Starting phenix.real_space_refine on Sun Mar 24 09:32:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/03_2024/6uks_20811_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/03_2024/6uks_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_20811/03_2024/6uks_20811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/03_2024/6uks_20811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/03_2024/6uks_20811_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uks_20811/03_2024/6uks_20811_trim_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 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. 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-5265/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: 17.43, per 1000 atoms: 0.43 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: 33.68 Conformation dependent library (CDL) restraints added in 4.7 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: 6.74 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: 15.86 Time building geometry restraints manager: 34.89 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: 18697 27.67 - 55.35: 762 55.35 - 83.02: 50 83.02 - 110.70: 0 110.70 - 138.37: 7 Dihedral angle restraints: 19516 sinusoidal: 10619 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 19513 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 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: 0.000 Normalize map: mean=0, sd=1: 0.880 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: 6.150 Check model and map are aligned: 0.560 Set scattering table: 0.420 Process input model: 129.170 Find NCS groups from input model: 2.500 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 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 : 14.491 138.374 7861 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 % Allowed : 1.59 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 214 HIS 0.007 0.001 HIS D 104 PHE 0.022 0.002 PHE B 148 TYR 0.018 0.002 TYR D 60 ARG 0.010 0.001 ARG C 56 *********************** 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 : 3.263 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: A 52 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6523 (mt-10) REVERT: A 204 ASP cc_start: 0.7838 (t70) cc_final: 0.7384 (t0) REVERT: A 276 GLN cc_start: 0.8513 (mt0) cc_final: 0.8280 (mt0) REVERT: B 52 GLU cc_start: 0.6897 (mt-10) cc_final: 0.6472 (tt0) REVERT: C 52 GLU cc_start: 0.6524 (mt-10) cc_final: 0.6235 (mt-10) REVERT: C 213 LYS cc_start: 0.8570 (ttpp) cc_final: 0.8235 (ttpt) REVERT: C 276 GLN cc_start: 0.8345 (mt0) cc_final: 0.8112 (mt0) REVERT: D 52 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6473 (mt-10) REVERT: D 213 LYS cc_start: 0.8659 (ttpp) cc_final: 0.8375 (ttpt) REVERT: D 276 GLN cc_start: 0.8348 (mt0) cc_final: 0.8132 (mt0) REVERT: E 213 LYS cc_start: 0.8715 (ttpp) cc_final: 0.8263 (ttmm) REVERT: E 276 GLN cc_start: 0.8408 (mt0) cc_final: 0.8180 (mt0) REVERT: F 52 GLU cc_start: 0.6727 (mt-10) cc_final: 0.6329 (mt-10) REVERT: F 66 TRP cc_start: 0.8699 (t60) cc_final: 0.8328 (t60) REVERT: F 276 GLN cc_start: 0.8478 (mt0) cc_final: 0.8256 (mt0) REVERT: G 52 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6416 (mt-10) REVERT: G 213 LYS cc_start: 0.8686 (ttpp) cc_final: 0.8345 (ttmm) REVERT: G 276 GLN cc_start: 0.8428 (mt0) cc_final: 0.8220 (mt0) outliers start: 7 outliers final: 3 residues processed: 516 average time/residue: 0.7919 time to fit residues: 614.3607 Evaluate side-chains 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 434 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 130 THR 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: 2.9990 chunk 105 optimal weight: 0.9990 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: 0.6980 chunk 228 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 GLN F 76 HIS ** F 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21196 Z= 0.226 Angle : 0.582 6.731 28819 Z= 0.301 Chirality : 0.039 0.131 3136 Planarity : 0.006 0.063 3668 Dihedral : 10.810 147.454 2971 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.86 % Allowed : 4.99 % Favored : 94.