Starting phenix.real_space_refine (version: dev) on Wed Dec 21 01:46:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/12_2022/6uks_20811_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 "A GLU 96": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 258": "OD1" <-> "OD2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 258": "OD1" <-> "OD2" Residue "C GLU 96": "OE1" <-> "OE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 258": "OD1" <-> "OD2" Residue "D GLU 96": "OE1" <-> "OE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 258": "OD1" <-> "OD2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 210": "OD1" <-> "OD2" Residue "E ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 258": "OD1" <-> "OD2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 210": "OD1" <-> "OD2" Residue "F ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 258": "OD1" <-> "OD2" Residue "G GLU 96": "OE1" <-> "OE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G ARG 185": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 210": "OD1" <-> "OD2" Residue "G ARG 218": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 258": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 40838 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "B" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "C" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "D" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "E" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "F" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "G" Number of atoms: 5802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 5802 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 18.29, per 1000 atoms: 0.45 Number of scatterers: 40838 At special positions: 0 Unit cell: (144.48, 143.62, 92.02, 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 77 16.00 P 21 15.00 Mg 7 11.99 O 3829 8.00 N 3612 7.00 C 13132 6.00 H 20160 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 32.20 Conformation dependent library (CDL) restraints added in 3.7 seconds 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 105 helices and 28 sheets defined 34.3% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.36 Creating SS restraints... Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 145 through 161 Processing helix chain 'A' and resid 188 through 190 No H-bonds generated for 'chain 'A' and resid 188 through 190' Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 216 No H-bonds generated for 'chain 'A' and resid 213 through 216' Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 263 through 269 Processing helix chain 'A' and resid 285 through 287 No H-bonds generated for 'chain 'A' and resid 285 through 287' Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 407 through 412 Processing helix chain 'A' and resid 414 through 417 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 145 through 161 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 198 through 209 Processing helix chain 'B' and resid 213 through 216 No H-bonds generated for 'chain 'B' and resid 213 through 216' Processing helix chain 'B' and resid 236 through 246 Processing helix chain 'B' and resid 263 through 269 Processing helix chain 'B' and resid 285 through 287 No H-bonds generated for 'chain 'B' and resid 285 through 287' Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 374 through 387 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 407 through 412 Processing helix chain 'B' and resid 414 through 417 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 145 through 161 Processing helix chain 'C' and resid 188 through 190 No H-bonds generated for 'chain 'C' and resid 188 through 190' Processing helix chain 'C' and resid 198 through 209 Processing helix chain 'C' and resid 213 through 216 No H-bonds generated for 'chain 'C' and resid 213 through 216' Processing helix chain 'C' and resid 236 through 246 Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 374 through 387 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 407 through 412 Processing helix chain 'C' and resid 414 through 417 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 145 through 161 Processing helix chain 'D' and resid 188 through 190 No H-bonds generated for 'chain 'D' and resid 188 through 190' Processing helix chain 'D' and resid 198 through 209 Processing helix chain 'D' and resid 213 through 216 No H-bonds generated for 'chain 'D' and resid 213 through 216' Processing helix chain 'D' and resid 236 through 246 Processing helix chain 'D' and resid 263 through 269 Processing helix chain 'D' and resid 285 through 287 No H-bonds generated for 'chain 'D' and resid 285 through 287' Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 374 through 387 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 414 through 417 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 87 through 89 No H-bonds generated for 'chain 'E' and resid 87 through 89' Processing helix chain 'E' and resid 145 through 161 Processing helix chain 'E' and resid 188 through 190 No H-bonds generated for 'chain 'E' and resid 188 through 190' Processing helix chain 'E' and resid 198 through 209 Processing helix chain 'E' and resid 213 through 216 No H-bonds generated for 'chain 'E' and resid 213 through 