Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 00:18:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/04_2023/7vy3_32193_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 16 5.49 5 Mg 25 5.21 5 S 69 5.16 5 C 13266 2.51 5 N 2513 2.21 5 O 2941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 18831 Number of models: 1 Model: "" Number of chains: 49 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1910 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" 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: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" 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: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: "V" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 441 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "W" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 339 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 318 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "Z" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "X" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 384 Unusual residues: {'BCL': 2, 'BPH': 1, 'LDA': 1, 'LMT': 2, 'PGV': 1, 'U10': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'PGV:plan-3': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-5': 1, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 2, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 270 Unusual residues: {'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'BCL': 1, 'LMT': 2} 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: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 260 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 2, 'PTY': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 16 Chain: "J" 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: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 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: 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: "P" 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: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'BCL': 2, 'LMT': 2, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" 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: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" 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: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" 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: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LDA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 11.45, per 1000 atoms: 0.61 Number of scatterers: 18831 At special positions: 0 Unit cell: (121.36, 125.46, 113.16, 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 69 16.00 P 16 15.00 Mg 25 11.99 O 2941 8.00 N 2513 7.00 C 13266 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.62 Conformation dependent library (CDL) restraints added in 2.5 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 5 sheets defined 63.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 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: 3.553A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.737A 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: 4.171A 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 removed outlier: 3.866A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 267 removed outlier: 3.509A pdb=" N VAL L 267 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 87 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 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.628A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) 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: 3.801A 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 229 removed outlier: 4.862A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.664A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.983A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 34 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: 3.705A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.508A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.569A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 13 through 44 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 13 through 44 Processing helix chain 'I' and resid 4 through 7 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 43 through 51 removed outlier: 3.505A pdb=" N ALA I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 13 through 37 removed outlier: 3.552A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 Processing helix chain 'P' and resid 15 through 44 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 51 Processing helix chain 'R' and resid 13 through 44 Processing helix chain 'S' and resid 4 through 7 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 13 through 44 Processing helix chain 'V' and resid 4 through 10 removed outlier: 3.830A pdb=" N ILE V 10 " --> pdb=" O ILE V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 37 Processing helix chain 'V' and resid 43 through 51 Processing helix chain 'W' and resid 13 through 44 removed outlier: 4.144A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 37 removed outlier: 3.943A pdb=" N PHE Y 17 " --> pdb=" O PRO Y 13 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL Y 18 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 43 through 46 No H-bonds generated for 'chain 'Y' and resid 43 through 