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.16), residues: 2506 helix: 0.26 (0.17), residues: 917 sheet: -2.23 (0.19), residues: 567 loop : -3.13 (0.17), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP G 62 HIS 0.002 0.001 HIS D 358 PHE 0.014 0.001 PHE G 95 TYR 0.029 0.001 TYR F 60 ARG 0.005 0.000 ARG C 346 *********************** 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 461 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 442 time to evaluate : 3.085 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: A 52 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6489 (mt-10) REVERT: A 162 GLU cc_start: 0.6211 (mp0) cc_final: 0.5987 (mp0) REVERT: B 213 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8262 (ttmm) REVERT: B 282 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7192 (mm-30) REVERT: C 52 GLU cc_start: 0.6509 (mt-10) cc_final: 0.6254 (mt-10) REVERT: C 58 ARG cc_start: 0.7602 (ttt-90) cc_final: 0.7289 (ttt180) REVERT: C 64 LEU cc_start: 0.7703 (mt) cc_final: 0.7478 (mt) REVERT: C 95 PHE cc_start: 0.6181 (m-80) cc_final: 0.5959 (m-10) REVERT: C 213 LYS cc_start: 0.8549 (ttpp) cc_final: 0.8247 (ttpt) REVERT: C 276 GLN cc_start: 0.8348 (mt0) cc_final: 0.8144 (mt0) REVERT: D 97 PHE cc_start: 0.8374 (m-80) cc_final: 0.8023 (m-10) REVERT: D 132 TRP cc_start: 0.7572 (t-100) cc_final: 0.7358 (t-100) REVERT: D 213 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8290 (ttmm) REVERT: E 97 PHE cc_start: 0.8396 (m-80) cc_final: 0.8149 (m-10) REVERT: E 213 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8262 (ttmm) REVERT: E 276 GLN cc_start: 0.8396 (mt0) cc_final: 0.8179 (mt0) REVERT: F 52 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6453 (mt-10) REVERT: F 86 HIS cc_start: 0.7886 (m170) cc_final: 0.7624 (m90) REVERT: F 123 MET cc_start: 0.6030 (ptm) cc_final: 0.5807 (ttp) REVERT: F 276 GLN cc_start: 0.8480 (mt0) cc_final: 0.8261 (mt0) REVERT: G 213 LYS cc_start: 0.8664 (ttpp) cc_final: 0.8348 (ttmm) outliers start: 19 outliers final: 10 residues processed: 453 average time/residue: 0.7100 time to fit residues: 490.1237 Evaluate side-chains 433 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 423 time to evaluate : 3.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 85 GLN Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 348 ASP Chi-restraints excluded: chain B residue 85 GLN Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain G residue 50 THR 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: 10.0000 chunk 155 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 204 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 78 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** F 127 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 332 ASN G 397 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 21196 Z= 0.366 Angle : 0.584 6.845 28819 Z= 0.299 Chirality : 0.041 0.140 3136 Planarity : 0.006 0.063 3668 Dihedral : 10.838 157.444 2968 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.77 % Allowed : 7.21 % Favored : 92.02 % 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: -2.09 (0.17), residues: 2506 helix: 0.66 (0.18), residues: 917 sheet: -2.08 (0.19), residues: 581 loop : -2.91 (0.18), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 62 HIS 0.003 0.001 HIS F 76 PHE 0.010 0.002 PHE A 95 TYR 0.026 0.001 TYR F 60 ARG 0.010 0.001 ARG E 58 *********************** 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 462 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 445 time to evaluate : 3.573 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: A 162 GLU cc_start: 0.6277 (mp0) cc_final: 0.6065 (mp0) REVERT: A 333 TYR cc_start: 0.8279 (m-80) cc_final: 0.7944 (m-80) REVERT: B 213 LYS cc_start: 0.8591 (ttpp) cc_final: 0.8229 (ttmm) REVERT: C 86 HIS cc_start: 0.7810 (m170) cc_final: 0.7578 (m170) REVERT: C 213 LYS cc_start: 0.8593 (ttpp) cc_final: 0.8230 (ttmm) REVERT: C 276 GLN cc_start: 0.8403 (mt0) cc_final: 0.8197 (mt0) REVERT: D 132 TRP cc_start: 0.7660 (t-100) cc_final: 0.7417 (t-100) REVERT: D 213 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8306 (ttmm) REVERT: E 97 PHE cc_start: 0.8492 (m-80) cc_final: 0.8205 (m-10) REVERT: E 213 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8216 (ttmm) REVERT: E 276 GLN cc_start: 0.8394 (mt0) cc_final: 0.8166 (mt0) REVERT: F 52 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6554 (mt-10) REVERT: F 276 GLN cc_start: 0.8514 (mt0) cc_final: 0.8286 (mt0) REVERT: G 52 GLU cc_start: 0.6779 (mt-10) cc_final: 0.6550 (mt-10) REVERT: G 213 LYS cc_start: 0.8662 (ttpp) cc_final: 0.8357 (ttmm) outliers start: 17 outliers final: 10 residues processed: 453 average time/residue: 0.7689 time to fit residues: 528.9074 Evaluate side-chains 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 427 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain E residue 317 ASP Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 317 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 226 optimal weight: 10.0000 chunk 172 optimal weight: 2.9990 chunk 118 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 153 optimal weight: 10.0000 chunk 230 optimal weight: 0.1980 chunk 243 optimal weight: 0.1980 chunk 120 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 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 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 76 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** F 127 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2293 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= 0.267 Angle : 0.547 7.077 28819 Z= 0.276 Chirality : 0.039 0.170 3136 Planarity : 0.005 0.062 3668 Dihedral : 10.872 158.170 2968 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.68 % Allowed : 8.34 % Favored : 90.98 % 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: -1.73 (0.17), residues: 2506 helix: 0.92 (0.18), residues: 917 sheet: -1.84 (0.20), residues: 581 loop : -2.69 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 66 HIS 0.005 0.001 HIS B 76 PHE 0.013 0.001 PHE D 105 TYR 0.023 0.001 TYR F 60 ARG 0.008 0.000 ARG E 58 *********************** 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 450 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 435 time to evaluate : 3.286 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: A 85 GLN cc_start: 0.7769 (tp40) cc_final: 0.7472 (tm-30) REVERT: A 86 HIS cc_start: 0.7642 (m170) cc_final: 0.7381 (m170) REVERT: A 333 TYR cc_start: 0.8277 (m-80) cc_final: 0.7917 (m-80) REVERT: B 52 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6580 (mt-10) REVERT: B 204 ASP cc_start: 0.7880 (t70) cc_final: 0.7525 (t70) REVERT: B 213 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8141 (ttmm) REVERT: C 213 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8210 (ttmm) REVERT: C 347 VAL cc_start: 0.8763 (t) cc_final: 0.8523 (m) REVERT: D 132 TRP cc_start: 0.7703 (t-100) cc_final: 0.7473 (t-100) REVERT: D 213 LYS cc_start: 0.8695 (ttpp) cc_final: 0.8319 (ttmm) REVERT: E 97 PHE cc_start: 0.8504 (m-80) cc_final: 0.8276 (m-10) REVERT: E 213 LYS cc_start: 0.8586 (ttpp) cc_final: 0.8182 (ttmm) REVERT: E 276 GLN cc_start: 0.8389 (mt0) cc_final: 0.8168 (mt0) REVERT: E 347 VAL cc_start: 0.8828 (t) cc_final: 0.8513 (m) REVERT: E 348 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7190 (m-30) REVERT: F 276 GLN cc_start: 0.8522 (mt0) cc_final: 0.8299 (mt0) REVERT: G 52 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6599 (mt-10) REVERT: G 213 LYS cc_start: 0.8654 (ttpp) cc_final: 0.8325 (ttmm) REVERT: G 277 SER cc_start: 0.8694 (p) cc_final: 0.8372 (t) outliers start: 15 outliers final: 7 residues processed: 441 average time/residue: 0.7587 time to fit residues: 507.4143 Evaluate side-chains 428 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 