Starting phenix.real_space_refine on Tue Mar 19 00:21:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/03_2024/7pds_13342_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 90 5.16 5 C 14281 2.51 5 N 3871 2.21 5 O 4280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 38": "OE1" <-> "OE2" Residue "A GLU 45": "OE1" <-> "OE2" Residue "A GLU 135": "OE1" <-> "OE2" Residue "A TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 345": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "B GLU 45": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B GLU 272": "OE1" <-> "OE2" Residue "B ARG 282": "NH1" <-> "NH2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B ARG 368": "NH1" <-> "NH2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B ARG 374": "NH1" <-> "NH2" Residue "B GLU 396": "OE1" <-> "OE2" Residue "C GLU 45": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C GLU 371": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 145": "OE1" <-> "OE2" Residue "D GLU 221": "OE1" <-> "OE2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 319": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "E GLU 124": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E GLU 358": "OE1" <-> "OE2" Residue "E GLU 371": "OE1" <-> "OE2" Residue "E GLU 372": "OE1" <-> "OE2" Residue "F GLU 45": "OE1" <-> "OE2" Residue "F GLU 108": "OE1" <-> "OE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F GLU 221": "OE1" <-> "OE2" Residue "F GLU 272": "OE1" <-> "OE2" Residue "F ARG 281": "NH1" <-> "NH2" Residue "F GLU 334": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 371": "OE1" <-> "OE2" Residue "F GLU 456": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22549 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3746 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 12, 'TRANS': 444} Chain breaks: 1 Chain: "B" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3670 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 13, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3698 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 13, 'TRANS': 437} Chain breaks: 1 Chain: "D" Number of atoms: 3724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3724 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 13, 'TRANS': 440} Chain breaks: 1 Chain: "E" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3708 Classifications: {'peptide': 453} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 440} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3709 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 12, 'TRANS': 438} Chain breaks: 3 Chain: "M" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Classifications: {'DNA': 5} Link IDs: {'rna3p': 4} 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: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 11.35, per 1000 atoms: 0.50 Number of scatterers: 22549 At special positions: 0 Unit cell: (136.12, 118.9, 145.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 90 16.00 P 23 15.00 Mg 4 11.99 O 4280 8.00 N 3871 7.00 C 14281 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.35 Conformation dependent library (CDL) restraints added in 4.0 seconds 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5118 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 121 helices and 22 sheets defined 40.0% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 18 through 20 No H-bonds generated for 'chain 'A' and resid 18 through 20' Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 100 through 112 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 137 through 141 Processing helix chain 'A' and resid 148 through 166 Processing helix chain 'A' and resid 186 through 197 removed outlier: 6.316A pdb=" N HIS A 196 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 213 Processing helix chain 'A' and resid 223 through 230 removed outlier: 5.823A pdb=" N ALA A 227 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 297 through 300 No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 303 through 320 removed outlier: 3.848A pdb=" N ASN A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 removed outlier: 3.572A pdb=" N LYS A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 357 Processing helix chain 'A' and resid 370 through 377 removed outlier: 3.607A pdb=" N VAL A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 401 through 404 No H-bonds generated for 'chain 'A' and resid 401 through 404' Processing helix chain 'A' and resid 413 through 418 Processing helix chain 'A' and resid 429 through 441 Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 100 through 113 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 137 through 141 removed outlier: 3.533A pdb=" N TYR B 141 " --> pdb=" O LEU B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 141' Processing helix chain 'B' and resid 148 through 166 Processing helix chain 'B' and resid 186 through 197 removed outlier: 6.566A pdb=" N HIS B 196 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N TRP B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 223 through 229 removed outlier: 5.979A pdb=" N ALA B 227 " --> pdb=" O GLU B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 Processing helix chain 'B' and resid 303 through 320 removed outlier: 4.017A pdb=" N ASN B 320 " --> pdb=" O TYR B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 326 No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 330 through 342 removed outlier: 3.560A pdb=" N LYS B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 357 removed outlier: 3.656A pdb=" N GLU B 352 " --> pdb=" O ALA