Starting phenix.real_space_refine (version: dev) on Fri Feb 24 08:48:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/02_2023/7pds_13342_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/02_2023/7pds_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_13342/02_2023/7pds_13342.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/02_2023/7pds_13342.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/02_2023/7pds_13342_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pds_13342/02_2023/7pds_13342_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.08, per 1000 atoms: 0.54 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: 8.67 Conformation dependent library (CDL) restraints added in 3.3 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: 2.25 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: 6.87 Time building geometry restraints manager: 9.17 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: 13204 28.69 - 57.38: 517 57.38 - 86.07: 48 86.07 - 114.77: 2 114.77 - 143.46: 4 Dihedral angle restraints: 13775 sinusoidal: 5803 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 13772 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 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. 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: 1.650 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: 11.680 Check model and map are aligned: 0.320 Process input model: 55.270 Find NCS groups from input model: 2.030 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.200 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 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 : 14.795 143.458 8657 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 % 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 *********************** 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 : 2.663 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 306 average time/residue: 0.3806 time to fit residues: 175.4862 Evaluate side-chains 187 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.669 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.6641 ------------------------------------------------------------------------------- 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: 0.0050 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: 0.8980 chunk 156 optimal weight: 3.9990 chunk 244 optimal weight: 4.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- 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** B 291 ASN C 147 ASN C 200 GLN C 229 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: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.0959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.082 23061 Z= 0.233 Angle : 0.472 6.163 31152 Z= 0.254 Chirality : 0.040 0.164 3306 Planarity : 0.004 0.052 3909 Dihedral : 9.363 161.939 3099 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 0.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 2681 helix: 0.53 (0.15), residues: 1161 sheet: -0.90 (0.30), residues: 261 loop : -1.32 (0.16), residues: 1259 *********************** 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 213 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 2.614 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 205 average time/residue: 0.3765 time to fit residues: 123.0290 Evaluate side-chains 182 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 167 time to evaluate : 2.679 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2126 time to fit residues: 9.7846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 135 optimal weight: 0.0050 chunk 75 optimal weight: 0.9980 chunk 203 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 chunk 242 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 196 optimal weight: 7.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- 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 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 HIS E 117 HIS E 443 ASN ** F 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 428 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: 0.8646 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 23061 Z= 0.247 Angle : 0.466 6.209 31152 Z= 0.252 Chirality : 0.040 0.167 3306 Planarity : 0.003 0.050 3909 Dihedral : 9.283 156.737 3099 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 0.88 % 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: -0.70 (0.15), residues: 2681 helix: 0.55 (0.15), residues: 1160 sheet: -0.83 (0.30), residues: 273 loop : -1.34 (0.16), residues: 1248 *********************** 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 211 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 190 time to evaluate : 2.490 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 199 average time/residue: 0.3463 time to fit residues: 109.1722 Evaluate side-chains 180 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 169 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2048 time to fit residues: 8.0562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 127 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 245 optimal weight: 8.9990 chunk 260 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 114 ASN C 117 HIS D 196 HIS F 426 GLN ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.1581 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= 0.287 Angle : 0.481 6.502 31152 Z= 0.258 Chirality : 0.040 0.170 3306 Planarity : 0.004 0.049 3909 Dihedral : 9.310 157.219 3099 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.08 % 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: -0.71 (0.15), residues: 2681 helix: 0.52 (0.15), residues: 1152 sheet: -0.90 (0.30), residues: 261 loop : -1.29 (0.16), residues: 1268 *********************** 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 204 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 2.766 Fit side-chains outliers start: 26 outliers final: 15 residues processed: 196 average time/residue: 0.3584 time to fit residues: 111.6058 Evaluate side-chains 176 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 161 time to evaluate : 2.511 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1987 time to fit residues: 9.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 193 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 221 optimal weight: 3.9990 chunk 179 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 132 optimal weight: 4.9990 chunk 233 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 291 ASN D 196 HIS D 215 GLN E 443 ASN F 196 HIS ** 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: 0.8668 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 23061 Z= 0.310 Angle : 0.491 9.659 31152 Z= 0.263 Chirality : 0.041 0.171 3306 Planarity : 0.004 0.049 3909 Dihedral : 9.322 159.241 3099 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.15), residues: 2681 helix: 0.50 (0.15), residues: 1143 sheet: -0.91 (0.29), residues: 279 loop : -1.27 (0.16), residues: 1259 *********************** 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 207 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 174 time to evaluate : 2.989 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 198 average time/residue: 0.3402 time to fit residues: 108.3403 Evaluate side-chains 176 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 