Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 10 02:29:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5v_14341/10_2023/7r5v_14341.pdb" } resolution = 4.55 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= 0.005 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1691 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 63 5.49 5 S 92 5.16 5 C 11668 2.51 5 N 3126 2.21 5 O 3558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H ASP 84": "OD1" <-> "OD2" Residue "H PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "I PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 342": "OE1" <-> "OE2" Residue "I PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 380": "NH1" <-> "NH2" Residue "I GLU 436": "OE1" <-> "OE2" Residue "I PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 566": "OE1" <-> "OE2" Residue "I TYR 643": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 86": "OE1" <-> "OE2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 102": "OE1" <-> "OE2" Residue "L PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 168": "OD1" <-> "OD2" Residue "L GLU 172": "OE1" <-> "OE2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L GLU 238": "OE1" <-> "OE2" Residue "L GLU 259": "OE1" <-> "OE2" Residue "L TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 337": "OE1" <-> "OE2" Residue "L PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 39": "OD1" <-> "OD2" Residue "M ASP 89": "OD1" <-> "OD2" Residue "N GLU 3": "OE1" <-> "OE2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "N ARG 196": "NH1" <-> "NH2" Residue "N GLU 244": "OE1" <-> "OE2" Residue "N GLU 246": "OE1" <-> "OE2" Residue "N ARG 330": "NH1" <-> "NH2" Residue "O TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 136": "OD1" <-> "OD2" Residue "O PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 137": "OD1" <-> "OD2" Residue "P GLU 146": "OE1" <-> "OE2" Residue "P ARG 223": "NH1" <-> "NH2" Residue "P GLU 248": "OE1" <-> "OE2" Residue "P PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 272": "OE1" <-> "OE2" Residue "Q ASP 82": "OD1" <-> "OD2" Residue "Q GLU 104": "OE1" <-> "OE2" Residue "Q GLU 122": "OE1" <-> "OE2" Residue "Q ARG 147": "NH1" <-> "NH2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "U GLU 250": "OE1" <-> "OE2" Residue "U GLU 257": "OE1" <-> "OE2" Residue "U PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 295": "OE1" <-> "OE2" Residue "U PHE 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 170": "OE1" <-> "OE2" Residue "R PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 18507 Number of models: 1 Model: "" Number of chains: 13 Chain: "H" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1013 Classifications: {'peptide': 124} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'TRANS': 123} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2686 Classifications: {'peptide': 328} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain breaks: 6 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "J" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 658 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "K" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1026 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 125} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2397 Classifications: {'peptide': 297} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 284} Chain breaks: 2 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2452 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 283} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 8, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1732 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 211} Chain breaks: 2 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "U" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1346 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 160} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "i" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 632 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "R" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 92 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Time building chain proxies: 9.70, per 1000 atoms: 0.52 Number of scatterers: 18507 At special positions: 0 Unit cell: (113.847, 177.834, 191.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 63 15.00 O 3558 8.00 N 3126 7.00 C 11668 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: 7.96 Conformation dependent library (CDL) restraints added in 2.7 seconds 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4170 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 11 sheets defined 63.6% alpha, 12.8% beta 20 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 6.11 Creating SS restraints... Processing helix chain 'H' and resid 40 through 64 Processing helix chain 'H' and resid 79 through 115 Processing helix chain 'H' and resid 125 through 183 removed outlier: 3.635A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS H 183 " --> pdb=" O LYS H 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 364 through 369 removed outlier: 4.192A pdb=" N ASN I 368 " --> pdb=" O GLY I 364 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 380 removed outlier: 3.516A pdb=" N LEU I 373 " --> pdb=" O ASN I 369 