B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 377 Processing helix chain 'B' and resid 413 through 418 Processing helix chain 'B' and resid 429 through 441 Processing helix chain 'B' and resid 468 through 472 removed outlier: 4.082A pdb=" N TYR B 472 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 80 through 93 Processing helix chain 'C' and resid 100 through 113 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 137 through 140 No H-bonds generated for 'chain 'C' and resid 137 through 140' Processing helix chain 'C' and resid 148 through 166 Processing helix chain 'C' and resid 186 through 197 removed outlier: 6.383A pdb=" N HIS C 196 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 223 through 230 removed outlier: 5.875A pdb=" N ALA C 227 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 Processing helix chain 'C' and resid 297 through 300 No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 303 through 319 Processing helix chain 'C' and resid 323 through 326 Processing helix chain 'C' and resid 330 through 342 removed outlier: 3.560A pdb=" N LYS C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 358 Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 418 Processing helix chain 'C' and resid 431 through 441 Processing helix chain 'C' and resid 468 through 470 No H-bonds generated for 'chain 'C' and resid 468 through 470' Processing helix chain 'D' and resid 17 through 20 Processing helix chain 'D' and resid 34 through 42 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'D' and resid 80 through 93 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 148 through 166 Processing helix chain 'D' and resid 186 through 194 Processing helix chain 'D' and resid 209 through 213 Processing helix chain 'D' and resid 223 through 230 removed outlier: 5.992A pdb=" N ALA D 227 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 323 through 326 No H-bonds generated for 'chain 'D' and resid 323 through 326' Processing helix chain 'D' and resid 330 through 342 removed outlier: 3.642A pdb=" N LYS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 357 Processing helix chain 'D' and resid 365 through 367 No H-bonds generated for 'chain 'D' and resid 365 through 367' Processing helix chain 'D' and resid 370 through 377 Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 431 through 441 Processing helix chain 'D' and resid 469 through 472 No H-bonds generated for 'chain 'D' and resid 469 through 472' Processing helix chain 'E' and resid 17 through 19 No H-bonds generated for 'chain 'E' and resid 17 through 19' Processing helix chain 'E' and resid 34 through 43 Processing helix chain 'E' and resid 80 through 94 Processing helix chain 'E' and resid 100 through 114 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 148 through 166 Processing helix chain 'E' and resid 186 through 197 removed outlier: 6.812A pdb=" N HIS E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N TRP E 197 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 212 No H-bonds generated for 'chain 'E' and resid 209 through 212' Processing helix chain 'E' and resid 223 through 230 removed outlier: 5.823A pdb=" N ALA E 227 " --> pdb=" O GLU E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 Processing helix chain 'E' and resid 303 through 319 Processing helix chain 'E' and resid 323 through 326 Processing helix chain 'E' and resid 330 through 342 Processing helix chain 'E' and resid 349 through 357 Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 413 through 419 Processing helix chain 'E' and resid 431 through 440 Processing helix chain 'E' and resid 469 through 472 No H-bonds generated for 'chain 'E' and resid 469 through 472' Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 45 through 47 No H-bonds generated for 'chain 'F' and resid 45 through 47' Processing helix chain 'F' and resid 80 through 93 Processing helix chain 'F' and resid 100 through 113 Processing helix chain 'F' and resid 118 through 123 Processing helix chain 'F' and resid 148 through 166 Processing helix chain 'F' and resid 186 through 197 removed outlier: 6.737A pdb=" N HIS F 196 " --> pdb=" O LYS F 192 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N TRP F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 212 Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.740A pdb=" N GLU F 234 " --> pdb=" O LYS F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 303 through 320 removed outlier: 3.887A pdb=" N ASN F 320 " --> pdb=" O TYR F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 323 through 326 Processing helix chain 'F' and resid 330 through 342 removed outlier: 3.676A pdb=" N LYS F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 358 Processing helix chain 'F' and resid 373 through 377 Processing helix chain 'F' and resid 413 through 418 Processing helix chain 'F' and resid 431 through 441 Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing sheet with id= A, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.787A pdb=" N VAL A 59 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 283 through 287 removed outlier: 6.651A pdb=" N MET A 175 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE A 286 " --> pdb=" O MET A 175 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE A 177 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 176 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 267 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 450 through 455 removed outlier: 6.052A pdb=" N GLY A 459 " --> pdb=" O TYR A 454 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.669A pdb=" N