Starting phenix.real_space_refine on Sat Feb 17 12:13:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yml_33931/02_2024/7yml_33931_updated.pdb" } resolution = 2.6 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= 0.004 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 25 5.21 5 S 72 5.16 5 C 13028 2.51 5 N 2496 2.21 5 O 2923 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18554 Number of models: 1 Model: "" Number of chains: 50 Chain: "L" Number of atoms: 2239 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Conformer: "B" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} bond proxies already assigned to first conformer: 2308 Chain: "M" Number of atoms: 2417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2417 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 291} Chain: "H" Number of atoms: 1956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1956 Classifications: {'peptide': 248} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 227} Chain: "A" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 374 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} 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: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: "E" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "F" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "K" Number of atoms: 452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 452 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 453 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 334 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: 462 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 56, 454 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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 Conformer: "B" Number of residues, atoms: 56, 454 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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 bond proxies already assigned to first conformer: 460 Chain: "T" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 338 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 457 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} 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: "W" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 309 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 39} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "Y" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 335 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain: "Z" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 224 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 29} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "X" Number of atoms: 502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 502 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 5, 'TRANS': 59} Chain: "L" Number of atoms: 513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 513 Unusual residues: {'BCL': 2, 'BPH': 1, 'LDA': 1, 'LMT': 3, 'PEE': 1, 'PGV': 1, 'U10': 2} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'PGV:plan-3': 1, 'U10:plan-9': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 13 Chain: "M" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 685 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'LDA': 4, 'LMT': 5, 'PGV': 4, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 20} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 124 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 112 Planarities with less than four sites: {'PGV:plan-3': 3, 'U10:plan-8': 1, 'U10:plan-9': 2, 'U10:plan-11': 2, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 2, 'U10:plan-3': 1} Unresolved non-hydrogen planarities: 56 Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 107 Unusual residues: {'LDA': 2, 'PGV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 93 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 208 Unusual residues: {'BCL': 1, 'LDA': 1, 'SPO': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 190 Unusual residues: {'BCL': 2, 'MYR': 1, 'SPO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" 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: "I" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 185 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" 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: "O" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 166 Unusual residues: {'BCL': 1, 'LDA': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 157 Unusual residues: {'BCL': 1, 'LDA': 2, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" 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: "S" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'BCL': 1, 'LMT': 2, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Chain: "T" 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: "V" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "W" 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: "Y" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 121 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "Z" 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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 70 Unusual residues: {'LMT': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 11.38, per 1000 atoms: 0.61 Number of scatterers: 18554 At special positions: 0 Unit cell: (128.74, 104.96, 126.28, 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 72 16.00 P 9 15.00 Mg 25 11.99 O 2923 8.00 N 2496 7.00 C 13028 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=25, symmetry=0 Number of additional bonds: simple=25, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.09 Conformation dependent library (CDL) restraints added in 3.2 seconds 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 81 helices and 5 sheets defined 63.