216' Processing helix chain 'E' and resid 236 through 246 Processing helix chain 'E' and resid 263 through 269 Processing helix chain 'E' and resid 285 through 287 No H-bonds generated for 'chain 'E' and resid 285 through 287' Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 358 through 368 Processing helix chain 'E' and resid 374 through 387 Processing helix chain 'E' and resid 393 through 402 Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 414 through 417 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 87 through 89 No H-bonds generated for 'chain 'F' and resid 87 through 89' Processing helix chain 'F' and resid 145 through 161 Processing helix chain 'F' and resid 188 through 190 No H-bonds generated for 'chain 'F' and resid 188 through 190' Processing helix chain 'F' and resid 198 through 209 Processing helix chain 'F' and resid 213 through 216 No H-bonds generated for 'chain 'F' and resid 213 through 216' Processing helix chain 'F' and resid 236 through 246 Processing helix chain 'F' and resid 263 through 269 Processing helix chain 'F' and resid 285 through 287 No H-bonds generated for 'chain 'F' and resid 285 through 287' Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 358 through 368 Processing helix chain 'F' and resid 374 through 387 Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 414 through 417 Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 87 through 89 No H-bonds generated for 'chain 'G' and resid 87 through 89' Processing helix chain 'G' and resid 145 through 161 Processing helix chain 'G' and resid 188 through 190 No H-bonds generated for 'chain 'G' and resid 188 through 190' Processing helix chain 'G' and resid 198 through 209 Processing helix chain 'G' and resid 213 through 216 No H-bonds generated for 'chain 'G' and resid 213 through 216' Processing helix chain 'G' and resid 236 through 246 Processing helix chain 'G' and resid 263 through 269 Processing helix chain 'G' and resid 285 through 287 No H-bonds generated for 'chain 'G' and resid 285 through 287' Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 358 through 368 Processing helix chain 'G' and resid 374 through 387 Processing helix chain 'G' and resid 393 through 402 Processing helix chain 'G' and resid 407 through 412 Processing helix chain 'G' and resid 414 through 417 Processing sheet with id= A, first strand: chain 'A' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG A 117 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY A 102 " --> pdb=" O ARG A 117 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 80 through 84 Processing sheet with id= C, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= D, first strand: chain 'A' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU A 351 " --> pdb=" O GLY A 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 227 " --> pdb=" O GLU A 351 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG A 325 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR A 226 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL A 327 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 228 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N MET A 329 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER A 277 " --> pdb=" O ILE A 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE A 328 " --> pdb=" O SER A 277 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL A 279 " --> pdb=" O PHE A 328 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR A 330 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 281 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER A 250 " --> pdb=" O LEU A 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 280 " --> pdb=" O SER A 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS A 252 " --> pdb=" O LEU A 280 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU A 282 " --> pdb=" O CYS A 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.767A pdb=" N ARG B 117 " --> pdb=" O GLY B 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY B 102 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 80 through 84 Processing sheet with id= G, first strand: chain 'B' and resid 169 through 172 Processing sheet with id= H, first strand: chain 'B' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU B 351 " --> pdb=" O GLY B 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU B 227 " --> pdb=" O GLU B 351 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 325 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR B 226 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL B 327 " --> pdb=" O TYR B 226 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU B 228 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET B 329 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER B 277 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE B 328 " --> pdb=" O SER B 277 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL B 279 " --> pdb=" O PHE B 328 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR B 330 " --> pdb=" O VAL B 279 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N LEU B 281 " --> pdb=" O THR B 330 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER B 250 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 280 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 252 " --> pdb=" O