VAL B 59 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 283 through 287 removed outlier: 6.658A pdb=" N MET B 175 " --> pdb=" O PHE B 284 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ILE B 286 " --> pdb=" O MET B 175 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 177 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 176 " --> pdb=" O PHE B 264 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 267 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 244 through 248 Processing sheet with id= G, first strand: chain 'B' and resid 410 through 412 Processing sheet with id= H, first strand: chain 'C' and resid 51 through 54 removed outlier: 3.860A pdb=" N VAL C 59 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 283 through 287 removed outlier: 6.422A pdb=" N MET C 175 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE C 286 " --> pdb=" O MET C 175 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ILE C 177 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE C 176 " --> pdb=" O PHE C 264 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR C 267 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 244 through 248 Processing sheet with id= K, first strand: chain 'C' and resid 410 through 412 Processing sheet with id= L, first strand: chain 'D' and resid 51 through 54 removed outlier: 3.548A pdb=" N VAL D 59 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 283 through 287 removed outlier: 6.399A pdb=" N MET D 175 " --> pdb=" O PHE D 284 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ILE D 286 " --> pdb=" O MET D 175 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE D 177 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE D 176 " --> pdb=" O PHE D 264 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 244 through 247 Processing sheet with id= O, first strand: chain 'D' and resid 449 through 453 Processing sheet with id= P, first strand: chain 'E' and resid 51 through 54 removed outlier: 3.682A pdb=" N VAL E 59 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 283 through 288 removed outlier: 6.485A pdb=" N MET E 175 " --> pdb=" O PHE E 284 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ILE E 286 " --> pdb=" O MET E 175 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE E 177 " --> pdb=" O ILE E 286 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N THR E 288 " --> pdb=" O ILE E 177 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR E 179 " --> pdb=" O THR E 288 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 176 " --> pdb=" O PHE E 264 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 244 through 248 Processing sheet with id= S, first strand: chain 'E' and resid 449 through 453 Processing sheet with id= T, first strand: chain 'F' and resid 52 through 54 Processing sheet with id= U, first strand: chain 'F' and resid 283 through 287 removed outlier: 6.408A pdb=" N MET F 175 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ILE F 286 " --> pdb=" O MET F 175 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE F 177 " --> pdb=" O ILE F 286 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE F 176 " --> pdb=" O PHE F 264 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 449 through 453 705 hydrogen bonds defined for protein. 2016 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: 6.41 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7304 1.36 - 1.51: 6656 1.51 - 1.65: 8957 1.65 - 1.80: 123 1.80 - 1.95: 21 Bond restraints: 23061 Sorted by residual: bond pdb=" N ILE B 243 " pdb=" CA ILE B 243 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.18e-02 7.18e+03 1.27e+01 bond pdb=" N VAL D 244 " pdb=" CA VAL D 244 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.14e-02 7.69e+03 1.06e+01 bond pdb=" N VAL D 51 " pdb=" CA VAL D 51 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" N VAL B 96 " pdb=" CA VAL B 96 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.19e-02 7.06e+03 1.04e+01 bond pdb=" N ASP C 129 " pdb=" CA ASP C 129 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.17e-02 7.31e+03 9.98e+00 ... (remaining 23056 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.09: 410 106.09 - 113.14: 12405 113.14 - 120.19: 8672 120.19 - 127.24: 9379 127.24 - 134.29: 286 Bond angle restraints: 31152 Sorted by residual: angle pdb=" N LYS C 292 " pdb=" CA LYS C 292 " pdb=" C LYS C 292 " ideal model delta sigma weight residual 113.38 106.47 6.91 1.23e+00 6.61e-01 3.16e+01 angle pdb=" CA ILE C 222 " pdb=" C ILE C 222 " pdb=" O ILE C 222 " ideal model delta sigma weight residual 122.63 118.15 4.48 8.70e-01 1.32e+00 2.65e+01 angle pdb=" PA AGS C 501 " pdb=" O3A AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sigma weight residual 119.76 134.01 -14.25 3.00e+00 1.11e-01 2.26e+01 angle pdb=" PA AGS A 501 " pdb=" O3A AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sigma weight residual 119.76 133.36 -13.60 3.00e+00 1.11e-01 2.06e+01 angle pdb=" PB AGS A 501 " pdb=" O3B AGS A 501 " pdb=" PG AGS A 501 " ideal model delta sigma weight residual 120.12 133.40 -13.28 3.00e+00 1.11e-01 1.96e+01 ... (remaining 31147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 13236 28.69 - 57.38: 559 57.38 - 86.07: 56 86.07 - 114.77: 2 114.77 - 143.46: 4 Dihedral angle restraints: 13857 sinusoidal: 5885 harmonic: 7972 Sorted by residual: dihedral pdb=" O1A AGS A 501 " pdb=" O3A AGS A 501 " pdb=" PA AGS A 501 " pdb=" PB AGS A 501 " ideal model delta sinusoidal sigma weight residual -67.73 75.73 -143.46 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" O1A AGS C 501 " pdb=" O3A AGS C 501 " pdb=" PA AGS C 501 " pdb=" PB AGS C 501 " ideal model delta sinusoidal sigma weight residual -67.73 61.20 -128.93 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" O1B AGS C 501 " pdb=" O3B AGS C 501 " pdb=" PB AGS C 501 " pdb=" PG AGS C 501 " ideal model delta sinusoidal sigma weight residual 68.91 -57.96 126.87 1 3.00e+01 1.11e-03 1.71e+01 ... (remaining 13854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2808 0.063 - 0.126: 441 0.126 - 0.189: 45 0.189 - 0.252: 9 0.252 - 0.316: 3 Chirality restraints: 3306 Sorted by residual: chirality pdb=" CA ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA LEU E 214 " pdb=" N LEU E 214 " pdb=" C LEU E 214 " pdb=" CB LEU E 214 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CA HIS B 378 " pdb=" N HIS B 378 " pdb=" C HIS B 378 " pdb=" CB HIS B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 3303 not shown) Planarity restraints: 3909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 258 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.18e+00 pdb=" N PRO A 259 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 259 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 259 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 94 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C TYR B 94 " -0.039 2.00e-02 2.50e+03 pdb=" O TYR B 94 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN B 95 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 167 " -0.034 5.00e-02 4.00e+02 5.22e-02 4.36e+00 pdb=" N PRO B 168 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 168 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 168 " -0.029 5.00e-02 4.00e+02 ... (remaining 3906 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 94 2.43 - 3.05: 14399 3.05 - 3.67: 33761 3.67 - 4.28: 53602 4.28 - 4.90: 89102 Nonbonded interactions: 190958 Sorted by model distance: nonbonded pdb=" S1G AGS A 501 " pdb="MG MG A 502 " model vdw 1.818 2.530 nonbonded pdb=" S1G AGS C 501 " pdb="MG MG C 502 " model vdw 1.839 2.530 nonbonded pdb=" O1B AGS B 501 " pdb="MG MG B 502 " model vdw 2.072 2.170 nonbonded pdb=" O1B AGS D 501 " pdb="MG MG D 502 " model vdw 2.111 2.170 nonbonded pdb=" O3G AGS B 501 " pdb="MG MG B 502 " model vdw 2.166 2.170 ... (remaining 190953 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 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 388 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'B' and (resid 15 through 248 or resid 251 through 381 or resid 395 or re \ sid 397 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'C' and (resid 15 through 248 or resid 251 through 381 or resid 386 throu \ gh 394 or (resid 401 and (name N or name CA or name C or name O or name CB )) or \ resid 402 through 472)) selection = (chain 'D' and (resid 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 394 or (resid 401 and (name N or name CA or name C or name O or name CB )) o \ r resid 402 through 472)) selection = (chain 'E' and (resid 15 through 248 or resid 251 through 381 or resid 386 or re \ sid 388 or resid 401 through 472)) selection = (chain 'F' and (resid 15 through 381 or resid 386 or resid 388 or (resid 401 and \ (name N or name CA or name C or name O or name CB )) or resid 402 through 472)) \ } 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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.950 Check model and map are aligned: 0.370 Set scattering table: 0.220 Process input model: 56.880 Find NCS groups from input model: 1.690 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 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 : 0.005 0.092 23061 Z= 0.324 Angle : 0.682 14.254 31152 Z= 0.439 Chirality : 0.047 0.316 3306 Planarity : 0.003 0.057 3909 Dihedral : 15.193 143.458 8739 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.25 % Allowed : 0.79 % Favored : 98.96 % 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: -0.79 (0.15), residues: 2681 helix: 0.46 (0.15), residues: 1153 sheet: -1.02 (0.30), residues: 279 loop : -1.32 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 197 HIS 0.009 0.001 HIS F 148 PHE 0.017 0.001 PHE F 116 TYR 0.015 0.001 TYR D 94 ARG 0.007 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 302 time to evaluate : 2.873 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7767 (tttp) cc_final: 0.7489 (ttmt) REVERT: A 292 LYS cc_start: 0.8149 (mmmm) cc_final: 0.7730 (mtpp) REVERT: A 452 THR cc_start: 0.8279 (m) cc_final: 0.7992 (p) REVERT: B 38 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 291 ASN cc_start: 0.7449 (m-40) cc_final: 0.7186 (m110) REVERT: B 330 LYS cc_start: 0.7540 (tttm) cc_final: 0.7257 (tttm) REVERT: B 405 TYR cc_start: 0.8659 (m-80) cc_final: 0.8173 (m-80) REVERT: B 453 ARG cc_start: 0.8119 (ptp-110) cc_final: 0.7580 (mtm180) REVERT: C 235 ASP cc_start: 0.7425 (t0) cc_final: 0.7193 (t0) REVERT: C 436 ASP cc_start: 0.7516 (m-30) cc_final: 0.6993 (m-30) REVERT: D 99 SER cc_start: 0.8842 (m) cc_final: 0.8601 (p) REVERT: D 206 LYS cc_start: 0.8412 (ptpp) cc_final: 0.8045 (mtpt) REVERT: D 209 GLU cc_start: 0.7662 (tp30) cc_final: 0.7442 (mm-30) REVERT: D 234 GLU cc_start: 0.7519 (mp0) cc_final: 0.7055 (mp0) REVERT: D 367 TYR cc_start: 0.7934 (m-80) cc_final: 0.7575 (m-80) REVERT: E 224 GLU cc_start: 0.7026 (mm-30) cc_final: 0.6646 (mm-30) REVERT: E 254 ARG cc_start: 0.6898 (ptp-110) cc_final: 0.6039 (ptm-80) REVERT: E 324 LYS cc_start: 0.8556 (ttpt) cc_final: 0.8192 (tttp) REVERT: E 341 GLU cc_start: 0.7313 (tm-30) cc_final: 0.7066 (tp30) REVERT: F 341 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6899 (mm-30) REVERT: F 453 ARG cc_start: 0.7814 (mtp85) cc_final: 0.7542 (mmm160) outliers start: 6 outliers final: 0 residues processed: 306 average time/residue: 0.3744 time to fit residues: 172.2155 Evaluate side-chains 201 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 0.7980 chunk 210 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 156 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN C 200 GLN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS D 426 GLN E 443 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 23061 Z= 0.274 Angle : 0.490 6.182 31152 Z= 0.264 Chirality : 0.040 0.167 3306 Planarity : 0.004 0.051 3909 Dihedral : 10.767 158.355 3181 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.92 % Allowed : 7.34 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2681 helix: 0.49 (0.15), residues: 1154 sheet: -0.90 (0.30), residues: 261 loop : -1.30 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 197 HIS 0.009 0.001 HIS D 196 PHE 0.015 0.002 PHE F 56 TYR 0.023 0.001 TYR A 472 ARG 0.007 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 2.792 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7829 (tttp) cc_final: 0.7571 (ttmt) REVERT: A 292 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7959 (mtpp) REVERT: B 453 ARG cc_start: 0.8045 (ptp-110) cc_final: 0.7444 (mtm180) REVERT: D 206 LYS cc_start: 0.8469 (ptpp) cc_final: 0.8070 (mtpt) REVERT: D 209 GLU cc_start: 0.7724 (tp30) cc_final: 0.7376 (tp30) REVERT: D 234 GLU cc_start: 0.7509 (mp0) cc_final: 0.6991 (mp0) REVERT: D 367 TYR cc_start: 0.7963 (m-80) cc_final: 0.7548 (m-80) REVERT: E 224 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6801 (mm-30) REVERT: E 254 ARG cc_start: 0.6936 (ptp-110) cc_final: 0.5973 (ptm-80) REVERT: E 324 LYS cc_start: 0.8524 (ttpt) cc_final: 0.8271 (tttp) REVERT: E 341 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6994 (tp30) REVERT: E 421 MET cc_start: 0.8707 (mtt) cc_final: 0.8504 (mtt) REVERT: F 28 GLN cc_start: 0.7451 (mm110) cc_final: 0.7155 (tp40) REVERT: F 318 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7656 (m-30) REVERT: F 341 GLU cc_start: 0.7437 (mm-30) cc_final: 0.6961 (mm-30) outliers start: 22 outliers final: 16 residues processed: 213 average time/residue: 0.3652 time to fit residues: 119.4711 Evaluate side-chains 194 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 2.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain F residue 318 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 203 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 67 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 217 optimal weight: 9.9990 chunk 242 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 196 optimal weight: 8.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 ASN B 291 ASN C 114 ASN ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS E 117 HIS ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23061 Z= 0.292 Angle : 0.492 6.291 31152 Z= 0.264 Chirality : 0.041 0.170 3306 Planarity : 0.004 0.051 3909 Dihedral : 10.530 155.378 3181 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.96 % Allowed : 9.25 % Favored : 88.79 % 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: -0.80 (0.15), residues: 2681 helix: 0.44 (0.15), residues: 1156 sheet: -0.93 (0.30), residues: 263 loop : -1.33 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 197 HIS 0.010 0.001 HIS D 196 PHE 0.014 0.002 PHE D 283 TYR 0.023 0.002 TYR A 472 ARG 0.009 0.000 ARG C 133 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 190 time to evaluate : 2.658 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7914 (tttp) cc_final: 0.7641 (ttmt) REVERT: A 292 LYS cc_start: 0.8277 (mmmm) cc_final: 0.8043 (mtpp) REVERT: B 453 ARG cc_start: 0.8063 (ptp-110) cc_final: 0.7564 (mtm180) REVERT: D 209 GLU cc_start: 0.7811 (tp30) cc_final: 0.7387 (tp30) REVERT: D 214 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8493 (mp) REVERT: D 234 GLU cc_start: 0.7501 (mp0) cc_final: 0.7084 (mp0) REVERT: D 367 TYR cc_start: 0.7989 (m-80) cc_final: 0.7560 (m-80) REVERT: E 165 ILE cc_start: 0.8784 (OUTLIER) cc_final: 0.8248 (tp) REVERT: E 221 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7571 (tm-30) REVERT: E 224 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6744 (mm-30) REVERT: E 254 ARG cc_start: 0.6950 (ptp-110) cc_final: 0.5896 (ptm-80) REVERT: E 324 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8291 (tttp) REVERT: E 341 GLU cc_start: 0.7326 (tm-30) cc_final: 0.7074 (tp30) REVERT: E 443 ASN cc_start: 0.7908 (t160) cc_final: 0.7707 (t0) REVERT: F 28 GLN cc_start: 0.7464 (mm110) cc_final: 0.7149 (tp40) REVERT: F 318 ASP cc_start: 0.7941 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: F 335 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5188 (tmm) outliers start: 47 outliers final: 30 residues processed: 219 average time/residue: 0.3455 time to fit residues: 118.6718 Evaluate side-chains 211 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 176 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 341 GLU Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 221 GLU Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 241 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 127 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 164 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 260 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 232 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN C 117 HIS C 229 GLN D 196 HIS F 196 HIS F 426 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23061 Z= 0.190 Angle : 0.432 6.401 31152 Z= 0.234 Chirality : 0.038 