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'L' and resid 8 through 10 No H-bonds generated for 'chain 'L' and resid 8 through 10' Processing helix chain 'L' and resid 34 through 57 Processing helix chain 'L' and resid 72 through 74 No H-bonds generated for 'chain 'L' and resid 72 through 74' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 85 through 112 Processing helix chain 'L' and resid 117 through 133 removed outlier: 3.783A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 139 Processing helix chain 'L' and resid 143 through 145 No H-bonds generated for 'chain 'L' and resid 143 through 145' Processing helix chain 'L' and resid 153 through 165 removed outlier: 4.200A pdb=" N TYR L 165 " --> pdb=" O THR L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 170 No H-bonds generated for 'chain 'L' and resid 168 through 170' Processing helix chain 'L' and resid 172 through 199 Processing helix chain 'L' and resid 210 through 220 Processing helix chain 'L' and resid 227 through 251 removed outlier: 3.781A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 260 through 268 removed outlier: 4.058A pdb=" N TRP L 264 " --> pdb=" O TRP L 260 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR L 265 " --> pdb=" O SER L 261 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP L 266 " --> pdb=" O ASP L 262 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TRP L 267 " --> pdb=" O TRP L 263 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL L 268 " --> pdb=" O TRP L 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 260 through 268' Processing helix chain 'M' and resid 27 through 29 No H-bonds generated for 'chain 'M' and resid 27 through 29' Processing helix chain 'M' and resid 37 through 40 Processing helix chain 'M' and resid 55 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 108 through 110 No H-bonds generated for 'chain 'M' and resid 108 through 110' Processing helix chain 'M' and resid 112 through 138 removed outlier: 3.507A pdb=" N ALA M 136 " --> pdb=" O VAL M 132 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 160 removed outlier: 3.519A pdb=" N ALA M 152 " --> pdb=" O ALA M 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 167 Processing helix chain 'M' and resid 170 through 172 No H-bonds generated for 'chain 'M' and resid 170 through 172' Processing helix chain 'M' and resid 178 through 191 removed outlier: 3.630A pdb=" N LEU M 182 " --> pdb=" O ILE M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 197 No H-bonds generated for 'chain 'M' and resid 195 through 197' Processing helix chain 'M' and resid 199 through 224 Processing helix chain 'M' and resid 226 through 228 No H-bonds generated for 'chain 'M' and resid 226 through 228' Processing helix chain 'M' and resid 233 through 238 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.624A pdb=" N TRP M 251 " --> pdb=" O ALA M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 288 removed outlier: 3.790A pdb=" N VAL M 275 " --> pdb=" O MET M 271 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N THR M 276 " --> pdb=" O ALA M 272 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY M 287 " --> pdb=" O ILE M 283 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR M 288 " --> pdb=" O LEU M 284 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 300 Processing helix chain 'H' and resid 12 through 35 Processing helix chain 'H' and resid 77 through 82 Processing helix chain 'H' and resid 107 through 110 No H-bonds generated for 'chain 'H' and resid 107 through 110' Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 137 through 139 No H-bonds generated for 'chain 'H' and resid 137 through 139' Processing helix chain 'H' and resid 195 through 197 No H-bonds generated for 'chain 'H' and resid 195 through 197' Processing helix chain 'H' and resid 212 through 214 No H-bonds generated for 'chain 'H' and resid 212 through 214' Processing helix chain 'H' and resid 229 through 245 removed outlier: 3.522A pdb=" N GLY H 242 " --> pdb=" O TYR H 238 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N TYR H 243 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N MET H 244 " --> pdb=" O ALA H 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 removed outlier: 4.039A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER A 37 " --> pdb=" O LEU A 33 " (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 51 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 51 Processing helix chain 'G' and resid 13 through 44 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 13 through 44 Processing helix chain 'K' and resid 4 through 9 removed outlier: 3.613A pdb=" N TRP K 8 " --> pdb=" O TYR K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 51 Processing helix chain 'N' and resid 13 through 44 removed outlier: 3.518A pdb=" N VAL N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 3.640A pdb=" N TRP O 8 " --> pdb=" O TYR O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 37 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 removed outlier: 3.551A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) 