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS I 378 " --> pdb=" O HIS I 374 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ARG I 380 " --> pdb=" O ILE I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 404 removed outlier: 3.706A pdb=" N LYS I 404 " --> pdb=" O CYS I 400 " (cutoff:3.500A) Processing helix chain 'I' and resid 412 through 427 removed outlier: 3.559A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 433 through 443 Processing helix chain 'I' and resid 451 through 459 removed outlier: 3.678A pdb=" N GLN I 457 " --> pdb=" O SER I 453 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU I 458 " --> pdb=" O GLN I 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 469 through 474 removed outlier: 3.679A pdb=" N LEU I 473 " --> pdb=" O GLU I 469 " (cutoff:3.500A) Processing helix chain 'I' and resid 474 through 483 Processing helix chain 'I' and resid 486 through 509 Processing helix chain 'I' and resid 530 through 551 Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.512A pdb=" N LEU I 558 " --> pdb=" O ASN I 554 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 576 Processing helix chain 'I' and resid 584 through 593 Processing helix chain 'I' and resid 596 through 617 Processing helix chain 'I' and resid 635 through 651 Processing helix chain 'I' and resid 685 through 687 No H-bonds generated for 'chain 'I' and resid 685 through 687' Processing helix chain 'I' and resid 688 through 698 Processing helix chain 'I' and resid 719 through 726 Processing helix chain 'I' and resid 728 through 738 Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 54 through 77 Processing helix chain 'K' and resid 85 through 150 removed outlier: 3.660A pdb=" N LEU K 89 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLU K 105 " --> pdb=" O ARG K 101 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N MET K 106 " --> pdb=" O GLN K 102 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL K 107 " --> pdb=" O ASP K 103 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 38 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 87 through 103 Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 189 through 205 Processing helix chain 'L' and resid 214 through 228 Processing helix chain 'L' and resid 257 through 268 Processing helix chain 'L' and resid 276 through 296 Processing helix chain 'L' and resid 298 through 302 Processing helix chain 'L' and resid 324 through 326 No H-bonds generated for 'chain 'L' and resid 324 through 326' Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.612A pdb=" N LEU L 338 " --> pdb=" O TYR L 334 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 36 Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.923A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 88 No H-bonds generated for 'chain 'M' and resid 86 through 88' Processing helix chain 'M' and resid 89 through 94 Processing helix chain 'M' and resid 113 through 125 removed outlier: 3.969A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 Processing helix chain 'M' and resid 161 through 170 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 17 through 19 No H-bonds generated for 'chain 'N' and resid 17 through 19' Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 38 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 4.023A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 4.423A pdb=" N LEU N 116 " --> pdb=" O LEU N 112 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 removed outlier: 4.186A pdb=" N LEU N 175 " --> pdb=" O ASN N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 304 through 313 removed outlier: 4.504A pdb=" N ALA N 310 " --> pdb=" O LEU N 306 " (cutoff:3.500A) Proline residue: N 311 - end of helix Processing helix chain 'N' and resid 320 through 325 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.655A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 161 through 169 Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 201 through 204 removed outlier: 3.740A pdb=" N LEU O 204 " --> pdb=" O PHE O 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 201 through 204' Processing helix chain 'O' and resid 261 through 278 Processing helix chain 'O' and resid 279 through 289 Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 removed outlier: 4.070A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.577A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 254 through 256 No H-bonds generated for 'chain 'P' and resid 254 through 256' Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'P' and resid 271 through 282 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.626A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 124 Processing helix chain 'Q' and resid 136 through 198 removed outlier: 4.157A pdb=" N GLU Q 170 " --> pdb=" O VAL Q 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Q 171 " --> pdb=" O GLU Q 167 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N MET Q 172 " --> pdb=" O THR Q 168 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY Q 174 " --> pdb=" O GLU Q 170 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 229 removed outlier: 3.972A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 232 No H-bonds generated for 'chain 'Q' and resid 230 through 232' Processing helix chain 'Q' and resid 234 through 247 