Starting phenix.real_space_refine on Sat Feb 24 11:31:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/02_2024/6d8c_7831_trim_updated.pdb" } resolution = 3.54 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= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4475 atoms to isotropic. 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 P 10 5.49 5 Mg 5 5.21 5 S 128 5.16 5 C 12425 2.51 5 N 3374 2.21 5 O 3723 1.98 5 H 19516 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J ASP 286": "OD1" <-> "OD2" Residue "J ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ASP 286": "OD1" <-> "OD2" Residue "L ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M ASP 286": "OD1" <-> "OD2" Residue "M ARG 335": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 372": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 39181 Number of models: 1 Model: "" Number of chains: 18 Chain: "D" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "H" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "A" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "J" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "B" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "K" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "C" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "E" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2012 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "M" Number of atoms: 5750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 5750 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Chain: "N" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.94, per 1000 atoms: 0.43 Number of scatterers: 39181 At special positions: 0 Unit cell: (95.76, 129.01, 202.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 10 15.00 Mg 5 11.99 O 3723 8.00 N 3374 7.00 C 12425 6.00 H 19516 1.00 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 31.83 Conformation dependent library (CDL) restraints added in 4.1 seconds 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 120 helices and 20 sheets defined 43.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'D' and resid 30 through 32 No H-bonds generated for 'chain 'D' and resid 30 through 32' Processing helix chain 'D' and resid 40 through 58 removed outlier: 3.795A pdb=" N HIS D 56 " --> pdb=" O TRP D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 70 No H-bonds generated for 'chain 'D' and resid 67 through 70' Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 100 through 116 Processing helix chain 'D' and resid 126 through 131 Processing helix chain 'D' and resid 134 through 147 removed outlier: 3.713A pdb=" N LEU D 138 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU D 144 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 79 through 90 removed outlier: 3.664A pdb=" N LYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 126 removed outlier: 4.273A pdb=" N THR H 120 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET H 123 " --> pdb=" O MET H 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU H 125 " --> pdb=" O GLN H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 145 Processing helix chain 'H' and resid 182 through 196 removed outlier: 4.119A pdb=" N THR H 194 " --> pdb=" O MET H 190 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU H 195 " --> pdb=" O LYS H 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG H 196 " --> pdb=" O ILE H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 216 removed outlier: 3.585A pdb=" N GLU H 207 " --> pdb=" O THR H 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE H 208 " --> pdb=" O ALA H 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS H 215 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU H 216 " --> pdb=" O ILE H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 removed outlier: 3.547A pdb=" N ALA H 228 " --> pdb=" O GLU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 254 No H-bonds generated for 'chain 'H' and resid 252 through 254' Processing helix chain 'H' and resid 258 through 260 No H-bonds generated for 'chain 'H' and resid 258 through 260' Processing helix chain 'H' and resid 274 through 283 Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'H' and resid 309 through 320 removed outlier: 3.551A pdb=" N ALA H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 346 Processing helix chain 'H' and resid 351 through 354 Processing helix chain 'H' and resid 359 through 365 removed outlier: 3.617A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL H 370 " --> pdb=" O PRO H 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS H 371 " --> pdb=" O SER H 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG H 372 " --> pdb=" O ILE H 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 40 through 58 removed outlier: 3.795A pdb=" N HIS A 56 " --> pdb=" O TRP A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 70 No H-bonds generated for 'chain 'A' and resid 67 through 70' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 134 through 147 removed outlier: 3.713A pdb=" N LEU A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 144 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'J' and resid 79 through 90 removed outlier: 3.664A pdb=" N LYS J 84 " --> pdb=" O ASP J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 126 removed outlier: 4.273A pdb=" N THR J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET J 123 " --> pdb=" O MET J 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE J 124 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU J 125 " --> pdb=" O GLN J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 145 Processing helix chain 'J' and resid 182 through 196 removed outlier: 4.119A pdb=" N THR J 194 " --> pdb=" O MET J 190 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU J 195 " --> pdb=" O LYS J 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG J 196 " --> pdb=" O ILE J 192 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 216 removed outlier: 3.585A pdb=" N GLU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE J 208 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS J 215 " --> pdb=" O ASP J 211 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU J 216 " --> pdb=" O ILE J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 232 removed outlier: 3.548A pdb=" N ALA J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 254 No H-bonds generated for 'chain 'J' and resid 252 through 254' Processing helix chain 'J' and resid 258 through 260 No H-bonds generated for 'chain 'J' and resid 258 through 260' Processing