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 9 removed outlier: 3.616A pdb=" N ILE S 7 " --> pdb=" O PHE S 4 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP S 8 " --> pdb=" O TYR S 5 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 44 through 50 removed outlier: 5.139A pdb=" N ALA S 49 " --> pdb=" O THR S 45 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 44 Processing helix chain 'V' and resid 4 through 9 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 45 removed outlier: 3.921A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU W 19 " --> pdb=" O GLN W 15 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 37 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 51 Processing helix chain 'Z' and resid 19 through 44 Processing helix chain 'X' and resid 15 through 53 Proline residue: X 36 - end of helix removed outlier: 3.889A pdb=" N MET X 53 " --> pdb=" O GLY X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 60 No H-bonds generated for 'chain 'X' and resid 58 through 60' Processing sheet with id= A, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.634A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 64 Processing sheet with id= C, first strand: chain 'H' and resid 90 through 92 Processing sheet with id= D, first strand: chain 'H' and resid 134 through 136 removed outlier: 6.820A pdb=" N GLU H 182 " --> pdb=" O VAL H 167 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N MET H 169 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N TYR H 180 " --> pdb=" O MET H 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 204 through 206 removed outlier: 3.830A pdb=" N GLY H 164 " --> pdb=" O VAL H 155 " (cutoff:3.500A) 857 hydrogen bonds defined for protein. 2493 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: 4.70 Time building geometry restraints manager: 8.46 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: 5532 1.37 - 1.54: 13298 1.54 - 1.71: 147 1.71 - 1.88: 140 1.88 - 2.05: 100 Bond restraints: 19217 Sorted by residual: bond pdb=" NA BCL Z 101 " pdb="MG BCL Z 101 " ideal model delta sigma weight residual 2.170 1.991 0.179 2.40e-02 1.74e+03 5.59e+01 bond pdb=" C8 U10 M 407 " pdb=" C9 U10 M 407 " ideal model delta sigma weight residual 1.470 1.320 0.150 2.00e-02 2.50e+03 5.59e+01 bond pdb=" C8 U10 L 303 " pdb=" C9 U10 L 303 " ideal model delta sigma weight residual 1.470 1.321 0.149 2.00e-02 2.50e+03 5.59e+01 bond pdb=" NA BCL A 101 " pdb="MG BCL A 101 " ideal model delta sigma weight residual 2.170 1.993 0.177 2.40e-02 1.74e+03 5.44e+01 bond pdb=" C8 U10 M 401 " pdb=" C9 U10 M 401 " ideal model delta sigma weight residual 1.470 1.323 0.147 2.00e-02 2.50e+03 5.44e+01 ... (remaining 19212 not shown) Histogram of bond angle deviations from ideal: 83.92 - 102.54: 362 102.54 - 121.16: 21152 121.16 - 139.79: 4729 139.79 - 158.41: 28 158.41 - 177.03: 49 Bond angle restraints: 26320 Sorted by residual: angle pdb=" C2 SPO R 101 " pdb=" C1 SPO R 101 " pdb=" C4 SPO R 101 " ideal model delta sigma weight residual 110.23 86.74 23.49 3.00e+00 1.11e-01 6.13e+01 angle pdb=" C1D BCL A 101 " pdb=" C2D BCL A 101 " pdb=" CMD BCL A 101 " ideal model delta sigma weight residual 125.57 139.44 -13.87 1.83e+00 2.99e-01 5.76e+01 angle pdb=" C1D BCL V 101 " pdb=" C2D BCL V 101 " pdb=" CMD BCL V 101 " ideal model delta sigma weight residual 125.57 139.33 -13.76 1.83e+00 2.99e-01 5.67e+01 angle pdb=" C1D BCL S 103 " pdb=" C2D BCL S 103 " pdb=" CMD BCL S 103 " ideal model delta sigma weight residual 125.57 139.32 -13.74 1.83e+00 2.99e-01 5.65e+01 angle pdb=" C1D BCL F 101 " pdb=" C2D BCL F 101 " pdb=" CMD BCL F 101 " ideal model delta sigma weight residual 125.57 139.10 -13.53 1.83e+00 2.99e-01 5.48e+01 ... (remaining 26315 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.10: 10485 35.10 - 70.20: 431 70.20 - 105.30: 113 105.30 - 140.41: 58 140.41 - 175.51: 19 Dihedral angle restraints: 11106 sinusoidal: 5779 harmonic: 5327 Sorted by residual: dihedral pdb=" C1 BCL M 403 " pdb=" CGA BCL M 403 " pdb=" O2A BCL M 403 " pdb=" CBA BCL M 403 " ideal model delta sinusoidal sigma weight residual 180.00 109.53 70.47 1 6.00e+00 2.78e-02 1.78e+02 dihedral pdb=" C1 BCL B 101 " pdb=" CGA BCL B 101 " pdb=" O2A BCL B 101 " pdb=" CBA BCL B 101 " ideal model delta sinusoidal sigma weight residual 180.00 110.38 69.62 1 6.00e+00 2.78e-02 1.74e+02 dihedral pdb=" CBD BCL Z 101 " pdb=" CGD BCL Z 101 " pdb=" O2D BCL Z 101 " pdb=" CED BCL Z 101 " ideal model delta sinusoidal sigma weight residual 180.00 135.84 44.16 1 5.00e+00 4.00e-02 1.09e+02 ... (remaining 11103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 2169 0.057 - 0.115: 405 0.115 - 0.172: 103 0.172 - 0.229: 29 0.229 - 0.287: 12 Chirality restraints: 2718 Sorted by residual: chirality pdb=" C05 PGV L 305 " pdb=" C04 PGV L 305 " pdb=" C06 PGV L 305 " pdb=" O05 PGV L 305 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C05 PGV H 304 " pdb=" C04 PGV H 304 " pdb=" C06 PGV H 304 " pdb=" O05 PGV H 304 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C05 PGV H 303 " pdb=" C04 PGV H 303 " pdb=" C06 PGV H 303 " pdb=" O05 PGV H 303 " 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 2715 not shown) Planarity restraints: 3109 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 403 " 0.372 3.00e-02 1.11e+03 3.02e-01 5.08e+02 pdb=" CBA BCL M 403 " 0.178 3.00e-02 1.11e+03 pdb=" CGA BCL M 403 " -0.086 3.00e-02 1.11e+03 pdb=" O1A BCL M 