0.163 3306 Planarity : 0.003 0.049 3909 Dihedral : 10.384 156.498 3181 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.58 % Allowed : 11.05 % Favored : 87.37 % 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: -0.64 (0.15), residues: 2681 helix: 0.63 (0.15), residues: 1159 sheet: -1.00 (0.30), residues: 271 loop : -1.29 (0.16), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 197 HIS 0.010 0.001 HIS D 196 PHE 0.011 0.001 PHE F 56 TYR 0.018 0.001 TYR A 472 ARG 0.002 0.000 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 185 time to evaluate : 2.637 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7927 (tttp) cc_final: 0.7619 (ttmt) REVERT: A 292 LYS cc_start: 0.8327 (mmmm) cc_final: 0.8102 (mtpp) REVERT: A 306 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8156 (t) REVERT: B 453 ARG cc_start: 0.8023 (ptp-110) cc_final: 0.7544 (mtm180) REVERT: C 158 MET cc_start: 0.9023 (mmm) cc_final: 0.8814 (mmm) REVERT: D 209 GLU cc_start: 0.7737 (tp30) cc_final: 0.7323 (tp30) REVERT: D 234 GLU cc_start: 0.7483 (mp0) cc_final: 0.7010 (mp0) REVERT: D 367 TYR cc_start: 0.7959 (m-80) cc_final: 0.7550 (m-80) REVERT: D 466 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8978 (t) REVERT: E 135 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7576 (mt-10) REVERT: E 254 ARG cc_start: 0.6930 (ptp-110) cc_final: 0.5920 (ptt180) REVERT: E 324 LYS cc_start: 0.8572 (ttpt) cc_final: 0.8291 (tttp) REVERT: E 443 ASN cc_start: 0.7826 (t160) cc_final: 0.7595 (t0) REVERT: F 28 GLN cc_start: 0.7480 (mm110) cc_final: 0.7182 (tp40) REVERT: F 341 GLU cc_start: 0.7477 (mm-30) cc_final: 0.6936 (mm-30) outliers start: 38 outliers final: 24 residues processed: 208 average time/residue: 0.3374 time to fit residues: 109.8991 Evaluate side-chains 198 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 0.0010 chunk 147 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 221 optimal weight: 7.9990 chunk 179 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 132 optimal weight: 0.4980 chunk 233 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 2.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN C 147 ASN D 196 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23061 Z= 0.261 Angle : 0.463 6.311 31152 Z= 0.249 Chirality : 0.040 0.167 3306 Planarity : 0.003 0.048 3909 Dihedral : 10.328 155.948 3181 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.21 % Allowed : 11.55 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 2681 helix: 0.60 (0.15), residues: 1151 sheet: -0.97 (0.30), residues: 271 loop : -1.29 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 197 HIS 0.011 0.001 HIS D 196 PHE 0.012 0.001 PHE D 283 TYR 0.020 0.001 TYR A 472 ARG 0.004 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 2.631 Fit side-chains revert: symmetry clash REVERT: A 92 LYS cc_start: 0.7910 (tttp) cc_final: 0.7607 (ttmt) REVERT: A 292 LYS cc_start: 0.8360 (mmmm) cc_final: 0.8151 (mtpp) REVERT: A 306 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8186 (t) REVERT: B 453 ARG cc_start: 0.8056 (ptp-110) cc_final: 0.7547 (mtm180) REVERT: D 214 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8548 (mp) REVERT: D 234 GLU cc_start: 0.7443 (mp0) cc_final: 0.6983 (mp0) REVERT: D 367 TYR cc_start: 0.7985 (m-80) cc_final: 0.7568 (m-80) REVERT: E 165 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8181 (tp) REVERT: E 254 ARG cc_start: 0.6891 (ptp-110) cc_final: 0.5962 (ptt180) REVERT: E 324 LYS cc_start: 0.8617 (ttpt) cc_final: 0.8339 (tttp) REVERT: E 443 ASN cc_start: 0.7857 (t160) cc_final: 0.7604 (t0) REVERT: F 28 GLN cc_start: 0.7493 (mm110) cc_final: 0.7171 (tp40) REVERT: F 335 MET cc_start: 0.6300 (OUTLIER) cc_final: 0.5233 (tmm) outliers start: 53 outliers final: 37 residues processed: 214 average time/residue: 0.3466 time to fit residues: 116.2452 Evaluate side-chains 212 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 171 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 187 SER Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 216 optimal weight: 0.3980 chunk 120 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 136 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN D 196 HIS D 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23061 Z= 0.158 Angle : 0.410 6.422 31152 Z= 0.221 Chirality : 0.037 0.159 3306 Planarity : 0.003 0.048 3909 Dihedral : 10.149 155.980 3181 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.96 % Allowed : 12.30 % Favored : 85.74 % 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: -0.47 (0.16), residues: 2681 helix: 0.82 (0.15), residues: 1153 sheet: -0.92 (0.30), residues: 269 loop : -1.24 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.010 0.001 HIS D 196 PHE 0.009 0.001 PHE F 56 TYR 0.015 0.001 TYR A 472 ARG 0.003 0.000 ARG C 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 2.670 Fit side-chains REVERT: A 92 LYS cc_start: 0.7892 (tttp) cc_final: 0.7589 (ttmt) REVERT: B 453 ARG cc_start: 0.8025 (ptp-110) cc_final: 0.7553 (mtm180) REVERT: C 436 ASP cc_start: 0.7633 (m-30) cc_final: 0.7123 (m-30) REVERT: D 209 GLU cc_start: 0.7665 (tp30) cc_final: 0.7269 (tp30) REVERT: D 234 GLU cc_start: 0.7398 (mp0) cc_final: 0.6920 (mp0) REVERT: D 367 TYR cc_start: 0.7953 (m-80) cc_final: 0.7555 (m-80) REVERT: E 135 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7577 (mt-10) REVERT: E 165 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8096 (tp) REVERT: E 254 ARG cc_start: 0.6890 (ptp-110) cc_final: 0.5943 (ptt180) REVERT: E 324 LYS cc_start: 0.8605 (ttpt) cc_final: 0.8333 (tttp) REVERT: E 409 ASP cc_start: 0.7451 (t70) cc_final: 