420 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 348 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 202 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 168 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 218 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN ** F 127 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 21196 Z= 0.303 Angle : 0.539 6.671 28819 Z= 0.273 Chirality : 0.040 0.160 3136 Planarity : 0.005 0.053 3668 Dihedral : 10.993 160.329 2968 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 0.63 % Allowed : 9.52 % Favored : 89.84 % 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: -1.48 (0.17), residues: 2506 helix: 1.15 (0.18), residues: 917 sheet: -1.72 (0.20), residues: 567 loop : -2.56 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 66 HIS 0.003 0.001 HIS F 249 PHE 0.011 0.001 PHE D 95 TYR 0.024 0.001 TYR B 60 ARG 0.015 0.000 ARG B 144 *********************** 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 448 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 434 time to evaluate : 3.548 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: A 86 HIS cc_start: 0.7635 (m170) cc_final: 0.7263 (m170) REVERT: A 333 TYR cc_start: 0.8304 (m-80) cc_final: 0.7924 (m-80) REVERT: B 52 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6545 (mt-10) REVERT: B 204 ASP cc_start: 0.7885 (t70) cc_final: 0.7521 (t70) REVERT: B 213 LYS cc_start: 0.8536 (ttpp) cc_final: 0.8111 (ttmm) REVERT: C 58 ARG cc_start: 0.7672 (tpt-90) cc_final: 0.7294 (ttt-90) REVERT: C 204 ASP cc_start: 0.7869 (t70) cc_final: 0.7472 (t0) REVERT: C 213 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8210 (ttmm) REVERT: C 347 VAL cc_start: 0.8779 (t) cc_final: 0.8567 (m) REVERT: D 132 TRP cc_start: 0.7725 (t-100) cc_final: 0.7499 (t-100) REVERT: D 213 LYS cc_start: 0.8671 (ttpp) cc_final: 0.8286 (ttmm) REVERT: E 86 HIS cc_start: 0.7820 (m170) cc_final: 0.7599 (m90) REVERT: E 213 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8223 (ttmm) REVERT: E 276 GLN cc_start: 0.8435 (mt0) cc_final: 0.8207 (mt0) REVERT: E 347 VAL cc_start: 0.8855 (t) cc_final: 0.8538 (m) REVERT: E 348 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.7202 (m-30) REVERT: F 86 HIS cc_start: 0.7807 (m170) cc_final: 0.7577 (m90) REVERT: F 276 GLN cc_start: 0.8532 (mt0) cc_final: 0.8288 (mt0) REVERT: G 213 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8220 (ttmm) outliers start: 14 outliers final: 10 residues processed: 439 average time/residue: 0.7506 time to fit residues: 498.0864 Evaluate side-chains 438 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 427 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain E residue 348 ASP Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 81 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 243 optimal weight: 0.0670 chunk 202 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 85 GLN ** 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21196 Z= 0.419 Angle : 0.574 6.521 28819 Z= 0.291 Chirality : 0.042 0.154 3136 Planarity : 0.005 0.052 3668 Dihedral : 11.178 163.437 2968 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.68 % Allowed : 10.70 % Favored : 88.62 % 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: -1.49 (0.17), residues: 2506 helix: 1.09 (0.17), residues: 917 sheet: -1.70 (0.20), residues: 567 loop : -2.54 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 176 HIS 0.010 0.001 HIS F 104 PHE 0.010 0.002 PHE A 179 TYR 0.025 0.001 TYR E 60 ARG 0.008 0.000 ARG E 58 *********************** 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 443 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 428 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 REVERT: A 86 HIS cc_start: 0.7639 (m170) cc_final: 0.7400 (m170) REVERT: A 333 TYR cc_start: 0.8316 (m-80) cc_final: 0.7883 (m-80) REVERT: B 52 GLU cc_start: 0.6824 (mt-10) cc_final: 0.6523 (mt-10) REVERT: B 85 GLN cc_start: 0.7827 (tp40) cc_final: 0.7602 (tm-30) REVERT: B 123 MET cc_start: 0.5541 (ttp) cc_final: 0.5269 (ttp) REVERT: B 204 ASP cc_start: 0.7894 (t70) cc_final: 0.7542 (t70) REVERT: B 213 LYS cc_start: 0.8518 (ttpp) cc_final: 0.8089 (ttmm) REVERT: C 204 ASP cc_start: 0.7862 (t70) cc_final: 0.7480 (t0) REVERT: C 213 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8215 (ttmm) REVERT: C 347 VAL cc_start: 0.8787 (t) cc_final: 0.8548 (m) REVERT: D 213 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8301 (ttmm) REVERT: E 90 ARG cc_start: 0.7883 (mmp-170) cc_final: 0.7677 (mmp80) REVERT: E 213 LYS cc_start: 0.8590 (ttpp) cc_final: 0.8213 (ttmm) REVERT: E 276 GLN cc_start: 0.8460 (mt0) cc_final: 0.8221 (mt0) REVERT: F 86 HIS cc_start: 0.7865 (m170) cc_final: 0.7643 (m90) REVERT: F 276 GLN cc_start: 0.8532 (mt0) cc_final: 0.8278 (mt0) REVERT: G 213 LYS cc_start: 0.8615 (ttpp) cc_final: 0.8210 (ttmm) outliers start: 15 outliers final: 12 residues processed: 433 average time/residue: 0.8196 time to fit residues: 533.1583 Evaluate side-chains 435 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 423 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 217 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE 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: 1.9990 chunk 138 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 137 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 242 optimal weight: 0.6980 chunk 152 optimal weight: 10.0000 chunk 148 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 127 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21196 Z= 0.219 Angle : 0.514 5.629 28819 Z= 0.259 Chirality : 0.039 0.153 3136 Planarity : 0.005 0.046 3668 Dihedral : 10.947 160.278 2968 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.45 % Allowed : 11.56 % Favored : 87.98 % 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: -1.16 (0.17), residues: 2506 helix: 1.38 (0.18), residues: 917 sheet: -1.50 (0.20), residues: 567 loop : -2.37 (0.20), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 66 HIS 0.007 0.001 HIS F 104 PHE 0.008 0.001 PHE G 148 TYR 0.031 0.001 TYR B 60 ARG 0.004 0.000 ARG B 58 *********************** 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 435 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 425 time to evaluate : 3.116 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: B 52 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6506 (mt-10) REVERT: B 123 MET cc_start: 0.5500 (ttp) cc_final: 0.5247 (ttp) REVERT: B 204 ASP cc_start: 0.7838 (t70) cc_final: 0.7474 (t70) REVERT: B 213 LYS cc_start: 0.8490 (ttpp) cc_final: 0.8066 (ttmm) REVERT: C 204 ASP cc_start: 0.7800 (t70) cc_final: 0.7407 (t0) REVERT: C 213 LYS cc_start: 0.8565 (ttpp) cc_final: 0.8207 (ttmm) REVERT: C 347 VAL cc_start: 0.8772 (t) cc_final: 0.8531 (m) REVERT: D 213 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8287 (ttmm) REVERT: E 213 LYS cc_start: 0.8581 (ttpp) cc_final: 0.8199 (ttmm) REVERT: E 276 GLN cc_start: 0.8428 (mt0) cc_final: 0.8201 (mt0) REVERT: E 347 VAL cc_start: 0.8834 (t) cc_final: 0.8546 (m) REVERT: F 86 HIS cc_start: 0.7838 (m170) cc_final: 0.7608 (m90) REVERT: F 276 GLN cc_start: 0.8512 (mt0) cc_final: 0.8281 (mt0) outliers start: 10 outliers final: 8 residues processed: 429 average time/residue: 0.7654 time to fit residues: 496.1811 Evaluate side-chains 426 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 418 time to evaluate : 2.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 52 GLU Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE 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: 4.9990 chunk 145 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 154 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 190 optimal weight: 10.0000 chunk 220 optimal weight: 3.