403 " 0.061 3.00e-02 1.11e+03 pdb=" O2A BCL M 403 " -0.525 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL B 101 " 0.359 3.00e-02 1.11e+03 2.94e-01 4.81e+02 pdb=" CBA BCL B 101 " 0.173 3.00e-02 1.11e+03 pdb=" CGA BCL B 101 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL B 101 " 0.061 3.00e-02 1.11e+03 pdb=" O2A BCL B 101 " -0.515 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL A 101 " 0.123 3.10e-02 1.04e+03 2.69e-01 3.77e+02 pdb=" C4C BCL A 101 " 0.056 3.10e-02 1.04e+03 pdb=" CHC BCL A 101 " -0.321 3.10e-02 1.04e+03 pdb=" CHD BCL A 101 " -0.269 3.10e-02 1.04e+03 pdb=" NC BCL A 101 " 0.411 3.10e-02 1.04e+03 ... (remaining 3106 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 203 2.61 - 3.18: 15008 3.18 - 3.75: 30807 3.75 - 4.33: 46297 4.33 - 4.90: 73026 Nonbonded interactions: 165341 Sorted by model distance: nonbonded pdb=" OE2 GLU M 233 " pdb="FE FE M 406 " model vdw 2.035 2.260 nonbonded pdb=" OE1 GLU M 233 " pdb="FE FE M 406 " model vdw 2.078 2.260 nonbonded pdb=" NE2 HIS M 218 " pdb="FE FE M 406 " model vdw 2.094 2.340 nonbonded pdb=" NE2 HIS L 191 " pdb="FE FE M 406 " model vdw 2.140 2.340 nonbonded pdb=" O6' LMT M 409 " pdb=" O1 LDA H 301 " model vdw 2.167 2.440 ... (remaining 165336 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 'B' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 through 48)) selection = (chain 'T' and ((resid 8 through 9 and (name N or name CA or name C or name O or \ name CB )) or resid 10 or (resid 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 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 8 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'O' 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 14 or resid 16 through 54)) 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'S' and (resid 1 through 2 or (resid 3 and (name N or name CA or name C o \ r name O or name CB )) or resid 4 through 14 or resid 16 through 54)) selection = (chain 'V' 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 or (resid 3 and (name N or name CA or name C \ or name O or name CB )) or resid 4 through 14 or resid 16 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=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: 3.580 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: 14.840 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 50.920 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.070 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:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 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 0.179 19217 Z= 1.004 Angle : 1.857 23.495 26320 Z= 0.775 Chirality : 0.056 0.287 2718 Planarity : 0.018 0.302 3109 Dihedral : 22.916 175.507 7672 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.88 % Allowed : 4.09 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1.32 (0.19), residues: 1793 helix: 1.44 (0.14), residues: 1098 sheet: -0.46 (1.04), residues: 28 loop : 0.12 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 8 HIS 0.007 0.001 HIS L 154 PHE 0.017 0.002 PHE L 147 TYR 0.032 0.002 TYR M 302 ARG 0.003 0.001 ARG T 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 1.789 Fit side-chains revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8672 (mttm) cc_final: 0.8460 (mmtp) REVERT: M 109 LYS cc_start: 0.8774 (ttmm) cc_final: 0.8561 (ttmm) REVERT: M 137 ASP cc_start: 0.8919 (t0) cc_final: 0.8547 (t70) REVERT: E 6 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4626 (tm) REVERT: I 15 ARG cc_start: 0.8331 (mmm-85) cc_final: 0.7187 (tmt170) REVERT: K 4 PHE cc_start: 0.8797 (m-80) cc_final: 0.8557 (m-10) REVERT: K 15 ARG cc_start: 0.8092 (mtt90) cc_final: 0.7828 (mtt90) REVERT: O 15 ARG cc_start: 0.7368 (mmm160) cc_final: 0.6438 (ttp-110) REVERT: P 24 MET cc_start: 0.8658 (mmm) cc_final: 0.8398 (mmm) REVERT: Q 6 LYS cc_start: 0.8828 (mmtp) cc_final: 0.8614 (ttmm) REVERT: R 13 ASP cc_start: 0.8016 (t0) cc_final: 0.7775 (t0) REVERT: S 5 TYR cc_start: 0.7954 (p90) cc_final: 0.6997 (p90) REVERT: T 17 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7723 (mp10) REVERT: V 11 PHE cc_start: 0.7278 (m-80) cc_final: 0.6788 (m-10) REVERT: V 30 LEU cc_start: 0.8317 (tt) cc_final: 0.8087 (tm) REVERT: W 17 GLN cc_start: 0.7268 (mm110) cc_final: 0.6977 (mm110) REVERT: X 9 ASP cc_start: 0.7256 (t0) cc_final: 0.6918 (t0) outliers start: 28 outliers final: 11 residues processed: 270 average time/residue: 1.2213 time to fit residues: 378.2298 Evaluate side-chains 225 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain Y residue 32 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 132 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 0.0370 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 77 ASN L 117 HIS M 12 GLN M 44 ASN M 110 GLN M 144 HIS H 44 ASN I 20 GLN ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 15 GLN O 51 HIS ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19217 Z= 0.189 Angle : 0.745 17.473 26320 Z= 0.287 Chirality : 0.042 0.488 2718 Planarity : 0.004 0.048 3109 Dihedral : 21.337 175.659 4601 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.28 % Allowed : 8.59 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.19 (0.19), residues: 1793 helix: 2.30 (0.14), residues: 1099 sheet: 0.04 (1.06), residues: 28 loop : 0.12 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.008 0.001 HIS L 154 PHE 0.019 0.001 PHE L 272 TYR 0.026 0.001 TYR M 302 ARG 0.003 0.000 ARG Y 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 231 time to evaluate : 1.