helix chain 'J' and resid 274 through 283 Processing helix chain 'J' and resid 290 through 295 Processing helix chain 'J' and resid 309 through 320 removed outlier: 3.552A pdb=" N ALA J 319 " --> pdb=" O LYS J 315 " (cutoff:3.500A) Processing helix chain 'J' and resid 338 through 346 Processing helix chain 'J' and resid 351 through 354 Processing helix chain 'J' and resid 359 through 365 removed outlier: 3.617A pdb=" N GLU J 364 " --> pdb=" O GLN J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL J 370 " --> pdb=" O PRO J 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS J 371 " --> pdb=" O SER J 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG J 372 " --> pdb=" O ILE J 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 40 through 58 removed outlier: 3.795A pdb=" N HIS B 56 " --> pdb=" O TRP B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 70 No H-bonds generated for 'chain 'B' and resid 67 through 70' Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 126 through 131 Processing helix chain 'B' and resid 134 through 147 removed outlier: 3.713A pdb=" N LEU B 138 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 144 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 55 through 60 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 79 through 90 removed outlier: 3.665A pdb=" N LYS K 84 " --> pdb=" O ASP K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 126 removed outlier: 4.273A pdb=" N THR K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET K 123 " --> pdb=" O MET K 119 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU K 125 " --> pdb=" O GLN K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 145 Processing helix chain 'K' and resid 182 through 196 removed outlier: 4.119A pdb=" N THR K 194 " --> pdb=" O MET K 190 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU K 195 " --> pdb=" O LYS K 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 196 " --> pdb=" O ILE K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 216 removed outlier: 3.586A pdb=" N GLU K 207 " --> pdb=" O THR K 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 215 " --> pdb=" O ASP K 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU K 216 " --> pdb=" O ILE K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 232 removed outlier: 3.546A pdb=" N ALA K 228 " --> pdb=" O GLU K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 254 No H-bonds generated for 'chain 'K' and resid 252 through 254' Processing helix chain 'K' and resid 258 through 260 No H-bonds generated for 'chain 'K' and resid 258 through 260' Processing helix chain 'K' and resid 274 through 283 Processing helix chain 'K' and resid 290 through 295 Processing helix chain 'K' and resid 309 through 320 removed outlier: 3.552A pdb=" N ALA K 319 " --> pdb=" O LYS K 315 " (cutoff:3.500A) Processing helix chain 'K' and resid 338 through 346 Processing helix chain 'K' and resid 351 through 354 Processing helix chain 'K' and resid 359 through 365 removed outlier: 3.617A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL K 370 " --> pdb=" O PRO K 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS K 371 " --> pdb=" O SER K 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG K 372 " --> pdb=" O ILE K 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 40 through 58 removed outlier: 3.795A pdb=" N HIS C 56 " --> pdb=" O TRP C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 70 No H-bonds generated for 'chain 'C' and resid 67 through 70' Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 126 through 131 Processing helix chain 'C' and resid 134 through 147 removed outlier: 3.712A pdb=" N LEU C 138 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLY C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 144 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 55 through 60 Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'L' and resid 79 through 90 removed outlier: 3.664A pdb=" N LYS L 84 " --> pdb=" O ASP L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 126 removed outlier: 4.273A pdb=" N THR L 120 " --> pdb=" O ARG L 116 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N MET L 123 " --> pdb=" O MET L 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE L 124 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU L 125 " --> pdb=" O GLN L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 145 Processing helix chain 'L' and resid 182 through 196 removed outlier: 4.118A pdb=" N THR L 194 " --> pdb=" O MET L 190 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU L 195 " --> pdb=" O LYS L 191 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG L 196 " --> pdb=" O ILE L 192 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 removed outlier: 3.585A pdb=" N GLU L 207 " --> pdb=" O THR L 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE L 208 " --> pdb=" O ALA L 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS L 215 " --> pdb=" O ASP L 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU L 216 " --> pdb=" O ILE L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 232 removed outlier: 3.547A pdb=" N ALA L 228 " --> pdb=" O GLU L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 254 No H-bonds generated for 'chain 'L' and resid 252 through 254' Processing helix chain 'L' and resid 258 through 260 No H-bonds generated for 'chain 'L' and resid 258 through 260' Processing helix chain 'L' and resid 274 through 283 Processing helix chain 'L' and resid 290 through 295 Processing helix chain 'L' and resid 309 through 320 removed outlier: 3.551A pdb=" N ALA L 319 " --> pdb=" O LYS L 315 " (cutoff:3.500A) Processing helix chain 'L' and resid 338 through 346 Processing helix chain 'L' and resid 351 through 354 Processing helix chain 'L' and resid 359 through 365 removed outlier: 3.617A pdb=" N GLU L 364 " --> pdb=" O GLN L 360 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL L 370 " --> pdb=" O PRO L 367 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N HIS L 371 " --> pdb=" O SER L 368 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG L 372 " --> pdb=" O ILE L 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 32 No H-bonds generated for 'chain 'E' and resid 30 through 32' Processing helix chain 'E' and resid 40 through 58 removed outlier: 3.795A pdb=" N HIS E 56 " --> pdb=" O TRP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 70 No H-bonds generated for 'chain 'E' and resid 67 through 70' Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 100 through 116 Processing helix chain 'E' and resid 