Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 09:18:10 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/10_2023/7vnm_32042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/10_2023/7vnm_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_32042/10_2023/7vnm_32042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/10_2023/7vnm_32042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/10_2023/7vnm_32042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnm_32042/10_2023/7vnm_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-1.21rc1-5097/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: 42 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: 10.90, per 1000 atoms: 0.53 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: 8.45 Conformation dependent library (CDL) restraints added in 2.5 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: 2.49 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: 5.94 Time building geometry restraints manager: 9.09 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: 10920 35.84 - 71.68: 342 71.68 - 107.53: 41 107.53 - 143.37: 3 143.37 - 179.21: 1 Dihedral angle restraints: 11307 sinusoidal: 5195 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 11304 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: 1.700 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: 0.020 Extract box with map and model: 7.170 Check model and map are aligned: 0.630 Set scattering table: 0.200 Process input model: 52.820 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 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:19.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.660 ------------------------------------------------------------------------------- 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 : 16.381 179.212 7377 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 *********************** 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 : 2.022 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 289 average time/residue: 1.2362 time to fit residues: 408.4152 Evaluate side-chains 242 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 241 time to evaluate : 1.983 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 2.4724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 199 GLN O 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 21391 Z= 0.378 Angle : 0.888 17.399 29397 Z= 0.360 Chirality : 0.044 0.178 2878 Planarity : 0.005 0.056 3587 Dihedral : 15.979 179.472 3650 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.38 % Allowed : 6.63 % Favored : 90.99 % 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: 2.06 (0.18), residues: 2052 helix: 2.08 (0.13), residues: 1370 sheet: -0.72 (0.82), residues: 34 loop : -0.00 (0.25), residues: 648 *********************** 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 298 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 256 time to evaluate : 1.933 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 21 residues processed: 272 average time/residue: 1.2432 time to fit residues: 386.5197 Evaluate side-chains 262 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 241 time to evaluate : 1.971 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 11 residues processed: 10 average time/residue: 0.7538 time to fit residues: 11.7722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 151 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 chunk 180 optimal weight: 2.9990 chunk 62 optimal weight: 0.0050 chunk 145 optimal weight: 3.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21391 Z= 0.150 Angle : 0.635 13.544 29397 Z= 0.260 Chirality : 0.036 0.132 2878 Planarity : 0.004 0.036 3587 Dihedral : 14.980 179.145 3650 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.15 % Allowed : 9.35 % Favored : 88.49 % 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: 2.78 (0.18), residues: 2052 helix: 2.68 (0.13), residues: 1369 sheet: -0.28 (0.88), residues: 34 loop : 0.15 (0.26), residues: 649 *********************** 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 293 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 255 time to evaluate : 1.955 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 275 average time/residue: 1.1997 time to fit residues: 378.2755 Evaluate side-chains 252 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 235 time to evaluate : 1.979 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 13 residues processed: 4 average time/residue: 0.2083 time to fit residues: 4.0054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2061 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= 0.268 Angle : 0.745 13.962 29397 Z= 0.305 Chirality : 0.040 0.143 2878 Planarity : 0.005 0.060 3587 Dihedral : 15.125 179.324 3650 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.27 % Allowed : 10.66 % 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: 2.59 (0.18), residues: 2052 helix: 2.48 (0.13), residues: 1377 sheet: -0.62 (0.85), residues: 34 loop : 0.20 (0.26), residues: 641 *********************** 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 279 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 239 time to evaluate : 2.263 Fit side-chains outliers start: 40 outliers final: 23 residues processed: 262 average time/residue: 1.2605 time to fit residues: 377.7464 Evaluate side-chains 258 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 235 time to evaluate : 1.977 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 7 average time/residue: 0.2239 time to fit residues: 5.1966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- 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** N 16 GLN W 20 GLN 7 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 21391 Z= 0.377 Angle : 0.863 15.173 29397 Z= 0.350 Chirality : 0.044 0.184 2878 Planarity : 0.005 0.056 3587 Dihedral : 15.576 179.502 3650 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.89 % Allowed : 10.94 % 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: 2.14 (0.18), residues: 2052 helix: 2.11 (0.13), residues: 1377 sheet: -0.87 (0.83), residues: 34 loop : 0.10 (0.26), residues: 641 *********************** 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 294 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 243 time to evaluate : 1.992 Fit side-chains outliers start: 51 outliers final: 29 residues processed: 276 average time/residue: 1.3129 time to fit residues: 412.3604 Evaluate side-chains 259 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 230 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 21 residues processed: 8 average time/residue: 0.4040 time to fit residues: 6.9755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 4.9990 chunk 174 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 