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8574 (mttm) cc_final: 0.8335 (mmtp) REVERT: M 109 LYS cc_start: 0.8778 (ttmm) cc_final: 0.8556 (ttmm) REVERT: M 137 ASP cc_start: 0.8854 (t0) cc_final: 0.8530 (t70) REVERT: E 6 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4425 (tm) REVERT: I 15 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.6953 (tmt170) REVERT: K 4 PHE cc_start: 0.8847 (m-80) cc_final: 0.8622 (m-10) REVERT: K 15 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7710 (mtt90) REVERT: O 15 ARG cc_start: 0.7190 (mmm160) cc_final: 0.6458 (ttp-170) REVERT: S 5 TYR cc_start: 0.7711 (p90) cc_final: 0.7091 (p90) REVERT: S 6 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8105 (mptp) REVERT: T 39 LEU cc_start: 0.8859 (tp) cc_final: 0.8547 (mt) REVERT: V 11 PHE cc_start: 0.7310 (m-80) cc_final: 0.6848 (m-10) REVERT: V 30 LEU cc_start: 0.8242 (tt) cc_final: 0.7917 (tm) REVERT: X 9 ASP cc_start: 0.7222 (t0) cc_final: 0.6713 (t0) outliers start: 34 outliers final: 12 residues processed: 249 average time/residue: 1.1067 time to fit residues: 316.3310 Evaluate side-chains 220 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 207 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 135 GLN H 176 GLN N 15 GLN N 17 GLN P 20 HIS S 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 19217 Z= 0.332 Angle : 0.779 16.296 26320 Z= 0.304 Chirality : 0.045 0.575 2718 Planarity : 0.004 0.050 3109 Dihedral : 19.009 178.794 4593 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.02 % Allowed : 9.66 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.21 (0.19), residues: 1793 helix: 2.36 (0.14), residues: 1115 sheet: -0.07 (1.07), residues: 28 loop : -0.01 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 156 HIS 0.013 0.002 HIS L 154 PHE 0.021 0.002 PHE H 20 TYR 0.030 0.002 TYR M 302 ARG 0.002 0.000 ARG L 218 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 215 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8635 (mttm) cc_final: 0.8415 (mmtp) REVERT: M 109 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8467 (ttmm) REVERT: M 137 ASP cc_start: 0.8862 (t0) cc_final: 0.8482 (t70) REVERT: B 36 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8345 (mp) REVERT: G 14 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: I 15 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.6948 (tmt170) REVERT: K 15 ARG cc_start: 0.8021 (mtt90) cc_final: 0.7685 (mtt90) REVERT: N 12 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8203 (p) REVERT: O 12 ASP cc_start: 0.8185 (t0) cc_final: 0.7870 (t0) REVERT: O 15 ARG cc_start: 0.7148 (mmm160) cc_final: 0.6412 (ttp-170) REVERT: S 5 TYR cc_start: 0.7508 (p90) cc_final: 0.7049 (p90) REVERT: S 6 LYS cc_start: 0.8529 (mtpt) cc_final: 0.8145 (mptp) REVERT: S 9 LEU cc_start: 0.7678 (mt) cc_final: 0.7462 (mm) REVERT: V 11 PHE cc_start: 0.7325 (m-80) cc_final: 0.6834 (m-10) REVERT: V 30 LEU cc_start: 0.8266 (tt) cc_final: 0.8000 (tm) REVERT: X 9 ASP cc_start: 0.7180 (t0) cc_final: 0.6851 (t0) outliers start: 45 outliers final: 25 residues processed: 244 average time/residue: 1.1580 time to fit residues: 323.1573 Evaluate side-chains 236 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 39 LEU Chi-restraints excluded: chain O residue 2 SER Chi-restraints excluded: chain P residue 17 GLN Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 34 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 17 GLN S 20 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19217 Z= 0.208 Angle : 0.703 14.254 26320 Z= 0.273 Chirality : 0.041 0.565 2718 Planarity : 0.003 0.049 3109 Dihedral : 17.366 176.506 4591 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.82 % Allowed : 11.07 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.40 (0.19), residues: 1793 helix: 2.52 (0.14), residues: 1119 sheet: 0.17 (1.08), residues: 28 loop : -0.00 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 156 HIS 0.009 0.001 HIS L 154 PHE 0.016 0.001 PHE H 20 TYR 0.026 0.001 TYR M 302 ARG 0.002 0.000 ARG W 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 220 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8585 (mttm) cc_final: 0.8376 (mmtp) REVERT: M 109 LYS cc_start: 0.8796 (ttmm) cc_final: 0.8484 (ttmm) REVERT: M 137 ASP cc_start: 0.8858 (t0) cc_final: 0.8482 (t70) REVERT: M 213 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.8890 (tp) REVERT: I 15 ARG cc_start: 0.8121 (mmm-85) cc_final: 0.6934 (tmt170) REVERT: K 15 ARG cc_start: 0.7978 (mtt90) cc_final: 0.7654 (mtt90) REVERT: N 12 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8040 (p) REVERT: N 14 GLU cc_start: 0.7905 (pm20) cc_final: 0.7649 (pm20) REVERT: O 12 ASP cc_start: 0.8219 (t0) cc_final: 0.7892 (t0) REVERT: O 15 ARG cc_start: 0.7147 (mmm160) cc_final: 0.6434 (ttp-170) REVERT: Q 6 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8262 (ttmm) REVERT: S 6 LYS cc_start: 0.8578 (mtpt) cc_final: 0.8322 (mttm) REVERT: T 17 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7454 (tp40) REVERT: V 11 PHE cc_start: 0.7338 (m-80) cc_final: 0.6870 (m-10) REVERT: V 30 LEU cc_start: 0.8281 (tt) cc_final: 0.7948 (tm) REVERT: X 9 ASP cc_start: 0.7205 (t0) cc_final: 0.6834 (t0) REVERT: X 15 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8241 (mtpt) outliers start: 42 outliers final: 21 residues processed: 240 average time/residue: 