LEU B 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU B 282 " --> pdb=" O CYS B 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG C 117 " --> pdb=" O GLY C 102 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLY C 102 " --> pdb=" O ARG C 117 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 80 through 84 Processing sheet with id= K, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= L, first strand: chain 'C' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU C 351 " --> pdb=" O GLY C 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU C 227 " --> pdb=" O GLU C 351 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 325 " --> pdb=" O ARG C 224 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR C 226 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL C 327 " --> pdb=" O TYR C 226 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU C 228 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET C 329 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER C 277 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE C 328 " --> pdb=" O SER C 277 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL C 279 " --> pdb=" O PHE C 328 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR C 330 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 281 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER C 250 " --> pdb=" O LEU C 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 280 " --> pdb=" O SER C 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 252 " --> pdb=" O LEU C 280 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLU C 282 " --> pdb=" O CYS C 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG D 117 " --> pdb=" O GLY D 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY D 102 " --> pdb=" O ARG D 117 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 80 through 84 Processing sheet with id= O, first strand: chain 'D' and resid 169 through 172 Processing sheet with id= P, first strand: chain 'D' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU D 351 " --> pdb=" O GLY D 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU D 227 " --> pdb=" O GLU D 351 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG D 325 " --> pdb=" O ARG D 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR D 226 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 327 " --> pdb=" O TYR D 226 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU D 228 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET D 329 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER D 277 " --> pdb=" O ILE D 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE D 328 " --> pdb=" O SER D 277 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL D 279 " --> pdb=" O PHE D 328 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR D 330 " --> pdb=" O VAL D 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU D 281 " --> pdb=" O THR D 330 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER D 250 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU D 280 " --> pdb=" O SER D 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS D 252 " --> pdb=" O LEU D 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU D 282 " --> pdb=" O CYS D 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 50 through 52 removed outlier: 3.767A pdb=" N ARG E 117 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 102 " --> pdb=" O ARG E 117 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 80 through 84 Processing sheet with id= S, first strand: chain 'E' and resid 169 through 172 Processing sheet with id= T, first strand: chain 'E' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU E 351 " --> pdb=" O GLY E 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU E 227 " --> pdb=" O GLU E 351 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG E 325 " --> pdb=" O ARG E 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR E 226 " --> pdb=" O ARG E 325 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL E 327 " --> pdb=" O TYR E 226 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU E 228 " --> pdb=" O VAL E 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET E 329 " --> pdb=" O LEU E 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER E 277 " --> pdb=" O ILE E 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE E 328 " --> pdb=" O SER E 277 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL E 279 " --> pdb=" O PHE E 328 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR E 330 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU E 281 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N SER E 250 " --> pdb=" O LEU E 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU E 280 " --> pdb=" O SER E 250 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS E 252 " --> pdb=" O LEU E 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU E 282 " --> pdb=" O CYS E 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG F 117 " --> pdb=" O GLY F 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY F 102 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 80 through 84 Processing sheet with id= W, first strand: chain 'F' and resid 169 through 172 Processing sheet with id= X, first strand: chain 'F' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU F 351 " --> pdb=" O GLY F 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 227 " --> pdb=" O GLU F 351 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG F 325 " --> pdb=" O ARG F 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR F 226 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL F 327 " --> pdb=" O TYR F 226 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU F 228 " --> pdb=" O VAL F 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET F 329 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER F 277 " --> pdb=" O ILE F 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE F 328 " --> pdb=" O SER F 277 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL F 279 " --> pdb=" O PHE F 328 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N THR F 330 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU F 281 " --> pdb=" O THR F 330 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER F 250 " --> pdb=" O LEU F 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU F 280 " --> pdb=" O SER F 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS F 252 " --> pdb=" O LEU F 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU F 282 " --> pdb=" O CYS F 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 50 through 52 removed outlier: 3.766A pdb=" N ARG G 117 " --> pdb=" O GLY G 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY G 102 " --> pdb=" O ARG G 117 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 80 through 84 Processing sheet with id= AA, first strand: chain 'G' and resid 169 through 172 Processing sheet with id= AB, first strand: chain 'G' and resid 350 through 352 removed outlier: 8.672A pdb=" N GLU G 351 " --> pdb=" O GLY G 225 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU G 227 " --> pdb=" O GLU G 351 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG G 325 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N TYR G 226 " --> pdb=" O ARG G 325 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL G 327 " --> pdb=" O TYR G 226 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU G 228 " --> pdb=" O VAL G 327 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET G 329 " --> pdb=" O LEU G 228 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER G 277 " --> pdb=" O ILE G 326 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N PHE G 328 " --> pdb=" O SER G 277 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL G 279 " --> pdb=" O PHE G 328 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N THR G 330 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU G 281 " --> pdb=" O THR G 330 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N SER G 250 " --> pdb=" O LEU G 278 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU G 280 " --> pdb=" O SER G 250 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS G 252 " --> pdb=" O LEU G 280 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N GLU G 282 " --> pdb=" O CYS G 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB 630 hydrogen bonds defined for protein. 1743 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: 15.26 Time building geometry restraints manager: 33.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.78 - 1.02: 20137 1.02 - 1.25: 3306 1.25 - 1.49: 9477 1.49 - 1.73: 8310 1.73 - 1.96: 126 Bond restraints: 41356 Sorted by residual: bond pdb=" NH2 ARG C 56 " pdb="HH22 ARG C 56 " ideal model delta sigma weight residual 0.860 0.937 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" OG1 THR G 130 " pdb=" HG1 THR G 130 " ideal model delta sigma weight residual 0.840 0.781 0.059 2.00e-02 2.50e+03 8.60e+00 bond pdb=" CG2 THR E 130 " pdb="HG22 THR E 130 " ideal model delta sigma weight residual 0.970 1.029 -0.059 2.00e-02 2.50e+03 8.57e+00 bond pdb=" OG1 THR E 130 " pdb=" HG1 THR E 130 " ideal model delta sigma weight residual 0.840 0.784 0.056 2.00e-02 2.50e+03 7.85e+00 bond pdb=" NH1 ARG C 56 " pdb="HH12 ARG C 56 " ideal model delta sigma weight residual 0.860 0.911 -0.051 2.00e-02 2.50e+03 6.52e+00 ... (remaining 41351 not shown) Histogram of bond angle deviations from ideal: 95.71 - 103.39: 327 103.39 - 111.07: 42869 111.07 - 118.75: 12180 118.75 - 126.42: 18549 126.42 - 134.10: 520 Bond angle restraints: 74445 Sorted by residual: angle pdb=" OG1 THR E 130 " pdb=" CB THR E 130 " pdb=" HB THR E 130 " ideal model delta sigma weight residual 109.00 95.71 13.29 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C SER A 59 " pdb=" N TYR A 60 " pdb=" CA TYR A 60 " ideal model delta sigma weight residual 120.38 126.28 -5.90 1.37e+00 5.33e-01 1.86e+01 angle pdb=" C SER F 59 " pdb=" N TYR F 60 " pdb=" CA TYR F 60 " ideal model delta sigma weight residual 120.38 126.27 -5.89 1.37e+00 5.33e-01 1.85e+01 angle pdb=" C SER B 59 " pdb=" N TYR B 60 " pdb=" CA TYR B 60 " ideal model delta sigma weight residual 120.38 126.25 -5.87 1.37e+00 5.33e-01 1.84e+01 angle pdb=" C SER D 59 " pdb=" N TYR D 60 " pdb=" CA TYR D 60 " ideal model delta sigma weight residual 120.38 126.23 -5.85 1.37e+00 5.33e-01 1.83e+01 ... (remaining 74440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 16191 27.67 - 55.35: 454 55.35 - 83.02: 36 83.02 - 110.70: 0 110.70 - 138.37: 7 Dihedral angle restraints: 16688 sinusoidal: 7791 harmonic: 8897 Sorted by residual: dihedral