 1 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.4039 (tmt) REVERT: A 52 ASN cc_start: 0.7575 (m110) cc_final: 0.7355 (m110) REVERT: K 10 ILE cc_start: 0.8577 (pt) cc_final: 0.8267 (pt) REVERT: R 26 SER cc_start: 0.8764 (m) cc_final: 0.8499 (m) REVERT: R 40 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8720 (tt) REVERT: U 1 MET cc_start: 0.3993 (mpm) cc_final: 0.3747 (mpm) REVERT: C 21 HIS cc_start: 0.2906 (OUTLIER) cc_final: 0.2014 (m-70) REVERT: 8 22 SER cc_start: 0.7817 (m) cc_final: 0.7584 (p) outliers start: 56 outliers final: 34 residues processed: 269 average time/residue: 1.2483 time to fit residues: 383.1482 Evaluate side-chains 280 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 236 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 168 HIS Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 8 residue 30 LEU Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain X residue 60 ASN Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21391 Z= 0.181 Angle : 0.670 13.534 29397 Z= 0.277 Chirality : 0.037 0.167 2878 Planarity : 0.004 0.039 3587 Dihedral : 15.118 179.401 3820 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.66 % Allowed : 11.73 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.68 (0.18), residues: 2052 helix: 2.54 (0.13), residues: 1378 sheet: -0.39 (0.86), residues: 34 loop : 0.24 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.011 0.001 HIS M 182 PHE 0.012 0.001 PHE H 20 TYR 0.024 0.001 TYR V 24 ARG 0.006 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 241 time to evaluate : 2.052 Fit side-chains REVERT: L 207 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.5665 (mpt90) REVERT: M 52 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.6822 (tm) REVERT: M 60 LEU cc_start: 0.8380 (tt) cc_final: 0.7810 (mt) REVERT: M 263 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7794 (tt0) REVERT: H 1 MET cc_start: 0.8166 (tpt) cc_final: 0.7484 (tpt) REVERT: H 89 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.7678 (mtp85) REVERT: H 154 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.6400 (ttm-80) REVERT: A 1 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.3884 (tmt) REVERT: A 12 ASP cc_start: 0.8502 (t70) cc_final: 0.8281 (t0) REVERT: K 10 ILE cc_start: 0.8422 (pt) cc_final: 0.8102 (pt) REVERT: R 26 SER cc_start: 0.8739 (m) cc_final: 0.8505 (m) REVERT: R 40 LEU cc_start: 0.9013 (tp) cc_final: 0.8703 (tt) REVERT: C 21 HIS cc_start: 0.2531 (OUTLIER) cc_final: 0.1560 (m-70) REVERT: 7 30 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7502 (tmm) REVERT: 2 25 MET cc_start: 0.2084 (OUTLIER) cc_final: 0.1259 (ttt) outliers start: 47 outliers final: 29 residues processed: 270 average time/residue: 1.2225 time to fit residues: 377.7056 Evaluate side-chains 276 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 238 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 7 residue 30 MET Chi-restraints excluded: chain 7 residue 33 LEU Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 179 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 117 optimal weight: 9.9990 chunk 189 optimal weight: 7.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21391 Z= 0.269 Angle : 0.743 12.968 29397 Z= 0.305 Chirality : 0.040 0.157 2878 Planarity : 0.004 0.041 3587 Dihedral : 15.371 179.441 3820 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.83 % Allowed : 11.62 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2052 helix: 2.41 (0.13), residues: 1376 sheet: -0.49 (0.86), residues: 34 loop : 0.19 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 271 HIS 0.012 0.002 HIS M 182 PHE 0.015 0.002 PHE O 25 TYR 0.012 0.001 TYR M 198 ARG 0.004 0.001 ARG H 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 239 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 207 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.5649 (mpt90) REVERT: M 52 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.6791 (tm) REVERT: M 60 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7828 (mt) REVERT: M 263 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: H 89 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7728 (mtp85) REVERT: H 154 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.6426 (ttm-80) REVERT: A 1 MET cc_start: 0.5626 (OUTLIER) cc_final: 0.3979 (tmt) REVERT: A 12 ASP cc_start: 0.8561 (t70) cc_final: 0.8332 (t0) REVERT: I 15 ARG cc_start: 0.7259 (OUTLIER) cc_final: 0.7025 (mtm-85) REVERT: K 10 ILE cc_start: 0.8523 (pt) cc_final: 0.8216 (pt) REVERT: R 26 SER cc_start: 0.8763 (m) cc_final: 0.8517 (m) REVERT: R 40 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8700 (tt) REVERT: V 24 TYR cc_start: 0.8012 (t80) cc_final: 0.7714 (t80) REVERT: 8 22 SER cc_start: 0.7757 (m) cc_final: 0.7544 (p) REVERT: X 58 GLN cc_start: 0.6864 (mt0) cc_final: 0.6625 (mt0) outliers start: 50 outliers final: 32 residues processed: 266 average time/residue: 1.3371 time to fit residues: 413.1105 Evaluate side-chains 279 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 238 time to evaluate : 2.