1.1725 time to fit residues: 320.5745 Evaluate side-chains 234 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain T residue 17 GLN Chi-restraints excluded: chain Y residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 69 optimal weight: 0.0770 chunk 144 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 151 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN H 52 ASN J 17 GLN N 17 GLN Q 51 HIS S 20 GLN V 20 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 19217 Z= 0.460 Angle : 0.841 15.234 26320 Z= 0.332 Chirality : 0.047 0.532 2718 Planarity : 0.004 0.050 3109 Dihedral : 17.701 179.855 4591 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.15 % Allowed : 11.34 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.04 (0.19), residues: 1793 helix: 2.25 (0.14), residues: 1115 sheet: -0.16 (1.07), residues: 28 loop : -0.14 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 156 HIS 0.012 0.002 HIS L 154 PHE 0.023 0.002 PHE H 20 TYR 0.032 0.002 TYR M 302 ARG 0.003 0.000 ARG S 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 214 time to evaluate : 1.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8661 (mttm) cc_final: 0.8448 (mmtp) REVERT: M 109 LYS cc_start: 0.8801 (ttmm) cc_final: 0.8496 (ttmm) REVERT: M 137 ASP cc_start: 0.8872 (t0) cc_final: 0.8481 (t70) REVERT: I 15 ARG cc_start: 0.8199 (mmm-85) cc_final: 0.6988 (tmt170) REVERT: K 15 ARG cc_start: 0.8050 (mtt90) cc_final: 0.7711 (mtt90) REVERT: K 20 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8634 (tt0) REVERT: N 12 THR cc_start: 0.8533 (OUTLIER) cc_final: 0.7941 (p) REVERT: N 14 GLU cc_start: 0.7924 (pm20) cc_final: 0.7514 (pm20) REVERT: O 12 ASP cc_start: 0.8260 (t0) cc_final: 0.7881 (t0) REVERT: O 15 ARG cc_start: 0.7178 (mmm160) cc_final: 0.6430 (ttp-170) REVERT: R 25 SER cc_start: 0.8713 (OUTLIER) cc_final: 0.8347 (p) REVERT: S 5 TYR cc_start: 0.7470 (p90) cc_final: 0.6914 (p90) REVERT: S 6 LYS cc_start: 0.8503 (mtpt) cc_final: 0.8182 (mptp) REVERT: S 9 LEU cc_start: 0.7657 (mt) cc_final: 0.7413 (mm) REVERT: V 11 PHE cc_start: 0.7291 (m-80) cc_final: 0.6799 (m-80) REVERT: V 30 LEU cc_start: 0.8275 (tt) cc_final: 0.8020 (tm) REVERT: X 9 ASP cc_start: 0.7204 (t0) cc_final: 0.6833 (t0) outliers start: 47 outliers final: 28 residues processed: 242 average time/residue: 1.1842 time to fit residues: 326.6478 Evaluate side-chains 236 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 205 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 76 LEU Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain K residue 20 GLN Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain W residue 28 SER Chi-restraints excluded: chain Y residue 31 ILE Chi-restraints excluded: chain X residue 34 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 0.0010 chunk 152 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 169 optimal weight: 0.3980 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN S 20 GLN T 20 HIS V 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19217 Z= 0.157 Angle : 0.665 16.069 26320 Z= 0.263 Chirality : 0.039 0.437 2718 Planarity : 0.003 0.049 3109 Dihedral : 16.399 173.206 4591 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.62 % Allowed : 12.42 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.41 (0.19), residues: 1793 helix: 2.56 (0.14), residues: 1118 sheet: 0.23 (1.09), residues: 28 loop : -0.05 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 156 HIS 0.007 0.001 HIS L 154 PHE 0.014 0.001 PHE L 147 TYR 0.024 0.001 TYR M 302 ARG 0.002 0.000 ARG M 163 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8575 (mttm) cc_final: 0.8353 (mmtp) REVERT: M 109 LYS cc_start: 0.8758 (ttmm) cc_final: 0.8442 (ttmm) REVERT: M 137 ASP cc_start: 0.8853 (t0) cc_final: 0.8524 (t70) REVERT: M 213 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.8893 (tp) REVERT: I 14 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7834 (mtt90) REVERT: I 15 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.6914 (tmt170) REVERT: K 15 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7675 (mtt90) REVERT: K 20 GLN cc_start: 0.8772 (tt0) cc_final: 0.8566 (tt0) REVERT: N 12 THR cc_start: 0.8516 (OUTLIER) cc_final: 0.8043 (p) REVERT: O 12 ASP cc_start: 0.8245 (t0) cc_final: 0.7916 (t0) REVERT: O 15 ARG cc_start: 0.7132 (mmm160) cc_final: 0.6408 (ttp-110) REVERT: R 25 SER cc_start: 0.8668 (OUTLIER) cc_final: 0.8313 (p) REVERT: S 3 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8085 (tptt) REVERT: S 5 TYR cc_start: 0.7423 (p90) cc_final: 0.6890 (p90) REVERT: S 6 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8228 (mptp) REVERT: V 30 LEU cc_start: 0.8291 (tt) cc_final: 0.7961 (tm) REVERT: V 34 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.8107 (mp) REVERT: X 9 ASP cc_start: 0.7186 (t0) cc_final: 0.6787 (t0) outliers start: 39 outliers final: 19 residues processed: 235 average time/residue: 1.1627 time to fit residues: 311.4174 Evaluate side-chains 235 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 211 time to evaluate : 2.