160 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- 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 H 199 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 21391 Z= 0.242 Angle : 0.725 13.377 29397 Z= 0.298 Chirality : 0.039 0.152 2878 Planarity : 0.004 0.041 3587 Dihedral : 14.975 179.375 3650 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.44 % Allowed : 11.79 % Favored : 85.77 % 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: 2.42 (0.18), residues: 2052 helix: 2.34 (0.13), residues: 1376 sheet: -0.80 (0.85), residues: 34 loop : 0.16 (0.25), residues: 642 *********************** 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 277 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 234 time to evaluate : 2.254 Fit side-chains outliers start: 43 outliers final: 28 residues processed: 261 average time/residue: 1.2405 time to fit residues: 370.4908 Evaluate side-chains 259 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 1.818 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 21 residues processed: 7 average time/residue: 0.2483 time to fit residues: 5.4331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 109 optimal weight: 4.9990 chunk 162 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 0.0270 chunk 120 optimal weight: 9.9990 chunk 117 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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: 0.8463 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 21391 Z= 0.264 Angle : 0.749 13.245 29397 Z= 0.306 Chirality : 0.040 0.163 2878 Planarity : 0.004 0.041 3587 Dihedral : 14.954 179.413 3650 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.66 % Allowed : 11.96 % 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: 2.38 (0.18), residues: 2052 helix: 2.31 (0.13), residues: 1377 sheet: -0.82 (0.85), residues: 34 loop : 0.14 (0.25), residues: 641 *********************** 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 283 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 236 time to evaluate : 2.199 Fit side-chains outliers start: 47 outliers final: 33 residues processed: 262 average time/residue: 1.2726 time to fit residues: 380.6068 Evaluate side-chains 265 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.996 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 23 residues processed: 11 average time/residue: 0.6127 time to fit residues: 11.1480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 115 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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: 0.8433 moved from start: 0.2572 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= 0.192 Angle : 0.671 13.053 29397 Z= 0.276 Chirality : 0.037 0.150 2878 Planarity : 0.004 0.038 3587 Dihedral : 14.607 179.407 3650 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.87 % Allowed : 12.81 % Favored : 85.32 % 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: 2.63 (0.18), residues: 2052 helix: 2.52 (0.13), residues: 1378 sheet: -0.72 (0.86), residues: 34 loop : 0.21 (0.25), residues: 640 *********************** 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 272 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 239 time to evaluate : 2.006 Fit side-chains outliers start: 33 outliers final: 24 residues processed: 265 average time/residue: 1.2434 time to fit residues: 377.5728 Evaluate side-chains 259 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.823 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.4574 time to fit residues: 4.9106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 179 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 117 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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: 0.8455 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21391 Z= 0.246 Angle : 0.725 13.010 29397 Z= 0.298 Chirality : 0.039 0.151 2878 Planarity : 0.004 0.039 3587 Dihedral : 14.752 179.426 3650 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.70 % Allowed : 13.10 % 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: 2.53 (0.18), residues: 2052 helix: 2.43 (0.13), residues: 1378 sheet: -0.77 (0.86), residues: 34 loop : 0.18 (0.25), residues: 640 *********************** 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 264 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 234 time to evaluate : 2.101 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 24 residues processed: 256 average time/residue: 1.2824 time to fit residues: 375.4383 Evaluate side-chains 257 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 1.982 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.2483 time to fit residues: 4.3746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 199 optimal weight: 0.0970 chunk 183 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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: 0.8466 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 21391 Z= 0.276 Angle : 0.762 12.948 29397 Z= 0.312 Chirality : 0.040 0.158 2878 Planarity : 0.005 0.042 3587 Dihedral : 14.959 179.416 3650 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.59 % Allowed : 13.15 % Favored : 85.26 % 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: 2.75 (0.18), residues: 2052 helix: 2.73 (0.13), residues: 1310 sheet: -0.84 (0.86), residues: 34 loop : 0.24 (0.24), residues: 708 ********************** 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 260 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 2.069 Fit side-chains revert: symmetry clash outliers start: 28 outliers final: 21 residues processed: 255 average time/residue: 1.3112 time to fit residues: 382.7192 Evaluate side-chains 251 residues out of total 1764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 230 time to evaluate : 2.147 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.6874 time to fit residues: 4.1595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 0.8980 chunk 146 optimal weight: 0.3980 chunk 23 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.098783 restraints weight = 22201.678| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.19 r_work: 0.2674 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21391 Z= 0.195 Angle : 0.681 12.864 29397 Z= 0.281 Chirality : 0.038 0.146 2878 Planarity : 0.004 0.038 3587 Dihedral : 14.605 179.407 3650 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.36 % Allowed : 13.32 % Favored : 85.32 % 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: 2.62 (0.18), residues: 2052 helix: 2.50 (0.13), residues: 1378 sheet: -0.67 (0.87), residues: 34 loop : 0.20 (0.25), residues: 640 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6495.55 seconds wall clock time: 116 minutes 41.10 seconds (7001.10 seconds total)