pdb=" O1A AGS C 800 " pdb=" O3A AGS C 800 " pdb=" PA AGS C 800 " pdb=" PB AGS C 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.64 -138.37 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS G 800 " pdb=" O3A AGS G 800 " pdb=" PA AGS G 800 " pdb=" PB AGS G 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.59 -138.32 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS F 800 " pdb=" O3A AGS F 800 " pdb=" PA AGS F 800 " pdb=" PB AGS F 800 " ideal model delta sinusoidal sigma weight residual -67.73 70.59 -138.32 1 3.00e+01 1.11e-03 1.86e+01 ... (remaining 16685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1938 0.038 - 0.076: 838 0.076 - 0.114: 286 0.114 - 0.152: 59 0.152 - 0.189: 15 Chirality restraints: 3136 Sorted by residual: chirality pdb=" CA PRO B 54 " pdb=" N PRO B 54 " pdb=" C PRO B 54 " pdb=" CB PRO B 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" CA PRO C 54 " pdb=" N PRO C 54 " pdb=" C PRO C 54 " pdb=" CB PRO C 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CA PRO D 54 " pdb=" N PRO D 54 " pdb=" C PRO D 54 " pdb=" CB PRO D 54 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.84e-01 ... (remaining 3133 not shown) Planarity restraints: 6062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 56 " -0.001 9.50e-02 1.11e+02 1.83e-02 7.55e+00 pdb=" NE ARG C 56 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 56 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG C 56 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 56 " -0.033 2.00e-02 2.50e+03 pdb="HH11 ARG C 56 " 0.016 2.00e-02 2.50e+03 pdb="HH12 ARG C 56 " -0.002 2.00e-02 2.50e+03 pdb="HH21 ARG C 56 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 56 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR F 130 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.41e+00 pdb=" N PRO F 131 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO F 131 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 131 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 130 " 0.045 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO D 131 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 131 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 131 " 0.038 5.00e-02 4.00e+02 ... (remaining 6059 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 3779 2.23 - 2.82: 87319 2.82 - 3.42: 97692 3.42 - 4.01: 134899 4.01 - 4.60: 209835 Nonbonded interactions: 533524 Sorted by model distance: nonbonded pdb="HH21 ARG B 223 " pdb=" OD1 ASP B 317 " model vdw 1.638 1.850 nonbonded pdb="HH21 ARG A 223 " pdb=" OD1 ASP A 317 " model vdw 1.638 1.850 nonbonded pdb="HH21 ARG C 223 " pdb=" OD1 ASP C 317 " model vdw 1.639 1.850 nonbonded pdb="HH21 ARG F 223 " pdb=" OD1 ASP F 317 " model vdw 1.639 1.850 nonbonded pdb="HH21 ARG E 223 " pdb=" OD1 ASP E 317 " model vdw 1.639 1.850 ... (remaining 533519 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 49 through 419) selection = (chain 'B' and resid 49 through 419) selection = (chain 'C' and resid 49 through 419) selection = (chain 'D' and resid 49 through 419) selection = (chain 'E' and resid 49 through 419) selection = (chain 'F' and resid 49 through 419) selection = (chain 'G' and resid 49 through 419) } 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 21 5.49 5 Mg 7 5.21 5 S 77 5.16 5 C 13132 2.51 5 N 3612 2.21 5 O 3829 1.98 5 H 20160 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.580 Extract box with map and model: 7.830 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.390 Process input model: 121.450 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 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 : 0.009 0.059 21196 Z= 0.561 Angle : 0.883 8.320 28819 Z= 0.470 Chirality : 0.048 0.189 3136 Planarity : 0.007 0.068 3668 Dihedral : 14.204 138.374 7784 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 0.32 % 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: -3.37 (0.15), residues: 2506 helix: -0.70 (0.16), residues: 917 sheet: -2.56 (0.19), residues: 602 loop : -3.47 (0.17), residues: 987 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 516 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 509 time to evaluate : 3.407 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: 7 outliers final: 3 residues processed: 516 average time/residue: 0.7259 time to fit residues: 564.1195 Evaluate side-chains 430 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 427 time to evaluate : 3.342 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4176 time to fit residues: 6.5754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 128 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 332 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN E 127 GLN E 397 GLN F 76 HIS F 127 GLN F 332 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 21196 Z= 0.240 Angle : 0.582 6.551 28819 Z= 0.300 Chirality : 0.039 0.134 3136 Planarity : 0.006 0.070 3668 Dihedral : 9.712 143.535 2891 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.86 % 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: -2.48 (0.16), residues: 2506 helix: 0.29 (0.17), residues: 917 sheet: -2.28 (0.19), residues: 602 loop : -3.10 (0.18), residues: 987 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 452 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 433 