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain V residue 34 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 20 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19217 Z= 0.259 Angle : 0.696 14.317 26320 Z= 0.278 Chirality : 0.040 0.389 2718 Planarity : 0.003 0.049 3109 Dihedral : 16.216 175.887 4587 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.89 % Allowed : 12.55 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 1793 helix: 2.53 (0.14), residues: 1120 sheet: 0.21 (1.08), residues: 28 loop : -0.07 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 156 HIS 0.011 0.001 HIS M 181 PHE 0.019 0.001 PHE F 17 TYR 0.029 0.001 TYR M 302 ARG 0.002 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8610 (mttm) cc_final: 0.8378 (mmtp) REVERT: M 109 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8444 (ttmm) REVERT: M 137 ASP cc_start: 0.8857 (t0) cc_final: 0.8457 (t70) REVERT: I 14 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7831 (mtt90) REVERT: I 15 ARG cc_start: 0.8142 (mmm-85) cc_final: 0.6935 (tmt170) REVERT: K 15 ARG cc_start: 0.7995 (mtt90) cc_final: 0.7704 (mtt90) REVERT: K 20 GLN cc_start: 0.8805 (tt0) cc_final: 0.8601 (tt0) REVERT: N 12 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8074 (p) REVERT: N 14 GLU cc_start: 0.7984 (pm20) cc_final: 0.7784 (pm20) REVERT: O 12 ASP cc_start: 0.8264 (t0) cc_final: 0.7897 (t0) REVERT: O 15 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6451 (ttp-110) REVERT: R 17 GLN cc_start: 0.8085 (tt0) cc_final: 0.7872 (tp40) REVERT: R 25 SER cc_start: 0.8682 (OUTLIER) cc_final: 0.8329 (p) REVERT: S 5 TYR cc_start: 0.7414 (p90) cc_final: 0.6874 (p90) REVERT: S 6 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8252 (mptp) REVERT: V 30 LEU cc_start: 0.8292 (tt) cc_final: 0.7941 (tm) REVERT: V 34 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.8146 (mp) REVERT: X 9 ASP cc_start: 0.7170 (t0) cc_final: 0.6868 (t0) outliers start: 43 outliers final: 25 residues processed: 236 average time/residue: 1.1674 time to fit residues: 314.5096 Evaluate side-chains 236 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 5 TYR Chi-restraints excluded: chain V residue 34 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 153 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 20 HIS S 20 GLN V 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 19217 Z= 0.293 Angle : 0.715 12.527 26320 Z= 0.287 Chirality : 0.041 0.360 2718 Planarity : 0.004 0.050 3109 Dihedral : 16.334 178.633 4587 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.68 % Allowed : 12.89 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.27 (0.19), residues: 1793 helix: 2.45 (0.14), residues: 1119 sheet: 0.13 (1.08), residues: 28 loop : -0.11 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 156 HIS 0.011 0.001 HIS M 181 PHE 0.020 0.001 PHE H 20 TYR 0.031 0.001 TYR M 302 ARG 0.002 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 210 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8615 (mttm) cc_final: 0.8392 (mmtp) REVERT: M 109 LYS cc_start: 0.8769 (ttmm) cc_final: 0.8443 (ttmm) REVERT: M 137 ASP cc_start: 0.8860 (t0) cc_final: 0.8461 (t70) REVERT: I 15 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.6963 (tmt170) REVERT: K 15 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7669 (mtt90) REVERT: K 20 GLN cc_start: 0.8815 (tt0) cc_final: 0.8609 (tt0) REVERT: N 12 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8054 (p) REVERT: N 14 GLU cc_start: 0.8023 (pm20) cc_final: 0.7821 (pm20) REVERT: O 12 ASP cc_start: 0.8265 (t0) cc_final: 0.7902 (t0) REVERT: O 15 ARG cc_start: 0.7120 (mmm160) cc_final: 0.6457 (ttp-110) REVERT: R 25 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8336 (p) REVERT: S 3 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.8178 (tptt) REVERT: S 5 TYR cc_start: 0.7391 (p90) cc_final: 0.6789 (p90) REVERT: S 6 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8164 (mptp) REVERT: V 30 LEU cc_start: 0.8261 (tt) cc_final: 0.7905 (tm) REVERT: V 34 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.8163 (mp) REVERT: X 9 ASP cc_start: 0.7227 (t0) cc_final: 0.6920 (t0) outliers start: 40 outliers final: 24 residues processed: 232 average time/residue: 1.1450 time to fit residues: 303.1665 Evaluate side-chains 236 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 225 VAL Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain H residue 233 ASP Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain D residue 12 ASP Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain S residue 3 LYS Chi-restraints excluded: chain V residue 34 ILE 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: 0.7980 chunk 157 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 123 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 148 optimal weight: 0.7980 chunk 156 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 63 GLN H 52 ASN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN V 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19217 Z= 0.163 Angle : 0.640 12.040 26320 Z= 0.258 Chirality : 0.037 0.351 2718 Planarity : 0.003 0.049 3109 Dihedral : 15.694 172.726 4587 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.08 % Allowed : 13.62 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.19), residues: 1793 helix: 2.66 (0.14), residues: 1116 sheet: 0.39 (1.10), residues: 28 loop : -0.05 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.007 0.001 HIS L 154 PHE 0.014 0.001 PHE F 17 TYR 0.024 0.001 TYR Q 5 ARG 0.003 0.000 ARG H 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 213 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8568 (mttm) cc_final: 0.8274 (mmtp) REVERT: M 109 LYS cc_start: 0.8760 (ttmm) cc_final: 0.8437 (ttmm) REVERT: M 137 ASP cc_start: 0.8822 (t0) cc_final: 0.8395 (t70) REVERT: I 14 