126 through 131 Processing helix chain 'E' and resid 134 through 147 removed outlier: 3.713A pdb=" N LEU E 138 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLY E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU E 144 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 60 Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'M' and resid 79 through 90 removed outlier: 3.665A pdb=" N LYS M 84 " --> pdb=" O ASP M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 126 removed outlier: 4.274A pdb=" N THR M 120 " --> pdb=" O ARG M 116 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N MET M 123 " --> pdb=" O MET M 119 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE M 124 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU M 125 " --> pdb=" O GLN M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 145 Processing helix chain 'M' and resid 182 through 196 removed outlier: 4.119A pdb=" N THR M 194 " --> pdb=" O MET M 190 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU M 195 " --> pdb=" O LYS M 191 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG M 196 " --> pdb=" O ILE M 192 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 removed outlier: 3.585A pdb=" N GLU M 207 " --> pdb=" O THR M 203 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE M 208 " --> pdb=" O ALA M 204 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS M 215 " --> pdb=" O ASP M 211 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU M 216 " --> pdb=" O ILE M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 232 removed outlier: 3.547A pdb=" N ALA M 228 " --> pdb=" O GLU M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 254 No H-bonds generated for 'chain 'M' and resid 252 through 254' Processing helix chain 'M' and resid 258 through 260 No H-bonds generated for 'chain 'M' and resid 258 through 260' Processing helix chain 'M' and resid 274 through 283 Processing helix chain 'M' and resid 290 through 295 Processing helix chain 'M' and resid 309 through 320 removed outlier: 3.552A pdb=" N ALA M 319 " --> pdb=" O LYS M 315 " (cutoff:3.500A) Processing helix chain 'M' and resid 338 through 346 Processing helix chain 'M' and resid 351 through 354 Processing helix chain 'M' and resid 359 through 365 removed outlier: 3.617A pdb=" N GLU M 364 " --> pdb=" O GLN M 360 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 373 removed outlier: 3.920A pdb=" N VAL M 370 " --> pdb=" O PRO M 367 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS M 371 " --> pdb=" O SER M 368 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG M 372 " --> pdb=" O ILE M 369 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.773A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 35 through 38 Processing sheet with id= C, first strand: chain 'H' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL H 163 " --> pdb=" O VAL H 152 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 238 through 240 removed outlier: 3.537A pdb=" N LYS H 238 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE H 248 " --> pdb=" O TYR H 240 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'J' and resid 132 through 136 removed outlier: 6.772A pdb=" N THR J 103 " --> pdb=" O TYR J 133 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA J 135 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU J 105 " --> pdb=" O ALA J 135 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU J 8 " --> pdb=" O LEU J 104 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N THR J 106 " --> pdb=" O LEU J 8 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N CYS J 10 " --> pdb=" O THR J 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'J' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL J 163 " --> pdb=" O VAL J 152 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS J 238 " --> pdb=" O ILE J 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE J 248 " --> pdb=" O TYR J 240 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 132 through 136 removed outlier: 6.772A pdb=" N THR K 103 " --> pdb=" O TYR K 133 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA K 135 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU K 105 " --> pdb=" O ALA K 135 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'K' and resid 35 through 38 Processing sheet with id= K, first strand: chain 'K' and resid 150 through 152 removed outlier: 3.591A pdb=" N VAL K 163 " --> pdb=" O VAL K 152 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS K 238 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE K 248 " --> pdb=" O TYR K 240 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'L' and resid 132 through 136 removed outlier: 6.773A pdb=" N THR L 103 " --> pdb=" O TYR L 133 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA L 135 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU L 105 " --> pdb=" O ALA L 135 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N LEU L 8 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N THR L 106 " --> pdb=" O LEU L 8 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N CYS L 10 " --> pdb=" O THR L 106 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'L' and resid 35 through 38 Processing sheet with id= O, first strand: chain 'L' and resid 150 through 152 removed outlier: 3.590A pdb=" N VAL L 163 " --> pdb=" O VAL L 152 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 238 through 240 removed outlier: 3.537A pdb=" N LYS L 238 " --> pdb=" O ILE L 250 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE L 248 " --> pdb=" O TYR L 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'M' and resid 132 through 136 removed outlier: 6.772A pdb=" N THR M 103 " --> pdb=" O TYR M 133 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N ALA M 135 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU M 105 " --> pdb=" O ALA M 135 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU M 8 " --> pdb=" O LEU M 104 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N THR M 106 " --> pdb=" O LEU M 8 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N CYS M 10 " --> pdb=" O THR M 106 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'M' and resid 35 through 38 Processing sheet with id= S, first strand: chain 'M' and resid 150 through 152 removed outlier: 3.590A pdb=" N VAL M 163 " --> pdb=" O VAL M 152 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'M' and resid 238 through 240 removed outlier: 3.538A pdb=" N LYS M 238 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE M 248 " --> pdb=" O TYR M 240 " (cutoff:3.500A) 605 hydrogen bonds defined for protein. 