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 85 GLN ** 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 21196 Z= 0.419 Angle : 0.566 5.806 28819 Z= 0.285 Chirality : 0.041 0.152 3136 Planarity : 0.005 0.071 3668 Dihedral : 11.184 166.000 2968 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 0.68 % Allowed : 11.61 % Favored : 87.71 % 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: -1.19 (0.17), residues: 2506 helix: 1.43 (0.18), residues: 896 sheet: -1.53 (0.20), residues: 567 loop : -2.38 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 176 HIS 0.007 0.001 HIS F 104 PHE 0.012 0.002 PHE F 309 TYR 0.025 0.001 TYR F 60 ARG 0.005 0.000 ARG D 343 *********************** 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 445 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 430 time to evaluate : 2.832 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: B 52 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6516 (mt-10) REVERT: B 123 MET cc_start: 0.5400 (ttp) cc_final: 0.5179 (ttp) REVERT: B 204 ASP cc_start: 0.7882 (t70) cc_final: 0.7526 (t70) REVERT: B 213 LYS cc_start: 0.8520 (ttpp) cc_final: 0.8103 (ttmm) REVERT: C 204 ASP cc_start: 0.7848 (t70) cc_final: 0.7467 (t0) REVERT: C 213 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8213 (ttmm) REVERT: C 347 VAL cc_start: 0.8797 (t) cc_final: 0.8574 (m) REVERT: D 213 LYS cc_start: 0.8681 (ttpp) cc_final: 0.8294 (ttmm) REVERT: E 213 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8212 (ttmm) REVERT: E 276 GLN cc_start: 0.8459 (mt0) cc_final: 0.8224 (mt0) REVERT: F 86 HIS cc_start: 0.7871 (m90) cc_final: 0.7658 (m90) REVERT: F 276 GLN cc_start: 0.8547 (mt0) cc_final: 0.8305 (mt0) REVERT: G 213 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8212 (ttmm) outliers start: 15 outliers final: 13 residues processed: 434 average time/residue: 0.7668 time to fit residues: 495.3489 Evaluate side-chains 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 424 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 283 ASP Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 232 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 226 optimal weight: 9.9990 chunk 136 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 177 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 85 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21196 Z= 0.283 Angle : 0.528 5.532 28819 Z= 0.267 Chirality : 0.039 0.148 3136 Planarity : 0.005 0.062 3668 Dihedral : 11.044 163.572 2968 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.68 % Allowed : 11.88 % Favored : 87.44 % 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: -1.00 (0.18), residues: 2506 helix: 1.57 (0.18), residues: 896 sheet: -1.38 (0.21), residues: 567 loop : -2.29 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 66 HIS 0.006 0.001 HIS F 104 PHE 0.009 0.001 PHE F 309 TYR 0.028 0.001 TYR E 60 ARG 0.006 0.000 ARG F 346 *********************** 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 437 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 422 time to evaluate : 3.479 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: B 123 MET cc_start: 0.5345 (ttp) cc_final: 0.5129 (ttp) REVERT: B 204 ASP cc_start: 0.7839 (t70) cc_final: 0.7470 (t70) REVERT: B 213 LYS cc_start: 0.8482 (ttpp) cc_final: 0.8064 (ttmm) REVERT: C 204 ASP cc_start: 0.7810 (t70) cc_final: 0.7431 (t0) REVERT: C 213 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8201 (ttmm) REVERT: C 347 VAL cc_start: 0.8788 (t) cc_final: 0.8548 (m) REVERT: D 213 LYS cc_start: 0.8661 (ttpp) cc_final: 0.8278 (ttmm) REVERT: E 213 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8245 (ttmm) REVERT: E 276 GLN cc_start: 0.8449 (mt0) cc_final: 0.8224 (mt0) REVERT: E 347 VAL cc_start: 0.8854 (t) cc_final: 0.8550 (m) REVERT: F 86 HIS cc_start: 0.7865 (m90) cc_final: 0.7652 (m90) REVERT: F 276 GLN cc_start: 0.8525 (mt0) cc_final: 0.8281 (mt0) REVERT: G 123 MET cc_start: 0.5448 (ttp) cc_final: 0.5244 (ttt) outliers start: 15 outliers final: 15 residues processed: 427 average time/residue: 0.7586 time to fit residues: 484.2368 Evaluate side-chains 435 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 420 time to evaluate : 3.