0.7250 (t70) REVERT: E 443 ASN cc_start: 0.7834 (t160) cc_final: 0.7573 (t0) REVERT: F 28 GLN cc_start: 0.7465 (mm110) cc_final: 0.7157 (tp40) REVERT: F 335 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5077 (tmm) REVERT: F 341 GLU cc_start: 0.7457 (mm-30) cc_final: 0.6906 (mm-30) outliers start: 47 outliers final: 36 residues processed: 217 average time/residue: 0.3226 time to fit residues: 109.9086 Evaluate side-chains 213 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 175 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 452 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 104 ASP Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 265 VAL Chi-restraints excluded: chain E residue 381 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 335 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 0.8980 chunk 219 optimal weight: 0.0870 chunk 145 optimal weight: 0.7980 chunk 259 optimal weight: 2.9990 chunk 162 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 119 optimal weight: 0.0270 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 ASN B 431 HIS D 196 HIS D 308 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23061 Z= 0.122 Angle : 0.392 6.239 31152 Z= 0.212 Chirality : 0.037 0.155 3306 Planarity : 0.003 0.049 3909 Dihedral : 9.857 154.979 3181 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.42 % Allowed : 12.96 % Favored : 85.62 % 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: -0.29 (0.16), residues: 2681 helix: 1.03 (0.15), residues: 1155 sheet: -0.81 (0.30), residues: 276 loop : -1.21 (0.16), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.012 0.001 HIS D 196 PHE 0.008 0.001 PHE F 56 TYR 0.014 0.001 TYR F 316 ARG 0.003 0.000 ARG F 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 190 time to evaluate : 2.788 Fit side-chains REVERT: A 92 LYS cc_start: 0.7887 (tttp) cc_final: 0.7583 (ttmt) REVERT: A 110 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7558 (tm-30) REVERT: A 436 ASP cc_start: 0.8134 (m-30) cc_final: 0.7851 (m-30) REVERT: B 453 ARG cc_start: 0.7981 (ptp-110) cc_final: 0.7533 (mtm180) REVERT: C 436 ASP cc_start: 0.7515 (m-30) cc_final: 0.7091 (m-30) REVERT: D 99 SER cc_start: 0.8833 (m) cc_final: 0.8631 (p) REVERT: D 209 GLU cc_start: 0.7664 (tp30) cc_final: 0.7299 (tp30) REVERT: D 234 GLU cc_start: 0.7369 (mp0) cc_final: 0.6704 (mp0) REVERT: D 367 TYR cc_start: 0.7938 (m-80) cc_final: 0.7532 (m-80) REVERT: E 165 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8164 (tp) REVERT: E 254 ARG cc_start: 0.6871 (ptp-110) cc_final: 0.5933 (ptt180) REVERT: E 324 LYS cc_start: 0.8599 (ttpt) cc_final: 0.8328 (tttp) REVERT: E 409 ASP cc_start: 0.7413 (t70) cc_final: 0.7210 (t70) REVERT: E 443 ASN cc_start: 0.7785 (t160) cc_final: 0.7371 (t0) REVERT: F 335 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5152 (tmm) REVERT: F 341 GLU cc_start: 0.7397 (mm-30) cc_final: 0.6828 (mm-30) outliers start: 34 outliers final: 29 residues processed: 210 average time/residue: 0.3570 time to fit residues: 118.0844 Evaluate side-chains 210 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 179 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 78 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 HIS B 291 ASN C 147 ASN D 196 HIS D 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23061 Z= 0.393 Angle : 0.527 6.843 31152 Z= 0.280 Chirality : 0.043 0.187 3306 Planarity : 0.004 0.046 3909 Dihedral : 10.071 153.562 3181 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.29 % Allowed : 12.63 % Favored : 85.08 % 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: -0.66 (0.15), residues: 2681 helix: 0.60 (0.15), residues: 1141 sheet: -0.88 (0.29), residues: 281 loop : -1.27 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 417 HIS 0.011 0.001 HIS D 196 PHE 0.016 0.002 PHE D 283 TYR 0.024 0.002 TYR A 472 ARG 0.005 0.001 ARG C 164 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 172 time to evaluate : 2.561 Fit side-chains REVERT: A 306 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8209 (t) REVERT: B 306 VAL cc_start: 0.8851 (OUTLIER) cc_final: 0.8631 (t) REVERT: B 453 ARG cc_start: 0.8079 (ptp-110) cc_final: 0.7560 (mtm180) REVERT: C 436 ASP cc_start: 0.7672 (m-30) cc_final: 0.7145 (m-30) REVERT: D 367 TYR cc_start: 0.7984 (m-80) cc_final: 0.7553 (m-80) REVERT: E 135 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7548 (mt-10) REVERT: E 165 ILE cc_start: 0.8789 (OUTLIER) cc_final: 0.8256 (tp) REVERT: E 254 ARG cc_start: 0.6918 (ptp-110) cc_final: 0.6049 (ptt180) REVERT: E 324 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8365 (tttp) REVERT: E 443 ASN cc_start: 0.7917 (t160) cc_final: 0.7628 (t0) REVERT: F 335 MET cc_start: 0.6287 (OUTLIER) cc_final: 0.5362 (tmm) outliers start: 55 outliers final: 42 residues processed: 211 average time/residue: 0.3372 time to fit residues: 112.2984 Evaluate side-chains 211 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 165 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 147 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 80 ASP Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 VAL Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain E residue 466 VAL Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 1.9990 chunk 226 optimal weight: 0.7980 chunk 241 optimal weight: 0.8980 chunk 145 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 218 optimal weight: 1.9990 chunk 228 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 HIS F 196 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23061 Z= 0.143 Angle : 0.413 6.302 31152 Z= 0.224 