1635 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: 14.98 Time building geometry restraints manager: 32.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 19481 1.02 - 1.22: 56 1.22 - 1.42: 8128 1.42 - 1.62: 11699 1.62 - 1.82: 218 Bond restraints: 39582 Sorted by residual: bond pdb=" C HYP O 1 " pdb=" N ALA O 2 " ideal model delta sigma weight residual 1.329 1.460 -0.131 1.40e-02 5.10e+03 8.71e+01 bond pdb=" C HYP P 1 " pdb=" N ALA P 2 " ideal model delta sigma weight residual 1.329 1.459 -0.130 1.40e-02 5.10e+03 8.63e+01 bond pdb=" C HYP N 1 " pdb=" N ALA N 2 " ideal model delta sigma weight residual 1.329 1.459 -0.130 1.40e-02 5.10e+03 8.59e+01 bond pdb=" C ALA O 5 " pdb=" N ALO O 6 " ideal model delta sigma weight residual 1.329 1.458 -0.129 1.40e-02 5.10e+03 8.47e+01 bond pdb=" C ALA N 5 " pdb=" N ALO N 6 " ideal model delta sigma weight residual 1.329 1.457 -0.128 1.40e-02 5.10e+03 8.38e+01 ... (remaining 39577 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.63: 2935 107.63 - 114.81: 47957 114.81 - 121.99: 13839 121.99 - 129.17: 6688 129.17 - 136.36: 206 Bond angle restraints: 71625 Sorted by residual: angle pdb=" N THR M 194 " pdb=" CA THR M 194 " pdb=" C THR M 194 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.16e+01 angle pdb=" N THR L 194 " pdb=" CA THR L 194 " pdb=" C THR L 194 " ideal model delta sigma weight residual 111.71 105.26 6.45 1.15e+00 7.56e-01 3.15e+01 angle pdb=" N THR H 194 " pdb=" CA THR H 194 " pdb=" C THR H 194 " ideal model delta sigma weight residual 111.71 105.27 6.44 1.15e+00 7.56e-01 3.14e+01 angle pdb=" N THR K 194 " pdb=" CA THR K 194 " pdb=" C THR K 194 " ideal model delta sigma weight residual 111.71 105.28 6.43 1.15e+00 7.56e-01 3.13e+01 angle pdb=" N THR J 194 " pdb=" CA THR J 194 " pdb=" C THR J 194 " ideal model delta sigma weight residual 111.71 105.29 6.42 1.15e+00 7.56e-01 3.12e+01 ... (remaining 71620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 18215 33.81 - 67.63: 344 67.63 - 101.44: 6 101.44 - 135.25: 5 135.25 - 169.06: 10 Dihedral angle restraints: 18580 sinusoidal: 10283 harmonic: 8297 Sorted by residual: dihedral pdb=" O2A ADP J 401 " pdb=" O3A ADP J 401 " pdb=" PA ADP J 401 " pdb=" PB ADP J 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.06 -169.06 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP K 401 " pdb=" O3A ADP K 401 " pdb=" PA ADP K 401 " pdb=" PB ADP K 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.00 -169.00 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PA ADP H 401 " pdb=" PB ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 109.00 -169.00 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 18577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2657 0.065 - 0.131: 383 0.131 - 0.196: 17 0.196 - 0.262: 8 0.262 - 0.327: 5 Chirality restraints: 3070 Sorted by residual: chirality pdb=" CA HIS J 161 " pdb=" N HIS J 161 " pdb=" C HIS J 161 " pdb=" CB HIS J 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA HIS M 161 " pdb=" N HIS M 161 " pdb=" C HIS M 161 " pdb=" CB HIS M 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA HIS H 161 " pdb=" N HIS H 161 " pdb=" C HIS H 161 " pdb=" CB HIS H 161 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 ... (remaining 3067 not shown) Planarity restraints: 5788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN K 263 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO K 264 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO K 264 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO K 264 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN M 263 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO M 264 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO M 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO M 264 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN L 263 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO L 264 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO L 264 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 264 " -0.033 5.00e-02 4.00e+02 ... (remaining 5785 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 512 2.08 - 2.71: 65663 2.71 - 3.34: 112850 3.34 - 3.97: 144495 3.97 - 4.60: 231695 Nonbonded interactions: 555215 Sorted by model distance: nonbonded pdb=" HE1 MET H 47 " pdb=" HG1 THR M 148 " model vdw 1.448 2.270 nonbonded pdb=" HG1 THR K 148 " pdb=" HE1 MET L 47 " model vdw 1.460 2.270 nonbonded pdb=" HG1 THR H 148 " pdb=" HE1 MET J 47 " model vdw 1.488 2.270 nonbonded pdb=" HE3 LYS D 127 " pdb=" HG2 GLU M 167 " model vdw 1.540 2.440 nonbonded pdb=" HG2 GLU K 167 " pdb=" HE3 LYS C 127 " model vdw 1.542 2.440 ... (remaining 555210 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.260 Construct map_model_manager: 0.550 Extract box with map and model: 4.380 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 123.980 Find NCS groups from input model: 2.150 Set up NCS constraints: 0.300 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.006 0.131 20066 Z= 0.387 Angle : 0.819 10.405 27190 Z= 0.481 Chirality : 0.046 0.327 3070 Planarity : 0.005 0.059 3436 Dihedral : 11.945 169.063 7543 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.85 % Allowed : 3.06 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.35 (0.15), residues: 2435 helix: -1.88 (0.12), residues: 1050 sheet: -1.71 (0.28), residues: 305 loop : -0.94 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 340 HIS 0.004 0.001 HIS J 73 PHE 0.010 0.001 PHE A 49 TYR 0.019 0.001 TYR K 166 ARG 0.004 0.001 ARG M 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 712 time to evaluate : 4.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 66 ASN cc_start: 0.8414 (t0) cc_final: 0.8202 (t0) REVERT: D 87 LYS cc_start: 0.8367 (mttt) cc_final: 0.8055 (mtmt) REVERT: D 92 LYS cc_start: 0.8069 (mttp) cc_final: 0.7858 (mtpp) REVERT: H 113 LYS cc_start: 0.7627 (mtpt) cc_final: 0.7231 (mtmt) REVERT: H 132 MET cc_start: 0.7891 (tmm) cc_final: 0.7586 (ttp) REVERT: H 171 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8823 (mt) REVERT: H 283 MET cc_start: 0.7860 (mmt) cc_final: 0.7602 (mmt) REVERT: H 361 GLU cc_start: 0.6217 (tt0) cc_final: 0.6002 (tt0) REVERT: A 119 ILE cc_start: 0.7738 (mt) cc_final: 0.7455 (mt) REVERT: J 176 MET cc_start: 0.7878 (mmm) cc_final: 0.7294 (mtp) REVERT: J 361 GLU cc_start: 0.6563 (tt0) cc_final: 0.6263 (tt0) REVERT: B 100 ARG cc_start: 0.7917 (ttt90) cc_final: 0.5919 (ptt180) REVERT: K 107 GLU cc_start: 0.7663 (pp20) cc_final: 0.7307 (pp20) REVERT: K 244 ASP cc_start: 0.5371 (OUTLIER) cc_final: 0.5001 (p0) REVERT: L 78 ASN cc_start: 0.7495 (m110) cc_final: 0.7224 (m-40) REVERT: L 132 MET cc_start: 0.8150 (tmm) cc_final: 0.7917 (ttp) REVERT: L 244 ASP cc_start: 0.5293 (OUTLIER) cc_final: 0.5024 (p0) REVERT: E 89 MET cc_start: 0.7801 (mmm) cc_final: 0.6451 (mmt) REVERT: E 100 ARG cc_start: 0.8061 (ttt90) cc_final: 0.6003 (ptt90) REVERT: M 12 ASN cc_start: 0.7717 (t0) cc_final: 0.7304 (t0) REVERT: M 44 MET cc_start: 0.8580 (mmt) cc_final: 0.8325 (mmt) REVERT: M 157 ASP cc_start: 0.7040 (t0) cc_final: 0.6820 (t0) REVERT: M 176 MET cc_start: 0.8081 (mmm) cc_final: 0.7759 (mtp) outliers start: 18 outliers final: 13 residues processed: 728 average time/residue: 0.8525 time to fit residues: 898.0552 Evaluate side-chains 397 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 381 time to evaluate : 3.