time to evaluate : 3.288 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: 19 outliers final: 10 residues processed: 443 average time/residue: 0.6998 time to fit residues: 475.2045 Evaluate side-chains 424 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 414 time to evaluate : 3.355 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4217 time to fit residues: 11.8927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 127 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 190 optimal weight: 0.8980 chunk 155 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 21196 Z= 0.222 Angle : 0.546 5.773 28819 Z= 0.276 Chirality : 0.039 0.138 3136 Planarity : 0.005 0.053 3668 Dihedral : 9.723 145.100 2891 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer Outliers : 0.45 % 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: -1.91 (0.17), residues: 2506 helix: 0.81 (0.18), residues: 917 sheet: -1.98 (0.20), residues: 581 loop : -2.81 (0.18), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 448 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 438 time to evaluate : 3.303 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 outliers start: 10 outliers final: 6 residues processed: 443 average time/residue: 0.7245 time to fit residues: 490.4093 Evaluate side-chains 429 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 423 time to evaluate : 3.537 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4072 time to fit residues: 8.9566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 5.9990 chunk 172 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 153 optimal weight: 4.9990 chunk 230 optimal weight: 2.9990 chunk 243 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 397 GLN ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 397 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 21196 Z= 0.277 Angle : 0.545 6.441 28819 Z= 0.273 Chirality : 0.039 0.193 3136 Planarity : 0.005 0.064 3668 Dihedral : 9.902 150.897 2891 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.41 % 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: -1.53 (0.17), residues: 2506 helix: 1.08 (0.18), residues: 917 sheet: -1.74 (0.20), residues: 581 loop : -2.58 (0.19), residues: 1008 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 447 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 438 time to evaluate : 3.495 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: 9 outliers final: 6 residues processed: 441 average time/residue: 0.7428 time to fit residues: 505.6828 Evaluate side-chains 434 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 428 time to evaluate : 3.313 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.7336 time to fit residues: 10.9822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 3.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 181 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 218 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 GLN ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 21196 Z= 0.275 Angle : 0.525 6.066 28819 Z= 0.265 Chirality : 0.039 0.156 3136 Planarity : 0.004 0.048 3668 Dihedral : 9.947 155.614 2891 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer Outliers : 0.14 % 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: -1.30 (0.17), residues: 2506 helix: 1.24 (0.18), residues: 917 sheet: -1.59 (0.20), residues: 567 loop : -2.43 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 3.355 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 outliers start: 3 outliers final: 2 residues processed: 434 average time/residue: 0.7442 time to fit residues: 496.9251 Evaluate side-chains 427 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 3.418 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4063 time to fit residues: 5.8665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 4.9990 chunk 219 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 0.7980 chunk 202 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.044 21196 Z= 0.433 Angle : 0.579 5.632 28819 Z= 0.292 Chirality : 0.042 0.148 3136 Planarity : 0.005 0.050 3668 Dihedral : 10.112 160.797 2891 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer Outliers : 0.32 % 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: -1.41 (0.17), residues: 2506 helix: 1.13 (0.18), residues: 917 sheet: -1.61 (0.20), residues: 567 loop : -2.50 (0.19), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 431 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 424 time to evaluate : 3.291 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: 7 outliers final: 6 residues processed: 424 average time/residue: 0.7787 time to fit residues: 506.4851 Evaluate side-chains 426 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 420 time to evaluate : 3.306 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.4876 time to fit residues: 10.0445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 235 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 0.5980 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 242 optimal weight: 0.5980 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 0.0670 chunk 112 optimal weight: 3.