Starting phenix.real_space_refine (version: dev) on Sat Apr 9 10:11:16 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/04_2022/6d8c_7831_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/04_2022/6d8c_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_7831/04_2022/6d8c_7831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/04_2022/6d8c_7831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/04_2022/6d8c_7831_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6d8c_7831/04_2022/6d8c_7831_trim_updated.pdb" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral 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-4553/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 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 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 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: 16.87, 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: 34.41 Conformation dependent library (CDL) restraints added in 3.2 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: 2.08 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: 15.59 Time building geometry restraints manager: 35.23 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: 15691 33.81 - 67.63: 109 67.63 - 101.44: 0 101.44 - 135.25: 5 135.25 - 169.06: 10 Dihedral angle restraints: 15815 sinusoidal: 7518 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 15812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2654 0.065 - 0.131: 383 0.131 - 0.196: 20 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 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. 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.280 Construct map_model_manager: 0.550 Extract box with map and model: 5.590 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.300 Process input model: 123.300 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 136.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 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= 0.392 Angle : 0.823 10.405 27190 Z= 0.480 Chirality : 0.046 0.327 3070 Planarity : 0.005 0.059 3436 Dihedral : 11.575 169.063 7495 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 % 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 *********************** 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 : 3.470 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 outliers start: 18 outliers final: 13 residues processed: 728 average time/residue: 0.8058 time to fit residues: 862.8637 Evaluate side-chains 392 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 379 time to evaluate : 3.479 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 13 average time/residue: 0.4642 time to fit residues: 15.2768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 206 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 142 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 280 ASN J 296 ASN K 137 GLN 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 20066 Z= 0.310 Angle : 0.652 6.841 27190 Z= 0.332 Chirality : 0.043 0.144 3070 Planarity : 0.005 0.053 3436 Dihedral : 10.490 171.266 2731 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.07 % 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: -1.08 (0.16), residues: 2435 helix: -0.22 (0.14), residues: 1075 sheet: -2.28 (0.27), residues: 295 loop : -0.56 (0.18), residues: 1065 *********************** 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 468 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 424 time to evaluate : 3.632 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 outliers start: 44 outliers final: 38 residues processed: 458 average time/residue: 0.8418 time to fit residues: 556.9857 Evaluate side-chains 380 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 342 time to evaluate : 3.346 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4733 time to fit residues: 37.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 123 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 151 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 222 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 198 optimal weight: 2.9990 chunk 221 optimal weight: 0.0570 chunk 75 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 overall best weight: 1.8704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 133 ASN C 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 20066 Z= 0.232 Angle : 0.589 6.887 27190 Z= 0.296 Chirality : 0.041 0.183 3070 Planarity : 0.004 0.052 3436 Dihedral : 10.164 160.411 2731 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.85 % 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: -0.31 (0.17), residues: 2435 helix: 0.63 (0.15), residues: 1050 sheet: -2.17 (0.28), residues: 285 loop : -0.33 (0.19), residues: 1100 *********************** 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 382 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 364 time to evaluate : 3.323 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 outliers start: 18 outliers final: 14 residues processed: 377 average time/residue: 0.8261 time to fit residues: 450.8345 Evaluate side-chains 332 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 318 time to evaluate : 3.474 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.4214 time to fit residues: 15.2603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 220 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 149 optimal weight: 4.9990 chunk 223 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 212 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 137 GLN M 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 20066 Z= 0.309 Angle : 0.618 9.953 27190 Z= 0.312 Chirality : 0.042 0.185 3070 Planarity : 0.004 0.041 3436 Dihedral : 10.185 169.376 2731 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer Outliers : 1.27 % 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: -0.14 (0.17), residues: 2435 helix: 0.80 (0.16), residues: 1055 sheet: -2.21 (0.28), residues: 285 loop : -0.22 (0.20), residues: 1095 *********************** 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 386 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 359 time to evaluate : 3.556 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 outliers start: 27 outliers final: 20 residues processed: 381 average time/residue: 0.8124 time to fit residues: 450.3528 Evaluate side-chains 325 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 305 time to evaluate : 3.304 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.4280 time to fit residues: 19.7896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 197 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 176 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 20066 Z= 0.320 Angle : 0.608 6.851 27190 Z= 0.308 Chirality : 0.042 0.176 3070 Planarity : 0.004 0.046 3436 Dihedral : 10.096 175.118 2731 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 1.69 % 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: -0.13 (0.17), residues: 2435 helix: 0.81 (0.16), residues: 1055 sheet: -2.28 (0.27), residues: 315 loop : -0.12 (0.20), residues: 1065 *********************** 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 384 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 348 time to evaluate : 3.489 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 outliers start: 36 outliers final: 29 residues processed: 378 average time/residue: 0.7849 time to fit residues: 438.3217 Evaluate side-chains 336 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 307 time to evaluate : 3.396 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4124 time to fit residues: 26.4890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 