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 207 ARG Chi-restraints excluded: chain L residue 216 PHE Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 30 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain I residue 12 ASP Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 40 LEU Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain N residue 40 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain C residue 21 HIS Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 8 residue 26 SER Chi-restraints excluded: chain 0 residue 13 THR Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 132 optimal weight: 30.0000 chunk 199 optimal weight: 0.0770 chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 169 optimal weight: 9.9990 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21391 Z= 0.165 Angle : 0.637 12.871 29397 Z= 0.265 Chirality : 0.036 0.130 2878 Planarity : 0.004 0.037 3587 Dihedral : 14.875 179.388 3820 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.04 % Allowed : 12.59 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % 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: 2.85 (0.18), residues: 2052 helix: 2.66 (0.13), residues: 1377 sheet: 0.42 (1.09), residues: 22 loop : 0.26 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.009 0.001 HIS M 182 PHE 0.012 0.001 PHE L 119 TYR 0.010 0.001 TYR K 41 ARG 0.008 0.000 ARG H 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4104 Ramachandran restraints generated. 2052 Oldfield, 0 Emsley, 2052 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 248 time to evaluate : 2.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: M 52 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.6832 (tm) REVERT: M 60 LEU cc_start: 0.8364 (tt) cc_final: 0.7794 (mt) REVERT: M 263 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7746 (tt0) REVERT: H 154 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.6406 (ttm-80) REVERT: A 1 MET cc_start: 0.5535 (OUTLIER) cc_final: 0.3863 (tmt) REVERT: A 12 ASP cc_start: 0.8457 (t70) cc_final: 0.8241 (t0) REVERT: K 10 ILE cc_start: 0.8387 (pt) cc_final: 0.8073 (pt) REVERT: R 26 SER cc_start: 0.8708 (m) cc_final: 0.8483 (m) REVERT: R 40 LEU cc_start: 0.9015 (tp) cc_final: 0.8712 (tt) REVERT: S 9 MET cc_start: 0.7471 (mmm) cc_final: 0.7209 (mmm) REVERT: V 24 TYR cc_start: 0.7938 (t80) cc_final: 0.7634 (t80) REVERT: X 58 GLN cc_start: 0.6911 (mt0) cc_final: 0.6648 (mt0) outliers start: 36 outliers final: 26 residues processed: 270 average time/residue: 1.2932 time to fit residues: 398.0278 Evaluate side-chains 274 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 244 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 31 VAL Chi-restraints excluded: chain L residue 132 VAL Chi-restraints excluded: chain L residue 244 SER Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 86 LEU Chi-restraints excluded: chain M residue 263 GLU Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 277 THR Chi-restraints excluded: chain H residue 128 HIS Chi-restraints excluded: chain H residue 154 ARG Chi-restraints excluded: chain H residue 185 ASP Chi-restraints excluded: chain H residue 188 THR Chi-restraints excluded: chain H residue 223 THR Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 22 SER Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 46 ILE Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain S residue 30 MET Chi-restraints excluded: chain 7 residue 3 LYS Chi-restraints excluded: chain 8 residue 12 LEU Chi-restraints excluded: chain 8 residue 28 LEU Chi-restraints excluded: chain 1 residue 34 ILE Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 2 residue 25 MET Chi-restraints excluded: chain 2 residue 40 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 163 optimal weight: 0.6980 chunk 20 optimal weight: 0.0670 chunk 29 optimal weight: 20.0000 chunk 139 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 128 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.136443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.100264 restraints weight = 22215.658| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.16 r_work: 0.2708 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21391 Z= 0.190 Angle : 0.661 12.840 29397 Z= 0.274 Chirality : 0.037 0.144 2878 Planarity : 0.004 0.037 3587 Dihedral : 14.920 179.438 3820 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.93 % Allowed : 12.87 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.18), residues: 2052 helix: 2.65 (0.13), residues: 1378 sheet: 0.36 (1.09), residues: 22 loop : 0.27 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.011 0.001 HIS M 182 PHE 0.012 0.001 PHE H 20 TYR 0.013 0.001 TYR B 9 ARG 0.004 0.000 ARG H 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6623.96 seconds wall clock time: 118 minutes 46.97 seconds (7126.97 seconds total)