162 time to evaluate : 2.794 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2020 time to fit residues: 9.1163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 87 optimal weight: 5.9990 chunk 234 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 152 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 260 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 chunk 86 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN D 196 HIS D 308 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1764 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= 0.131 Angle : 0.411 11.874 31152 Z= 0.221 Chirality : 0.037 0.161 3306 Planarity : 0.003 0.050 3909 Dihedral : 9.089 158.813 3099 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2681 helix: 0.83 (0.15), residues: 1152 sheet: -0.94 (0.30), residues: 267 loop : -1.23 (0.16), residues: 1262 *********************** 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 198 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 182 time to evaluate : 2.954 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 193 average time/residue: 0.3661 time to fit residues: 112.4275 Evaluate side-chains 179 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 170 time to evaluate : 2.804 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2069 time to fit residues: 7.2289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 190 optimal weight: 5.9990 chunk 147 optimal weight: 1.9990 chunk 219 optimal weight: 0.0000 chunk 145 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 overall best weight: 1.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 431 HIS C 147 ASN D 196 HIS D 308 GLN E 443 ASN ** 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: 0.8644 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 23061 Z= 0.232 Angle : 0.443 8.275 31152 Z= 0.238 Chirality : 0.039 0.166 3306 Planarity : 0.003 0.049 3909 Dihedral : 9.035 158.072 3099 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.83 % 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: -0.50 (0.16), residues: 2681 helix: 0.77 (0.15), residues: 1150 sheet: -0.87 (0.29), residues: 282 loop : -1.23 (0.16), residues: 1249 *********************** 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 187 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 167 time to evaluate : 2.739 Fit side-chains outliers start: 20 outliers final: 14 residues processed: 177 average time/residue: 0.3736 time to fit residues: 104.5745 Evaluate side-chains 177 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 163 time to evaluate : 2.848 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2144 time to fit residues: 9.5060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 160 optimal weight: 0.0870 chunk 103 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 164 optimal weight: 0.6980 chunk 176 optimal weight: 0.4980 chunk 128 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 203 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 23061 Z= 0.176 Angle : 0.425 12.048 31152 Z= 0.228 Chirality : 0.038 0.163 3306 Planarity : 0.003 0.050 3909 Dihedral : 8.955 158.485 3099 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 0.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.16), residues: 2681 helix: 0.85 (0.15), residues: 1149 sheet: -0.92 (0.30), residues: 270 loop : -1.22 (0.16), residues: 1262 *********************** 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 182 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 2.909 Fit side-chains outliers start: 8 outliers final: 3 residues processed: 180 average time/residue: 0.3961 time to fit residues: 112.4117 Evaluate side-chains 169 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 166 time to evaluate : 2.539 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2103 time to fit residues: 4.7624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 248 optimal weight: 0.2980 chunk 226 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 218 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 240 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 196 HIS F 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: 0.8640 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 23061 Z= 0.214 Angle : 0.440 10.131 31152 Z= 0.235 Chirality : 0.039 0.166 3306 Planarity : 0.003 0.049 3909 Dihedral : 8.913 157.985 3099 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2681 helix: 0.80 (0.15), residues: 1149 sheet: -0.87 (0.29), residues: 282 loop : -1.23 (0.16), residues: 1250 *********************** 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 174 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 2.713 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 170 average time/residue: 0.3786 time to fit residues: 100.6317 Evaluate side-chains 167 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 162 time to evaluate : 2.803 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2212 time to fit residues: 6.0757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 255 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 121 optimal weight: 5.9990 chunk 177 optimal weight: 0.9990 chunk 267 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 213 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 196 HIS ** F 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.1953 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= 0.204 Angle : 0.435 9.716 31152 Z= 0.233 Chirality : 0.039 0.166 3306 Planarity : 0.003 0.049 3909 Dihedral : 8.810 157.981 3099 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2681 helix: 0.82 (0.15), residues: 1149 sheet: -0.91 (0.30), residues: 272 loop : -1.23 (0.16), residues: 1260 ********************** 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 172 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 168 time to evaluate : 2.571 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 170 average time/residue: 0.3813 time to fit residues: 103.0733 Evaluate side-chains 164 residues out of total 2400 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 162 time to evaluate : 2.896 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2024 time to fit residues: 4.4711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 59 optimal weight: 4.9990 chunk 213 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 219 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 187 optimal weight: 4.9990 overall best weight: 1.2180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.109898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.092090 restraints weight = 34242.566| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.44 r_work: 0.2975 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 23061 Z= 0.175 Angle : 0.421 9.158 31152 Z= 0.226 Chirality : 0.038 0.164 3306 Planarity : 0.003 0.049 3909 Dihedral : 8.719 158.199 3099 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 0.21 % 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: -0.40 (0.16), residues: 2681 helix: 0.90 (0.15), residues: 1150 sheet: -0.90 (0.30), residues: 268 loop : -1.22 (0.16), residues: 1263 =============================================================================== Job complete usr+sys time: 4095.98 seconds wall clock time: 76 minutes 3.09 seconds (4563.09 seconds total)