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 244 ASP Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain N residue 7 CYS Chi-restraints excluded: chain O residue 7 CYS Chi-restraints excluded: chain P residue 7 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 0.0970 chunk 185 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 137 GLN H 275 HIS H 280 ASN A 68 GLN J 87 HIS J 137 GLN J 280 ASN J 296 ASN K 137 GLN K 280 ASN K 296 ASN L 137 GLN L 275 HIS L 280 ASN M 87 HIS M 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20066 Z= 0.231 Angle : 0.605 6.471 27190 Z= 0.304 Chirality : 0.041 0.163 3070 Planarity : 0.005 0.055 3436 Dihedral : 11.666 169.153 2808 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.02 % Allowed : 10.25 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.96 (0.16), residues: 2435 helix: -0.15 (0.15), residues: 1070 sheet: -1.72 (0.27), residues: 325 loop : -0.60 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP M 340 HIS 0.005 0.001 HIS L 161 PHE 0.016 0.001 PHE M 262 TYR 0.011 0.001 TYR M 91 ARG 0.005 0.001 ARG L 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 420 time to evaluate : 3.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8265 (mttp) cc_final: 0.7880 (mttm) REVERT: D 117 GLU cc_start: 0.7949 (tp30) cc_final: 0.7617 (tp30) REVERT: D 124 ILE cc_start: 0.8584 (pt) cc_final: 0.8370 (pt) REVERT: H 132 MET cc_start: 0.7894 (tmm) cc_final: 0.7499 (ttp) REVERT: H 283 MET cc_start: 0.8441 (mmt) cc_final: 0.7789 (mmt) REVERT: A 117 GLU cc_start: 0.7785 (tp30) cc_final: 0.7505 (tp30) REVERT: A 119 ILE cc_start: 0.8161 (mt) cc_final: 0.7849 (mt) REVERT: J 176 MET cc_start: 0.7756 (mmm) cc_final: 0.7289 (mtp) REVERT: J 211 ASP cc_start: 0.8217 (t0) cc_final: 0.7933 (t0) REVERT: J 318 THR cc_start: 0.8741 (m) cc_final: 0.8333 (p) REVERT: B 51 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7636 (mmt-90) REVERT: B 100 ARG cc_start: 0.7691 (ttt90) cc_final: 0.6223 (ptt90) REVERT: K 107 GLU cc_start: 0.7669 (pp20) cc_final: 0.7281 (pp20) REVERT: K 244 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.5927 (p0) REVERT: L 78 ASN cc_start: 0.7872 (m110) cc_final: 0.7471 (m-40) REVERT: L 82 MET cc_start: 0.8914 (tpp) cc_final: 0.8676 (tpp) REVERT: L 137 GLN cc_start: 0.8237 (tt0) cc_final: 0.8025 (tt0) REVERT: L 244 ASP cc_start: 0.6451 (OUTLIER) cc_final: 0.5966 (p0) REVERT: E 33 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6030 (ptpp) REVERT: E 87 LYS cc_start: 0.7976 (mtpt) cc_final: 0.7581 (mtmt) REVERT: E 100 ARG cc_start: 0.7853 (ttt90) cc_final: 0.6177 (ptt90) REVERT: M 44 MET cc_start: 0.8660 (mmt) cc_final: 0.8332 (mmt) REVERT: M 157 ASP cc_start: 0.6888 (t0) cc_final: 0.6663 (t70) REVERT: M 198 TYR cc_start: 0.8835 (m-80) cc_final: 0.8564 (m-10) outliers start: 43 outliers final: 35 residues processed: 455 average time/residue: 0.8723 time to fit residues: 565.9231 Evaluate side-chains 387 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 349 time to evaluate : 3.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 33 LYS Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 136 ILE Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain J residue 10 CYS Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 103 THR Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 171 LEU Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 296 ASN Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 139 VAL Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 171 LEU Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 33 LYS Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 171 LEU Chi-restraints excluded: chain M residue 286 ASP Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 348 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 151 optimal weight: 8.9990 chunk 61 optimal weight: 8.9990 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN J 246 GLN J 296 ASN C 101 GLN M 137 GLN M 353 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 20066 Z= 0.346 Angle : 0.648 7.215 27190 Z= 0.332 Chirality : 0.043 0.238 3070 Planarity : 0.005 0.068 3436 Dihedral : 11.325 161.023 2801 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.16 % Allowed : 12.79 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.55 (0.17), residues: 2435 helix: 0.42 (0.15), residues: 1060 sheet: -2.35 (0.27), residues: 295 loop : -0.41 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 340 HIS 0.007 0.001 HIS K 161 PHE 0.016 0.002 PHE M 262 TYR 0.012 0.002 TYR K 279 ARG 0.005 0.001 ARG M 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 391 time to evaluate : 2.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8354 (mttp) cc_final: 0.7934 (mttm) REVERT: D 100 ARG cc_start: 0.8399 (ttt-90) cc_final: 0.7952 (ttp80) REVERT: H 283 MET cc_start: 0.8474 (mmt) cc_final: 0.7999 (mmt) REVERT: H 360 GLN cc_start: 0.7271 (pp30) cc_final: 0.7050 (pp30) REVERT: J 82 MET cc_start: 0.9056 (tpt) cc_final: 0.8663 (tpt) REVERT: J 176 MET cc_start: 0.7949 (mmm) cc_final: 0.7471 (mtp) REVERT: B 92 LYS cc_start: 0.7955 (tmmt) cc_final: 0.7480 (mmmt) REVERT: B 100 ARG cc_start: 0.7760 (ttt90) cc_final: 0.6104 (ptt180) REVERT: K 107 GLU cc_start: 0.7730 (pp20) cc_final: 0.7106 (pp20) REVERT: C 55 GLU cc_start: 0.7823 (tt0) cc_final: 0.7548 (tt0) REVERT: L 16 LEU cc_start: 0.8591 (mt) cc_final: 0.8360 (mt) REVERT: L 78 ASN cc_start: 0.8032 (m110) cc_final: 0.7434 (m-40) REVERT: L 161 HIS cc_start: 0.7267 (OUTLIER) cc_final: 0.5748 (m-70) REVERT: L 244 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7189 (p0) REVERT: L 361 GLU cc_start: 0.6890 (tt0) cc_final: 0.6440 (tt0) REVERT: E 33 LYS cc_start: 0.6911 (ttpp) cc_final: 0.6661 (ttpp) REVERT: E 100 ARG cc_start: 0.7832 (ttt90) cc_final: 0.6129 (ptt180) REVERT: E 127 LYS cc_start: 0.7569 (tttm) cc_final: 0.6912 (ttmt) REVERT: M 44 MET cc_start: 0.8696 (mmt) cc_final: 0.8427 (mmt) outliers start: 46 outliers final: 36 residues processed: 431 average time/residue: 0.9173 time to fit residues: 564.0593 Evaluate side-chains 354 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 316 time to evaluate : 3.