Chirality : 0.037 0.162 3306 Planarity : 0.003 0.048 3909 Dihedral : 9.881 153.150 3181 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.79 % Allowed : 13.09 % Favored : 85.12 % 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: -0.41 (0.16), residues: 2681 helix: 0.90 (0.15), residues: 1151 sheet: -0.87 (0.30), residues: 266 loop : -1.24 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.012 0.001 HIS D 196 PHE 0.009 0.001 PHE F 56 TYR 0.021 0.001 TYR F 198 ARG 0.008 0.000 ARG D 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 2.527 Fit side-chains REVERT: B 453 ARG cc_start: 0.8022 (ptp-110) cc_final: 0.7552 (mtm180) REVERT: C 436 ASP cc_start: 0.7630 (m-30) cc_final: 0.7115 (m-30) REVERT: D 214 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mp) REVERT: D 367 TYR cc_start: 0.7944 (m-80) cc_final: 0.7550 (m-80) REVERT: E 165 ILE cc_start: 0.8676 (OUTLIER) cc_final: 0.8116 (tp) REVERT: E 254 ARG cc_start: 0.6872 (ptp-110) cc_final: 0.6037 (ptt180) REVERT: E 324 LYS cc_start: 0.8634 (ttpt) cc_final: 0.8315 (ttmm) REVERT: E 415 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: E 443 ASN cc_start: 0.7841 (t160) cc_final: 0.7563 (t0) REVERT: F 176 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8211 (tt) REVERT: F 335 MET cc_start: 0.6213 (OUTLIER) cc_final: 0.5191 (tmm) REVERT: F 341 GLU cc_start: 0.7387 (mm-30) cc_final: 0.6884 (mm-30) outliers start: 43 outliers final: 33 residues processed: 207 average time/residue: 0.3286 time to fit residues: 107.2001 Evaluate side-chains 212 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 174 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 chunk 267 optimal weight: 8.9990 chunk 246 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 164 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23061 Z= 0.217 Angle : 0.438 6.141 31152 Z= 0.235 Chirality : 0.039 0.164 3306 Planarity : 0.003 0.048 3909 Dihedral : 9.786 152.419 3181 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.67 % Allowed : 13.38 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.16), residues: 2681 helix: 0.87 (0.15), residues: 1151 sheet: -0.85 (0.30), residues: 271 loop : -1.25 (0.16), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 197 HIS 0.011 0.001 HIS D 196 PHE 0.009 0.001 PHE D 283 TYR 0.020 0.001 TYR F 198 ARG 0.010 0.000 ARG D 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5362 Ramachandran restraints generated. 2681 Oldfield, 0 Emsley, 2681 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 173 time to evaluate : 2.653 Fit side-chains REVERT: B 453 ARG cc_start: 0.8041 (ptp-110) cc_final: 0.7566 (mtm180) REVERT: C 436 ASP cc_start: 0.7645 (m-30) cc_final: 0.7081 (m-30) REVERT: D 214 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8531 (mp) REVERT: D 367 TYR cc_start: 0.7962 (m-80) cc_final: 0.7561 (m-80) REVERT: E 135 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7553 (mt-10) REVERT: E 165 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8139 (tp) REVERT: E 254 ARG cc_start: 0.6876 (ptp-110) cc_final: 0.6028 (ptt180) REVERT: E 324 LYS cc_start: 0.8650 (ttpt) cc_final: 0.8325 (ttmm) REVERT: E 415 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: E 443 ASN cc_start: 0.7849 (t160) cc_final: 0.7570 (t0) REVERT: F 176 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8233 (tt) REVERT: F 335 MET cc_start: 0.6226 (OUTLIER) cc_final: 0.5245 (tmm) outliers start: 40 outliers final: 33 residues processed: 202 average time/residue: 0.3586 time to fit residues: 114.8218 Evaluate side-chains 208 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 170 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 105 THR Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 104 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 245 ASP Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 425 ASP Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 341 GLU Chi-restraints excluded: chain C residue 379 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 468 LEU Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 93 LEU Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 173 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 452 THR Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 415 GLU Chi-restraints excluded: chain E residue 425 ASP Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 335 MET Chi-restraints excluded: chain F residue 406 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 59 optimal weight: 5.9990 chunk 213 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 219 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 HIS D 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.110278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.091471 restraints weight = 34287.866| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.60 r_work: 0.2970 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23061 Z= 0.151 Angle : 0.407 6.233 31152 Z= 0.220 Chirality : 0.038 0.160 3306 Planarity : 0.003 0.049 3909 Dihedral : 9.556 151.271 3181 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.63 % Allowed : 13.51 % Favored : 84.87 % 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: -0.32 (0.16), residues: 2681 helix: 1.01 (0.15), residues: 1152 sheet: -0.84 (0.31), residues: 267 loop : -1.22 (0.16), residues: 1262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 197 HIS 0.011 0.001 HIS D 196 PHE 0.008 0.001 PHE F 56 TYR 0.020 0.001 TYR F 198 ARG 0.010 0.000 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4338.38 seconds wall clock time: 80 minutes 40.18 seconds (4840.18 seconds total)