46' Processing helix chain 'Z' and resid 19 through 44 removed outlier: 3.629A pdb=" N SER Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 37 Processing helix chain 'X' and resid 18 through 54 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.573A 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 65 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: 6.695A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.538A 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: 3.656A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2547 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: 5.07 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 5433 1.37 - 1.54: 13750 1.54 - 1.71: 111 1.71 - 1.88: 133 1.88 - 2.05: 100 Bond restraints: 19527 Sorted by residual: bond pdb=" CA7 CDL M 408 " pdb=" OA8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL H 307 " pdb=" OA8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL H 307 " pdb=" OB8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDL M 408 " pdb=" OB8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 ... (remaining 19522 not shown) Histogram of bond angle deviations from ideal: 83.96 - 102.73: 367 102.73 - 121.50: 21883 121.50 - 140.27: 4369 140.27 - 159.04: 28 159.04 - 177.81: 49 Bond angle restraints: 26696 Sorted by residual: angle pdb=" C2 SPO P 102 " pdb=" C1 SPO P 102 " pdb=" C4 SPO P 102 " ideal model delta sigma weight residual 110.23 85.50 24.73 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C1D BCL 1 101 " pdb=" C2D BCL 1 101 " pdb=" CMD BCL 1 101 " ideal model delta sigma weight residual 125.57 139.20 -13.63 1.83e+00 2.99e-01 5.56e+01 angle pdb=" C1D BCL M 402 " pdb=" C2D BCL M 402 " pdb=" CMD BCL M 402 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL Y 103 " pdb=" C2D BCL Y 103 " pdb=" CMD BCL Y 103 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.13 -13.55 1.83e+00 2.99e-01 5.50e+01 ... (remaining 26691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 9791 35.92 - 71.85: 373 71.85 - 107.77: 35 107.77 - 143.69: 7 143.69 - 179.61: 12 Dihedral angle restraints: 10218 sinusoidal: 4895 harmonic: 5323 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.95 -179.05 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL B 103 " pdb=" CGA BCL B 103 " pdb=" O2A BCL B 103 " pdb=" CBA BCL B 103 " ideal model delta sinusoidal sigma weight residual 180.00 116.19 63.81 1 6.00e+00 2.78e-02 1.49e+02 dihedral pdb=" CBD BCL Z 102 " pdb=" CGD BCL Z 102 " pdb=" O2D BCL Z 102 " pdb=" CED BCL Z 102 " ideal model delta sinusoidal sigma weight residual 180.00 140.82 39.18 1 5.00e+00 4.00e-02 8.63e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2177 0.059 - 0.118: 360 0.118 - 0.177: 102 0.177 - 0.236: 18 0.236 - 0.295: 10 Chirality restraints: 2667 Sorted by residual: chirality pdb=" C05 PGV H 301 " pdb=" C04 PGV H 301 " pdb=" C06 PGV H 301 " pdb=" O05 PGV H 301 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C05 PGV M 409 " pdb=" C04 PGV M 409 " pdb=" C06 PGV M 409 " pdb=" O05 PGV M 409 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C05 PGV F 102 " pdb=" C04 PGV F 102 " pdb=" C06 PGV F 102 " pdb=" O05 PGV F 102 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2664 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 D 105 " 0.062 2.00e-02 2.50e+03 1.93e-01 6.53e+02 pdb=" C1M U10 D 105 " -0.255 2.00e-02 2.50e+03 pdb=" C2 U10 D 105 " 0.145 2.00e-02 2.50e+03 pdb=" C3 U10 D 105 " 0.096 2.00e-02 2.50e+03 pdb=" C4 U10 D 105 " -0.289 2.00e-02 2.50e+03 pdb=" C5 U10 D 105 " -0.037 2.00e-02 2.50e+03 pdb=" C6 U10 D 105 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL B 103 " 0.343 3.00e-02 1.11e+03 2.80e-01 4.36e+02 pdb=" CBA BCL B 103 " 0.182 3.00e-02 1.11e+03 pdb=" CGA BCL B 103 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL B 103 " 0.037 3.00e-02 1.11e+03 pdb=" O2A BCL B 103 " -0.485 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 1 101 " -0.310 3.10e-02 1.04e+03 2.87e-01 4.30e+02 pdb=" C4C BCL 1 101 " -0.265 3.10e-02 1.04e+03 pdb=" CHC BCL 1 101 " 0.055 3.10e-02 1.04e+03 pdb=" CHD BCL 1 101 " 0.028 3.10e-02 1.04e+03 pdb=" NC BCL 1 101 " 0.492 3.10e-02 1.04e+03 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 176 2.61 - 3.18: 14761 3.18 - 3.75: 31504 3.75 - 4.33: 46656 4.33 - 4.90: 73889 Nonbonded interactions: 166986 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 2.032 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 404 " model vdw 2.066 2.260 nonbonded pdb=" OG SER A 37 " pdb=" O2' LMT A 102 " model vdw 2.102 2.440 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 404 " model vdw 2.119 2.340 nonbonded pdb=" OE1 GLN S 20 " pdb=" OH TYR T 23 " model vdw 2.184 2.440 ... (remaining 166981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) selection = (chain 'O' and resid 3 through 45) selection = (chain 'V' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) } ncs_group { reference = (chain 'B' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'E' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'G' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'J' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'N' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'P' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'R' and resid 7 through 48) selection = (chain 'T' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'W' and resid 7 through 48) } ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 54)) selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'I' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'S' and (resid 1 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } 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=0.50 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: 2.250 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: 11.990 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 50.020 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.019 0.183 19527 Z= 0.959 Angle : 1.837 24.733 26696 Z= 0.773 Chirality : 0.053 0.295 2667 Planarity : 0.017 0.287 3163 Dihedral : 18.697 179.613 6802 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.19), residues: 1789 helix: 1.12 (0.14), residues: 1147 sheet: -0.62 (1.08), residues: 24 loop : 0.25 (0.26), residues: 618 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.932 Fit side-chains outliers start: 35 outliers final: 15 residues processed: 317 average time/residue: 1.2242 time to fit residues: 440.4617 Evaluate side-chains 225 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 210 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 3 average time/residue: 0.5923 time to fit residues: 4.5514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 30.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 301 HIS H 199 GLN H 206 ASN A 20 GLN B 15 GLN E 17 GLN F 20 GLN I 20 GLN N 17 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 GLN 1 20 GLN X 66 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 19527 Z= 0.175 Angle : 0.673 14.990 26696 Z= 0.265 Chirality : 0.037 0.224 2667 Planarity : 0.004 0.038 3163 Dihedral : 19.293 179.768 3612 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.09 (0.19), residues: 1789 helix: 2.02 (0.14), residues: 1162 sheet: -0.56 (1.11), residues: 24 loop : 0.31 (0.26), residues: 603 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 221 time to evaluate : 1.838 Fit side-chains outliers start: 51 outliers final: 19 residues processed: 250 average time/residue: 1.2244 time to fit residues: 347.6377 Evaluate side-chains 226 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 207 time to evaluate : 2.017 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 14 residues processed: 5 average time/residue: 0.4411 time to fit residues: 5.4191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 127 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN K 20 GLN N 17 GLN S 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 19527 Z= 0.236 Angle : 0.701 15.432 26696 Z= 0.278 Chirality : 0.039 0.239 2667 Planarity : 0.004 0.038 3163 Dihedral : 19.009 179.621 3612 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.16 (0.19), residues: 1789 helix: 2.11 (0.14), residues: 1157 sheet: -0.66 (1.09), residues: 24 loop : 0.27 (0.26), residues: 608 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.954 Fit side-chains outliers start: 50 outliers final: 21 residues processed: 242 average time/residue: 1.3571 time to fit residues: 370.8580 Evaluate side-chains 225 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 204 time to evaluate : 1.878 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 18 residues processed: 3 average time/residue: 0.2297 time to fit residues: 3.4642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 chunk 169 optimal weight: 0.7980 chunk 83 optimal weight: 0.3980 chunk 151 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 19527 Z= 0.141 Angle : 0.607 12.007 26696 Z= 0.236 Chirality : 0.036 0.231 2667 Planarity : 0.003 0.038 3163 Dihedral : 17.930 179.748 3612 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.57 (0.19), residues: 1789 helix: 2.50 (0.14), residues: 1158 sheet: -0.39 (1.13), residues: 24 loop : 0.27 (0.26), residues: 607 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 220 time to evaluate : 2.003 Fit side-chains outliers start: 40 outliers final: 20 residues processed: 245 average time/residue: 1.3094 time to fit residues: 363.7688 Evaluate side-chains 227 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 207 time to evaluate : 1.930 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 5 average time/residue: 0.7786 time to fit residues: 7.1277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 144 optimal weight: 0.0040 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 86 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 264 GLN H 44 ASN A 42 ASN E 15 GLN E 17 GLN I 20 GLN S 20 GLN X 26 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 19527 Z= 0.285 Angle : 0.736 14.985 26696 Z= 0.292 Chirality : 0.041 0.233 2667 Planarity : 0.004 0.041 3163 Dihedral : 18.387 179.527 3612 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.18 (0.19), residues: 1789 helix: 2.14 (0.14), residues: 1164 sheet: -0.62 (1.10), residues: 24 loop : 0.22 (0.27), residues: 601 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 206 time to evaluate : 2.224 Fit side-chains outliers start: 46 outliers final: 25 residues processed: 234 average time/residue: 1.3543 time to fit residues: 357.4778 Evaluate side-chains 224 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 199 time to evaluate : 1.838 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 18 residues processed: 7 average time/residue: 0.6078 time to fit residues: 7.6223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN N 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 19527 Z= 0.308 Angle : 0.757 15.176 26696 Z= 0.301 Chirality : 0.042 0.224 2667 Planarity : 0.004 0.041 3163 Dihedral : 18.524 179.436 3612 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 3.