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 278 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 106 THR Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 142 LEU Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 248 ILE Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 244 ASP Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 348 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 223 optimal weight: 0.4980 chunk 236 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 353 GLN B 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20066 Z= 0.212 Angle : 0.561 7.947 27190 Z= 0.278 Chirality : 0.040 0.154 3070 Planarity : 0.004 0.051 3436 Dihedral : 11.143 166.199 2795 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.02 % Allowed : 14.49 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.17), residues: 2435 helix: 0.85 (0.16), residues: 1055 sheet: -2.27 (0.28), residues: 295 loop : -0.31 (0.19), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 340 HIS 0.007 0.001 HIS M 161 PHE 0.013 0.001 PHE K 262 TYR 0.012 0.001 TYR L 279 ARG 0.005 0.000 ARG E 116 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 347 time to evaluate : 4.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8355 (mttp) cc_final: 0.7948 (mtpp) REVERT: D 100 ARG cc_start: 0.8454 (ttt-90) cc_final: 0.8068 (ttp80) REVERT: H 283 MET cc_start: 0.8406 (mmt) cc_final: 0.7992 (mmt) REVERT: H 353 GLN cc_start: 0.7508 (mm-40) cc_final: 0.7247 (mp10) REVERT: J 195 GLU cc_start: 0.7528 (mm-30) cc_final: 0.6923 (mm-30) REVERT: J 299 MET cc_start: 0.8665 (tpt) cc_final: 0.8370 (tpt) REVERT: B 92 LYS cc_start: 0.8001 (tmmt) cc_final: 0.7508 (mtpt) REVERT: B 100 ARG cc_start: 0.7779 (ttt90) cc_final: 0.6052 (ptt180) REVERT: K 65 LEU cc_start: 0.9091 (mt) cc_final: 0.8859 (mt) REVERT: K 107 GLU cc_start: 0.7759 (pp20) cc_final: 0.7130 (pp20) REVERT: K 162 ASN cc_start: 0.8074 (t0) cc_final: 0.7482 (t0) REVERT: K 244 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7207 (p0) REVERT: L 78 ASN cc_start: 0.8117 (m110) cc_final: 0.7490 (m-40) REVERT: L 244 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.6988 (p0) REVERT: L 372 ARG cc_start: 0.7284 (ptp-170) cc_final: 0.6907 (ptp-170) REVERT: E 100 ARG cc_start: 0.7855 (ttt90) cc_final: 0.6189 (ptt90) REVERT: M 44 MET cc_start: 0.8730 (mmt) cc_final: 0.8357 (mmt) REVERT: M 121 GLN cc_start: 0.8044 (tm-30) cc_final: 0.7647 (tt0) outliers start: 43 outliers final: 34 residues processed: 385 average time/residue: 0.8749 time to fit residues: 489.1241 Evaluate side-chains 355 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 319 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 10 CYS Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 162 ASN Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 348 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 0.0670 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 202 optimal weight: 10.0000 chunk 163 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.2980 chunk 212 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 overall best weight: 2.6724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 20066 Z= 0.315 Angle : 0.601 6.792 27190 Z= 0.303 Chirality : 0.042 0.154 3070 Planarity : 0.005 0.045 3436 Dihedral : 11.012 168.776 2793 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.63 % Allowed : 15.00 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.19 (0.17), residues: 2435 helix: 0.85 (0.16), residues: 1070 sheet: -2.24 (0.28), residues: 295 loop : -0.36 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP M 340 HIS 0.006 0.001 HIS K 161 PHE 0.014 0.001 PHE K 262 TYR 0.009 0.001 TYR H 143 ARG 0.005 0.001 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 350 time to evaluate : 3.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8319 (mttp) cc_final: 0.7980 (mtpp) REVERT: H 283 MET cc_start: 0.8316 (mmt) cc_final: 0.7709 (mmt) REVERT: A 131 ASP cc_start: 0.7885 (m-30) cc_final: 0.7600 (m-30) REVERT: J 195 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7137 (mm-30) REVERT: J 299 MET cc_start: 0.8759 (tpt) cc_final: 0.8538 (tpt) REVERT: B 92 LYS cc_start: 0.7991 (tmmt) cc_final: 0.7521 (mtpt) REVERT: B 100 ARG cc_start: 0.7871 (ttt90) cc_final: 0.6055 (ptt180) REVERT: K 162 ASN cc_start: 0.8169 (t0) cc_final: 0.7599 (t0) REVERT: K 244 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7631 (p0) REVERT: C 60 VAL cc_start: 0.7964 (OUTLIER) cc_final: 0.7720 (t) REVERT: L 78 ASN cc_start: 0.8171 (m110) cc_final: 0.7625 (m110) REVERT: L 244 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7133 (p0) REVERT: L 372 ARG cc_start: 0.7385 (ptp-170) cc_final: 0.7099 (ptp-170) REVERT: E 76 ARG cc_start: 0.8870 (mtt90) cc_final: 0.8585 (mtt90) REVERT: E 100 ARG cc_start: 0.7830 (ttt90) cc_final: 0.6074 (ptt180) REVERT: M 44 MET cc_start: 0.8716 (mmt) cc_final: 0.8333 (mmt) REVERT: M 121 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7864 (tm-30) outliers start: 56 outliers final: 44 residues processed: 398 average time/residue: 0.8784 time to fit residues: 511.7963 Evaluate side-chains 360 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 313 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain J residue 351 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 286 ASP Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 278 THR Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Chi-restraints excluded: chain M residue 348 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 139 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 275 HIS ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.5968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20066 Z= 0.187 Angle : 0.543 8.353 27190 Z= 0.266 Chirality : 0.040 0.151 3070 Planarity : 0.004 0.045 3436 Dihedral : 10.753 174.626 2793 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.12 % Allowed : 16.18 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.11 (0.17), residues: 2435 helix: 1.14 (0.16), residues: 1055 sheet: -2.13 (0.28), residues: 310 loop : -0.18 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP M 340 HIS 0.005 0.001 HIS K 161 PHE 0.014 0.001 PHE K 262 TYR 0.009 0.001 TYR L 279 ARG 0.004 