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 3.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 166 optimal weight: 1.9990 chunk 251 optimal weight: 4.9990 chunk 231 optimal weight: 0.6980 chunk 199 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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** ** B 85 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 21196 Z= 0.288 Angle : 0.527 5.437 28819 Z= 0.265 Chirality : 0.040 0.185 3136 Planarity : 0.005 0.050 3668 Dihedral : 11.022 163.614 2968 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.86 % Allowed : 11.97 % Favored : 87.17 % 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: -0.87 (0.18), residues: 2506 helix: 1.70 (0.18), residues: 896 sheet: -1.29 (0.21), residues: 567 loop : -2.24 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 66 HIS 0.006 0.001 HIS F 104 PHE 0.009 0.001 PHE F 309 TYR 0.026 0.001 TYR E 60 ARG 0.005 0.000 ARG F 346 ********************** 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 447 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 428 time to evaluate : 3.177 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: B 204 ASP cc_start: 0.7866 (t70) cc_final: 0.7533 (t70) REVERT: B 213 LYS cc_start: 0.8516 (ttpp) cc_final: 0.8102 (ttmm) REVERT: C 204 ASP cc_start: 0.7814 (t70) cc_final: 0.7435 (t0) REVERT: C 213 LYS cc_start: 0.8550 (ttpp) cc_final: 0.8197 (ttmm) REVERT: C 347 VAL cc_start: 0.8796 (t) cc_final: 0.8565 (m) REVERT: D 213 LYS cc_start: 0.8663 (ttpp) cc_final: 0.8279 (ttmm) REVERT: E 213 LYS cc_start: 0.8626 (ttpp) cc_final: 0.8243 (ttmm) REVERT: E 276 GLN cc_start: 0.8447 (mt0) cc_final: 0.8226 (mt0) REVERT: F 86 HIS cc_start: 0.7866 (m90) cc_final: 0.7659 (m90) REVERT: F 276 GLN cc_start: 0.8526 (mt0) cc_final: 0.8288 (mt0) outliers start: 19 outliers final: 17 residues processed: 433 average time/residue: 0.7991 time to fit residues: 511.3387 Evaluate side-chains 441 residues out of total 2205 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 424 time to evaluate : 3.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 348 ASP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 113 ILE Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 308 THR Chi-restraints excluded: chain F residue 285 ASP Chi-restraints excluded: chain F residue 335 ASP Chi-restraints excluded: chain G residue 104 HIS Chi-restraints excluded: chain G residue 319 VAL Chi-restraints excluded: chain G residue 342 ILE 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: 0.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 200 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 175 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 85 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** ** E 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 GLN F 76 HIS ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 127 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.129012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.095920 restraints weight = 85102.226| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.45 r_work: 0.2990 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3254 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= 0.288 Angle : 0.526 5.410 28819 Z= 0.265 Chirality : 0.039 0.151 3136 Planarity : 0.005 0.053 3668 Dihedral : 11.010 163.619 2968 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 0.77 % Allowed : 12.43 % Favored : 86.80 % 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: -0.83 (0.18), residues: 2506 helix: 1.70 (0.18), residues: 896 sheet: -1.23 (0.21), residues: 567 loop : -2.23 (0.20), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 66 HIS 0.006 0.001 HIS F 104 PHE 0.008 0.001 PHE F 309 TYR 0.025 0.001 TYR E 60 ARG 0.006 0.000 ARG F 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10315.40 seconds wall clock time: 181 minutes 12.05 seconds (10872.05 seconds total)