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.19), residues: 1789 helix: 1.94 (0.14), residues: 1155 sheet: -0.63 (1.08), residues: 24 loop : 0.13 (0.26), residues: 610 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 198 time to evaluate : 1.986 Fit side-chains outliers start: 48 outliers final: 23 residues processed: 231 average time/residue: 1.3206 time to fit residues: 345.8347 Evaluate side-chains 218 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 2.054 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.3028 time to fit residues: 3.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 142 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 168 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 GLN E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 19527 Z= 0.169 Angle : 0.641 13.119 26696 Z= 0.252 Chirality : 0.037 0.233 2667 Planarity : 0.003 0.039 3163 Dihedral : 17.498 179.648 3612 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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 (0.19), residues: 1789 helix: 2.32 (0.14), residues: 1166 sheet: -0.29 (1.16), residues: 24 loop : 0.22 (0.26), residues: 599 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.980 Fit side-chains outliers start: 35 outliers final: 22 residues processed: 229 average time/residue: 1.3326 time to fit residues: 345.0164 Evaluate side-chains 222 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 200 time to evaluate : 1.908 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.2481 time to fit residues: 3.1325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.0170 chunk 100 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 132 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 overall best weight: 2.1624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN N 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 19527 Z= 0.249 Angle : 0.709 14.324 26696 Z= 0.281 Chirality : 0.039 0.233 2667 Planarity : 0.004 0.041 3163 Dihedral : 17.628 179.544 3612 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.20 (0.19), residues: 1789 helix: 2.17 (0.14), residues: 1163 sheet: -0.46 (1.13), residues: 24 loop : 0.18 (0.26), residues: 602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 203 time to evaluate : 1.966 Fit side-chains outliers start: 37 outliers final: 26 residues processed: 227 average time/residue: 1.4164 time to fit residues: 360.9867 Evaluate side-chains 224 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 1.912 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.4038 time to fit residues: 6.2892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 123 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 148 optimal weight: 5.9990 chunk 156 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 19527 Z= 0.190 Angle : 0.660 14.920 26696 Z= 0.261 Chirality : 0.038 0.234 2667 Planarity : 0.003 0.040 3163 Dihedral : 17.104 179.636 3612 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.37 (0.19), residues: 1789 helix: 2.33 (0.14), residues: 1161 sheet: -0.33 (1.15), residues: 24 loop : 0.18 (0.26), residues: 604 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 203 time to evaluate : 2.037 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 226 average time/residue: 1.3150 time to fit residues: 337.0463 Evaluate side-chains 219 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 198 time to evaluate : 1.986 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.3474 time to fit residues: 3.5185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 174 optimal weight: 0.0970 chunk 160 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 19527 Z= 0.304 Angle : 0.765 15.735 26696 Z= 0.303 Chirality : 0.042 0.245 2667 Planarity : 0.004 0.042 3163 Dihedral : 17.591 179.417 3612 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.19), residues: 1789 helix: 1.98 (0.14), residues: 1155 sheet: -0.60 (1.10), residues: 24 loop : 0.10 (0.26), residues: 610 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.971 Fit side-chains outliers start: 26 outliers final: 23 residues processed: 220 average time/residue: 1.3319 time to fit residues: 330.8891 Evaluate side-chains 221 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 1.918 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 20 residues processed: 3 average time/residue: 0.2938 time to fit residues: 3.7670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 15 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.107301 restraints weight = 28151.747| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.45 r_work: 0.2885 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 19527 Z= 0.156 Angle : 0.631 15.838 26696 Z= 0.249 Chirality : 0.037 0.229 2667 Planarity : 0.003 0.039 3163 Dihedral : 16.480 179.641 3612 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.19), residues: 1789 helix: 2.43 (0.14), residues: 1161 sheet: -0.19 (1.17), residues: 24 loop : 0.18 (0.26), residues: 604 =============================================================================== Job complete usr+sys time: 6180.72 seconds wall clock time: 111 minutes 21.40 seconds (6681.40 seconds total)