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7840 (mtt90) REVERT: I 15 ARG cc_start: 0.8136 (mmm-85) cc_final: 0.6947 (tmt170) REVERT: K 15 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7704 (mtt90) REVERT: K 20 GLN cc_start: 0.8770 (tt0) cc_final: 0.8562 (tt0) REVERT: N 12 THR cc_start: 0.8481 (OUTLIER) cc_final: 0.8052 (p) REVERT: O 12 ASP cc_start: 0.8279 (t0) cc_final: 0.7934 (t0) REVERT: O 15 ARG cc_start: 0.7151 (mmm160) cc_final: 0.6472 (ttp-110) REVERT: Q 5 TYR cc_start: 0.8583 (p90) cc_final: 0.8313 (p90) REVERT: R 25 SER cc_start: 0.8651 (OUTLIER) cc_final: 0.8314 (p) REVERT: S 5 TYR cc_start: 0.7417 (p90) cc_final: 0.7031 (p90) REVERT: S 6 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8230 (mptp) REVERT: V 30 LEU cc_start: 0.8268 (tt) cc_final: 0.7937 (tm) REVERT: V 34 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8105 (mp) REVERT: X 9 ASP cc_start: 0.7165 (t0) cc_final: 0.6888 (t0) outliers start: 31 outliers final: 17 residues processed: 228 average time/residue: 1.2350 time to fit residues: 324.9161 Evaluate side-chains 224 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 204 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain H residue 228 THR Chi-restraints excluded: chain A residue 35 LEU Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 28 SER Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 34 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 0.0970 chunk 115 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 14 optimal weight: 0.0470 chunk 107 optimal weight: 0.9980 chunk 85 optimal weight: 0.2980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN A 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19217 Z= 0.168 Angle : 0.636 12.298 26320 Z= 0.258 Chirality : 0.037 0.341 2718 Planarity : 0.003 0.049 3109 Dihedral : 15.410 174.005 4587 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 14.23 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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 (0.19), residues: 1793 helix: 2.68 (0.14), residues: 1113 sheet: 0.37 (1.10), residues: 28 loop : -0.05 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 156 HIS 0.009 0.001 HIS M 181 PHE 0.014 0.001 PHE H 20 TYR 0.024 0.001 TYR Q 5 ARG 0.002 0.000 ARG H 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3586 Ramachandran restraints generated. 1793 Oldfield, 0 Emsley, 1793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 212 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 83 LYS cc_start: 0.8563 (mttm) cc_final: 0.8324 (mmtp) REVERT: M 109 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8449 (ttmm) REVERT: M 137 ASP cc_start: 0.8823 (t0) cc_final: 0.8409 (t70) REVERT: M 213 LEU cc_start: 0.9576 (OUTLIER) cc_final: 0.8857 (tp) REVERT: I 14 ARG cc_start: 0.8046 (mtm110) cc_final: 0.7838 (mtt90) REVERT: I 15 ARG cc_start: 0.8122 (mmm-85) cc_final: 0.6936 (tmt170) REVERT: K 15 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7693 (mtt90) REVERT: N 12 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8055 (p) REVERT: O 12 ASP cc_start: 0.8277 (t0) cc_final: 0.7926 (t0) REVERT: O 15 ARG cc_start: 0.7131 (mmm160) cc_final: 0.6453 (ttp-110) REVERT: Q 5 TYR cc_start: 0.8622 (p90) cc_final: 0.8368 (p90) REVERT: R 25 SER cc_start: 0.8662 (OUTLIER) cc_final: 0.8374 (p) REVERT: S 5 TYR cc_start: 0.7464 (p90) cc_final: 0.6979 (p90) REVERT: S 12 ASP cc_start: 0.7862 (t0) cc_final: 0.7559 (t70) REVERT: V 30 LEU cc_start: 0.8269 (tt) cc_final: 0.7941 (tm) REVERT: X 9 ASP cc_start: 0.7191 (t0) cc_final: 0.6880 (t0) outliers start: 26 outliers final: 16 residues processed: 227 average time/residue: 1.2211 time to fit residues: 315.1249 Evaluate side-chains 233 residues out of total 1496 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 40 ILE Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 274 VAL Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain M residue 60 LEU Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 215 PHE Chi-restraints excluded: chain M residue 274 MET Chi-restraints excluded: chain H residue 126 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain I residue 3 LYS Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain Q residue 16 VAL Chi-restraints excluded: chain R residue 25 SER Chi-restraints excluded: chain V residue 20 GLN Chi-restraints excluded: chain Y residue 46 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 142 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN V 20 GLN Z 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079507 restraints weight = 43087.480| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 2.00 r_work: 0.2756 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19217 Z= 0.263 Angle : 0.695 15.578 26320 Z= 0.284 Chirality : 0.039 0.331 2718 Planarity : 0.003 0.050 3109 Dihedral : 15.590 174.623 4584 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.41 % Allowed : 14.70 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.75 % 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: 2.40 (0.19), residues: 1793 helix: 2.56 (0.14), residues: 1115 sheet: 0.34 (1.11), residues: 28 loop : -0.05 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP V 8 HIS 0.011 0.001 HIS M 181 PHE 0.019 0.001 PHE F 17 TYR 0.029 0.001 TYR M 302 ARG 0.002 0.000 ARG H 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6263.65 seconds wall clock time: 113 minutes 7.32 seconds (6787.32 seconds total)