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 335 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8359 (mttp) cc_final: 0.7933 (mtpp) REVERT: H 283 MET cc_start: 0.8277 (mmt) cc_final: 0.7672 (mmt) REVERT: A 33 LYS cc_start: 0.6850 (pttp) cc_final: 0.6537 (tmmt) REVERT: A 131 ASP cc_start: 0.7837 (m-30) cc_final: 0.7531 (m-30) REVERT: J 82 MET cc_start: 0.8940 (tpt) cc_final: 0.8407 (tpt) REVERT: J 195 GLU cc_start: 0.7504 (mm-30) cc_final: 0.7014 (mm-30) REVERT: B 100 ARG cc_start: 0.7848 (ttt90) cc_final: 0.6121 (ptt90) REVERT: K 162 ASN cc_start: 0.8135 (t0) cc_final: 0.7525 (t0) REVERT: K 244 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7525 (p0) REVERT: L 78 ASN cc_start: 0.8115 (m110) cc_final: 0.7540 (m-40) REVERT: L 125 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: L 162 ASN cc_start: 0.8647 (t0) cc_final: 0.8280 (t0) REVERT: L 244 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7019 (p0) REVERT: L 372 ARG cc_start: 0.7335 (ptp-170) cc_final: 0.7053 (ptp-170) REVERT: E 76 ARG cc_start: 0.8855 (mtt90) cc_final: 0.8557 (mtt90) REVERT: E 100 ARG cc_start: 0.7806 (ttt90) cc_final: 0.6171 (ptt90) REVERT: M 44 MET cc_start: 0.8735 (mmt) cc_final: 0.8239 (mmt) outliers start: 45 outliers final: 37 residues processed: 375 average time/residue: 0.8647 time to fit residues: 471.3895 Evaluate side-chains 355 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 315 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 173 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20066 Z= 0.204 Angle : 0.543 6.515 27190 Z= 0.267 Chirality : 0.040 0.149 3070 Planarity : 0.004 0.042 3436 Dihedral : 10.550 179.413 2793 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.01 % Allowed : 16.04 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.24 (0.17), residues: 2435 helix: 1.28 (0.16), residues: 1055 sheet: -2.03 (0.29), residues: 310 loop : -0.16 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 340 HIS 0.006 0.001 HIS K 161 PHE 0.012 0.001 PHE K 262 TYR 0.007 0.001 TYR J 279 ARG 0.005 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 328 time to evaluate : 3.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8212 (mttp) cc_final: 0.7854 (mtpp) REVERT: H 283 MET cc_start: 0.8246 (mmt) cc_final: 0.7720 (mmt) REVERT: A 131 ASP cc_start: 0.7918 (m-30) cc_final: 0.7603 (m-30) REVERT: J 195 GLU cc_start: 0.7483 (mm-30) cc_final: 0.6992 (mm-30) REVERT: B 100 ARG cc_start: 0.7842 (ttt90) cc_final: 0.6105 (ptt90) REVERT: K 162 ASN cc_start: 0.8150 (t0) cc_final: 0.7591 (t0) REVERT: K 244 ASP cc_start: 0.8067 (OUTLIER) cc_final: 0.7840 (p0) REVERT: L 125 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: L 244 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7062 (p0) REVERT: E 76 ARG cc_start: 0.8849 (mtt90) cc_final: 0.8575 (mtt90) REVERT: E 100 ARG cc_start: 0.7801 (ttt90) cc_final: 0.6094 (ptt180) REVERT: M 44 MET cc_start: 0.8715 (mmt) cc_final: 0.8229 (mmt) outliers start: 64 outliers final: 54 residues processed: 385 average time/residue: 0.8363 time to fit residues: 469.9324 Evaluate side-chains 373 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 316 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 108 SER Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 244 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 162 ASN Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 278 THR Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 146 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 185 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.6174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20066 Z= 0.194 Angle : 0.539 6.417 27190 Z= 0.265 Chirality : 0.040 0.149 3070 Planarity : 0.004 0.042 3436 Dihedral : 10.431 176.186 2793 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.63 % Allowed : 16.56 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.17), residues: 2435 helix: 1.27 (0.16), residues: 1070 sheet: -1.97 (0.29), residues: 310 loop : -0.25 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 340 HIS 0.005 0.001 HIS K 161 PHE 0.011 0.001 PHE K 262 TYR 0.007 0.001 TYR K 218 ARG 0.006 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 325 time to evaluate : 3.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8200 (mttp) cc_final: 0.7846 (mtpp) REVERT: H 283 MET cc_start: 0.8225 (mmt) cc_final: 0.7701 (mmt) REVERT: A 131 ASP cc_start: 0.7917 (m-30) cc_final: 0.7392 (m-30) REVERT: J 195 GLU cc_start: 0.7458 (mm-30) cc_final: 0.6988 (mm-30) REVERT: B 100 ARG cc_start: 0.7818 (ttt90) cc_final: 0.6099 (ptt90) REVERT: K 162 ASN cc_start: 0.8145 (t0) cc_final: 0.7574 (t0) REVERT: C 115 ASP cc_start: 0.7299 (m-30) cc_final: 0.7093 (m-30) REVERT: L 78 ASN cc_start: 0.8185 (m110) cc_final: 0.7541 (m110) REVERT: L 125 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: L 244 ASP cc_start: 0.7763 (OUTLIER) cc_final: 0.7051 (p0) REVERT: E 76 ARG cc_start: 0.8860 (mtt90) cc_final: 0.8579 (mtt90) REVERT: E 100 ARG cc_start: 0.7802 (ttt90) cc_final: 0.6166 (ptt90) REVERT: M 44 MET cc_start: 0.8708 (mmt) cc_final: 0.8228 (mmt) REVERT: M 161 HIS cc_start: 0.7928 (OUTLIER) cc_final: 0.7079 (m-70) outliers start: 56 outliers final: 51 residues processed: 374 average time/residue: 0.8363 time to fit residues: 454.6271 Evaluate side-chains 364 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 310 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 277 THR Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 45 VAL Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 0.9980 chunk 226 optimal weight: 3.9990 chunk 206 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 0.8980 chunk 172 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 198 optimal weight: 3.9990 chunk 208 optimal weight: 6.9990 chunk 219 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.6244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20066 Z= 0.167 Angle : 0.525 6.340 27190 Z= 0.256 Chirality : 0.039 0.150 3070 Planarity : 0.004 0.042 3436 Dihedral : 10.103 169.968 2791 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.63 % Allowed : 16.70 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.18), residues: 2435 helix: 1.50 (0.16), residues: 1055 sheet: -1.88 (0.29), residues: 310 loop : -0.12 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 340 HIS 0.005 0.001 HIS K 161 PHE 0.010 0.001 PHE K 262 TYR 0.009 0.001 TYR L 218 ARG 0.006 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 338 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 92 LYS cc_start: 0.8186 (mttp) cc_final: 0.7836 (mtpp) REVERT: H 195 GLU cc_start: 0.7032 (mm-30) cc_final: 0.6742 (mm-30) REVERT: H 283 MET cc_start: 0.8205 (mmt) cc_final: 0.7737 (mmt) REVERT: A 131 ASP cc_start: 0.7887 (m-30) cc_final: 0.7563 (m-30) REVERT: J 195 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6962 (mm-30) REVERT: J 269 MET cc_start: 0.8299 (mtp) cc_final: 0.8036 (mtp) REVERT: B 100 ARG cc_start: 0.7824 (ttt90) cc_final: 0.6021 (ptt180) REVERT: K 162 ASN cc_start: 0.8122 (t0) cc_final: 0.7611 (t0) REVERT: L 125 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: L 244 ASP cc_start: 0.7877 (OUTLIER) cc_final: 0.7163 (p0) REVERT: E 76 ARG cc_start: 0.8788 (mtt90) cc_final: 0.8492 (mtt90) REVERT: E 100 ARG cc_start: 0.7785 (ttt90) cc_final: 0.6161 (ptt90) REVERT: M 44 MET cc_start: 0.8755 (mmt) cc_final: 0.8285 (mmt) REVERT: M 161 HIS cc_start: 0.7985 (OUTLIER) cc_final: 0.7359 (m-70) REVERT: M 211 ASP cc_start: 0.8378 (t0) cc_final: 0.7953 (t0) outliers start: 56 outliers final: 49 residues processed: 386 average time/residue: 0.8815 time to fit residues: 497.7739 Evaluate side-chains 373 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 321 time to evaluate : 3.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 192 ILE Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.6980 chunk 232 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 110 optimal weight: 0.0470 chunk 161 optimal weight: 0.7980 chunk 244 optimal weight: 3.9990 chunk 224 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20066 Z= 0.166 Angle : 0.529 9.190 27190 Z= 0.257 Chirality : 0.039 0.150 3070 Planarity : 0.004 0.042 3436 Dihedral : 9.844 163.402 2787 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.40 % Allowed : 17.45 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.55 (0.18), residues: 2435 helix: 1.59 (0.16), residues: 1055 sheet: -1.78 (0.29), residues: 310 loop : -0.10 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 340 HIS 0.005 0.001 HIS K 161 PHE 0.010 0.001 PHE K 262 TYR 0.007 0.001 TYR L 218 ARG 0.006 0.000 ARG A 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4870 Ramachandran restraints generated. 2435 Oldfield, 0 Emsley, 2435 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 323 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 195 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6697 (mm-30) REVERT: H 283 MET cc_start: 0.8197 (mmt) cc_final: 0.7758 (mmt) REVERT: H 287 ILE cc_start: 0.8590 (tp) cc_final: 0.8330 (tp) REVERT: A 131 ASP cc_start: 0.7870 (m-30) cc_final: 0.7545 (m-30) REVERT: J 195 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7020 (mm-30) REVERT: B 100 ARG cc_start: 0.7843 (ttt90) cc_final: 0.6021 (ptt180) REVERT: K 162 ASN cc_start: 0.8160 (t0) cc_final: 0.7633 (t0) REVERT: L 125 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: L 244 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7205 (p0) REVERT: E 76 ARG cc_start: 0.8786 (mtt90) cc_final: 0.8484 (mtt90) REVERT: E 100 ARG cc_start: 0.7779 (ttt90) cc_final: 0.6159 (ptt90) REVERT: M 44 MET cc_start: 0.8751 (mmt) cc_final: 0.8214 (mmt) REVERT: M 161 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7465 (m-70) outliers start: 51 outliers final: 47 residues processed: 366 average time/residue: 0.8334 time to fit residues: 440.5774 Evaluate side-chains 365 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 315 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 142 LEU Chi-restraints excluded: chain H residue 154 ASP Chi-restraints excluded: chain H residue 160 THR Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 257 CYS Chi-restraints excluded: chain H residue 265 SER Chi-restraints excluded: chain H residue 281 SER Chi-restraints excluded: chain H residue 300 SER Chi-restraints excluded: chain H residue 348 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain J residue 16 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 244 ASP Chi-restraints excluded: chain J residue 257 CYS Chi-restraints excluded: chain J residue 286 ASP Chi-restraints excluded: chain J residue 300 SER Chi-restraints excluded: chain J residue 348 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain K residue 16 LEU Chi-restraints excluded: chain K residue 160 THR Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 203 THR Chi-restraints excluded: chain K residue 222 ASP Chi-restraints excluded: chain K residue 257 CYS Chi-restraints excluded: chain K residue 300 SER Chi-restraints excluded: chain K residue 348 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 85 ILE Chi-restraints excluded: chain L residue 119 MET Chi-restraints excluded: chain L residue 125 GLU Chi-restraints excluded: chain L residue 161 HIS Chi-restraints excluded: chain L residue 203 THR Chi-restraints excluded: chain L residue 222 ASP Chi-restraints excluded: chain L residue 244 ASP Chi-restraints excluded: chain L residue 257 CYS Chi-restraints excluded: chain L residue 348 SER Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 126 SER Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 160 THR Chi-restraints excluded: chain M residue 161 HIS Chi-restraints excluded: chain M residue 162 ASN Chi-restraints excluded: chain M residue 222 ASP Chi-restraints excluded: chain M residue 263 GLN Chi-restraints excluded: chain M residue 296 ASN Chi-restraints excluded: chain M residue 300 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 2.9990 chunk 207 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 194 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.096650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.085804 restraints weight = 103780.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.088734 restraints weight = 38331.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.090402 restraints weight = 19351.118| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.6457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20066 Z= 0.261 Angle : 0.566 8.214 27190 Z= 0.280 Chirality : 0.041 0.148 3070 Planarity : 0.004 0.042 3436 Dihedral : 9.906 162.567 2787 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.78 % Allowed : 16.79 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.17), residues: 2435 helix: 1.34 (0.16), residues: 1070 sheet: -1.80 (0.28), residues: 320 loop : -0.22 (0.20), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 340 HIS 0.005 0.001 HIS J 161 PHE 0.013 0.001 PHE K 262 TYR 0.009 0.001 TYR H 143 ARG 0.007 0.000 ARG C 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9772.63 seconds wall clock time: 173 minutes 23.15 seconds (10403.15 seconds total)