79 optimal weight: 3.9990 chunk 213 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 237 optimal weight: 0.5980 chunk 196 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 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** D 56 HIS B 86 GLN K 275 HIS ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.6079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 20066 Z= 0.194 Angle : 0.549 6.288 27190 Z= 0.271 Chirality : 0.040 0.155 3070 Planarity : 0.004 0.040 3436 Dihedral : 9.848 177.869 2731 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.56 % 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: 0.12 (0.17), residues: 2435 helix: 1.06 (0.16), residues: 1055 sheet: -2.17 (0.28), residues: 305 loop : -0.07 (0.20), residues: 1075 *********************** 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 353 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 341 time to evaluate : 3.426 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 outliers start: 12 outliers final: 8 residues processed: 351 average time/residue: 0.7764 time to fit residues: 404.6936 Evaluate side-chains 322 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 314 time to evaluate : 3.415 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4368 time to fit residues: 10.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 228 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 134 optimal weight: 0.8980 chunk 199 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 109 optimal weight: 0.0070 overall best weight: 1.3402 ------------------------------------------------------------------------------- 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** D 68 GLN B 86 GLN ** L 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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= 0.187 Angle : 0.545 7.191 27190 Z= 0.267 Chirality : 0.040 0.142 3070 Planarity : 0.004 0.040 3436 Dihedral : 9.570 170.229 2731 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.61 % 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: 0.31 (0.18), residues: 2435 helix: 1.24 (0.16), residues: 1055 sheet: -2.02 (0.29), residues: 305 loop : -0.01 (0.20), residues: 1075 *********************** 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 349 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 336 time to evaluate : 3.498 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 outliers start: 13 outliers final: 8 residues processed: 346 average time/residue: 0.8175 time to fit residues: 422.3139 Evaluate side-chains 333 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 325 time to evaluate : 3.133 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.4366 time to fit residues: 10.6249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 141 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 185 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** M 162 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 20066 Z= 0.301 Angle : 0.596 9.254 27190 Z= 0.298 Chirality : 0.042 0.161 3070 Planarity : 0.004 0.039 3436 Dihedral : 9.679 172.435 2731 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer Outliers : 0.75 % 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: 0.10 (0.17), residues: 2435 helix: 1.03 (0.16), residues: 1070 sheet: -2.02 (0.29), residues: 305 loop : -0.13 (0.20), residues: 1060 *********************** 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 348 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 3.476 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 outliers start: 16 outliers final: 12 residues processed: 341 average time/residue: 0.7925 time to fit residues: 399.4709 Evaluate side-chains 330 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 318 time to evaluate : 3.256 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4284 time to fit residues: 13.6770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 214 optimal weight: 1.9990 chunk 226 optimal weight: 0.9980 chunk 206 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 198 optimal weight: 5.9990 chunk 208 optimal weight: 0.0170 chunk 219 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 20066 Z= 0.146 Angle : 0.530 8.078 27190 Z= 0.256 Chirality : 0.039 0.141 3070 Planarity : 0.003 0.040 3436 Dihedral : 9.143 162.078 2731 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.09 % 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: 0.38 (0.18), residues: 2435 helix: 1.50 (0.16), residues: 1045 sheet: -2.10 (0.27), residues: 345 loop : -0.05 (0.20), residues: 1045 *********************** 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 343 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 341 time to evaluate : 3.456 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 outliers start: 2 outliers final: 2 residues processed: 343 average time/residue: 0.8106 time to fit residues: 409.8085 Evaluate side-chains 324 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 3.336 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4727 time to fit residues: 5.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 144 optimal weight: 0.9980 chunk 232 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 0.0670 chunk 161 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.1322 ------------------------------------------------------------------------------- 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 ** 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: 0.8247 moved from start: 0.6452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 20066 Z= 0.169 Angle : 0.533 6.701 27190 Z= 0.260 Chirality : 0.039 0.146 3070 Planarity : 0.004 0.063 3436 Dihedral : 8.955 161.060 2731 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer Outliers : 0.19 % 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: 0.48 (0.18), residues: 2435 helix: 1.52 (0.16), residues: 1055 sheet: -1.84 (0.29), residues: 315 loop : -0.10 (0.20), residues: 1065 ********************** 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 325 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 321 time to evaluate : 3.344 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 outliers start: 4 outliers final: 2 residues processed: 324 average time/residue: 0.7945 time to fit residues: 379.2425 Evaluate side-chains 317 residues out of total 2126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 315 time to evaluate : 3.622 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4953 time to fit residues: 6.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 245 random chunks: chunk 154 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 28 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 199 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.100280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.089376 restraints weight = 102399.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.092381 restraints weight = 37366.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094100 restraints weight = 18744.325| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 20066 Z= 0.148 Angle : 0.525 6.851 27190 Z= 0.254 Chirality : 0.039 0.145 3070 Planarity : 0.004 0.052 3436 Dihedral : 8.705 158.495 2731 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.24 % 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: 0.59 (0.18), residues: 2435 helix: 1.61 (0.16), residues: 1055 sheet: -1.66 (0.30), residues: 310 loop : -0.09 (0.20), residues: 1070 =============================================================================== Job complete usr+sys time: 8971.18 seconds wall clock time: 159 minutes 50.48 seconds (9590.48 seconds total)