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 HIS ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 21196 Z= 0.159 Angle : 0.502 4.953 28819 Z= 0.252 Chirality : 0.038 0.146 3136 Planarity : 0.004 0.059 3668 Dihedral : 9.888 155.902 2891 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer Outliers : 0.14 % 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: -0.95 (0.18), residues: 2506 helix: 1.52 (0.18), residues: 917 sheet: -1.37 (0.21), residues: 567 loop : -2.23 (0.20), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 428 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 425 time to evaluate : 3.518 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: 3 outliers final: 2 residues processed: 425 average time/residue: 0.7464 time to fit residues: 482.0676 Evaluate side-chains 411 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 409 time to evaluate : 3.739 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5779 time to fit residues: 6.6002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 150 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 145 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 21196 Z= 0.353 Angle : 0.545 5.339 28819 Z= 0.273 Chirality : 0.040 0.159 3136 Planarity : 0.005 0.057 3668 Dihedral : 10.021 163.152 2891 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 0.23 % 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: -1.03 (0.18), residues: 2506 helix: 1.49 (0.18), residues: 917 sheet: -1.39 (0.20), residues: 567 loop : -2.33 (0.20), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 421 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 416 time to evaluate : 3.284 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 outliers start: 5 outliers final: 5 residues processed: 417 average time/residue: 0.7417 time to fit residues: 465.3859 Evaluate side-chains 420 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 415 time to evaluate : 3.314 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4388 time to fit residues: 8.1558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 226 optimal weight: 7.9990 chunk 136 optimal weight: 0.2980 chunk 98 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 214 optimal weight: 0.7980 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 21196 Z= 0.165 Angle : 0.503 4.797 28819 Z= 0.252 Chirality : 0.038 0.153 3136 Planarity : 0.004 0.065 3668 Dihedral : 9.868 159.374 2891 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 0.18 % 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: -0.73 (0.18), residues: 2506 helix: 1.70 (0.18), residues: 917 sheet: -1.20 (0.21), residues: 567 loop : -2.14 (0.20), residues: 1022 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 425 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 421 time to evaluate : 3.455 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 outliers start: 4 outliers final: 3 residues processed: 421 average time/residue: 0.7391 time to fit residues: 469.3167 Evaluate side-chains 422 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 419 time to evaluate : 3.373 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4802 time to fit residues: 6.7756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 199 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 21196 Z= 0.343 Angle : 0.545 5.735 28819 Z= 0.271 Chirality : 0.040 0.161 3136 Planarity : 0.004 0.056 3668 Dihedral : 9.976 164.009 2891 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer Outliers : 0.23 % 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: -0.75 (0.18), residues: 2506 helix: 1.78 (0.18), residues: 896 sheet: -1.22 (0.21), residues: 567 loop : -2.17 (0.20), residues: 1043 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5012 Ramachandran restraints generated. 2506 Oldfield, 0 Emsley, 2506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Residue SER 237 is missing expected H atoms. Skipping. Evaluate side-chains 428 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 423 time to evaluate : 3.382 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: 5 outliers final: 4 residues processed: 424 average time/residue: 0.7442 time to fit residues: 474.3370 Evaluate side-chains 423 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 419 time to evaluate : 3.442 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4224 time to fit residues: 7.7171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 212 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 200 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 76 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.128983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.095735 restraints weight = 85003.944| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.48 r_work: 0.2988 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 21196 Z= 0.300 Angle : 0.534 6.124 28819 Z= 0.268 Chirality : 0.040 0.152 3136 Planarity : 0.004 0.053 3668 Dihedral : 9.966 164.162 2891 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 0.00 % 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: -0.71 (0.18), residues: 2506 helix: 1.78 (0.18), residues: 896 sheet: -1.15 (0.21), residues: 567 loop : -2.14 (0.20), residues: 1043 =============================================================================== Job complete usr+sys time: 9867.28 seconds wall clock time: 173 minutes 21.43 seconds (10401.43 seconds total)