Processing helix chain 'Q' and resid 248 through 264 removed outlier: 3.903A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS Q 264 " --> pdb=" O GLU Q 260 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 269 Proline residue: U 256 - end of helix Processing helix chain 'U' and resid 271 through 375 Proline residue: U 332 - end of helix removed outlier: 4.376A pdb=" N LYS U 335 " --> pdb=" O GLU U 331 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLN U 336 " --> pdb=" O PRO U 332 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU U 337 " --> pdb=" O GLN U 333 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 395 removed outlier: 3.822A pdb=" N LEU U 390 " --> pdb=" O SER U 386 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS U 393 " --> pdb=" O ALA U 389 " (cutoff:3.500A) Processing helix chain 'U' and resid 398 through 412 Processing helix chain 'R' and resid 168 through 177 Processing sheet with id=AA1, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.810A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 117 through 124 removed outlier: 3.810A pdb=" N ALA L 136 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N LEU L 304 " --> pdb=" O SER L 242 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N SER L 242 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE L 252 " --> pdb=" O TRP L 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER N 298 " --> pdb=" O ASP L 251 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE N 334 " --> pdb=" O GLN N 268 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'M' and resid 128 through 131 removed outlier: 8.671A pdb=" N LEU M 129 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE M 99 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N CYS M 131 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ALA M 101 " --> pdb=" O CYS M 131 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA M 16 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N HIS M 47 " --> pdb=" O ALA M 16 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE M 18 " --> pdb=" O HIS M 47 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N ALA M 49 " --> pdb=" O ILE M 18 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU M 20 " --> pdb=" O ALA M 49 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'N' and resid 120 through 124 removed outlier: 4.258A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'O' and resid 113 through 114 removed outlier: 6.536A pdb=" N VAL O 124 " --> pdb=" O PHE O 139 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE O 139 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE O 126 " --> pdb=" O SER O 137 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N SER O 137 " --> pdb=" O ILE O 126 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N THR O 128 " --> pdb=" O LEU O 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 210 through 211 removed outlier: 3.870A pdb=" N ASP O 249 " --> pdb=" O LEU O 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'P' and resid 76 through 78 removed outlier: 3.710A pdb=" N LYS P 100 " --> pdb=" O LEU P 88 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'P' and resid 76 through 78 removed outlier: 6.784A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 195 through 196 removed outlier: 4.018A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) 1142 hydrogen bonds defined for protein. 3363 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 6.76 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4311 1.33 - 1.45: 4111 1.45 - 1.58: 10300 1.58 - 1.70: 124 1.70 - 1.82: 140 Bond restraints: 18986 Sorted by residual: bond pdb=" N ARG N 194 " pdb=" CA ARG N 194 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.24e-02 6.50e+03 8.66e+00 bond pdb=" N SER N 195 " pdb=" CA SER N 195 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.42e+00 bond pdb=" N VAL P 174 " pdb=" CA VAL P 174 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.08e+00 bond pdb=" N GLU N 127 " pdb=" CA GLU N 127 " ideal model delta sigma weight residual 1.454 1.491 -0.036 1.32e-02 5.74e+03 7.61e+00 bond pdb=" N VAL H 94 " pdb=" CA VAL H 94 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.45e+00 ... (remaining 18981 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.50: 803 106.50 - 113.43: 10552 113.43 - 120.35: 7253 120.35 - 127.28: 7037 127.28 - 134.20: 265 Bond angle restraints: 25910 Sorted by residual: angle pdb=" N GLU H 86 " pdb=" CA GLU H 86 " pdb=" CB GLU H 86 " ideal model delta sigma weight residual 110.28 116.35 -6.07 1.55e+00 4.16e-01 1.53e+01 angle pdb=" CA ALA N 130 " pdb=" C ALA N 130 " pdb=" O ALA N 130 " ideal model delta sigma weight residual 122.13 117.88 4.25 1.13e+00 7.83e-01 1.42e+01 angle pdb=" CA GLU N 127 " pdb=" C GLU N 127 " pdb=" O GLU N 127 " ideal model delta sigma weight residual 121.87 117.79 4.08 1.10e+00 8.26e-01 1.38e+01 angle pdb=" N GLN M 144 " pdb=" CA GLN M 144 " pdb=" CB GLN M 144 " ideal model delta sigma weight residual 110.28 115.74 -5.46 1.55e+00 4.16e-01 1.24e+01 angle pdb=" N GLU O 25 " pdb=" CA GLU O 25 " pdb=" CB GLU O 25 " ideal model delta sigma weight residual 110.39 116.20 -5.81 1.66e+00 3.63e-01 1.23e+01 ... (remaining 25905 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 9884 17.72 - 35.45: 1015 35.45 - 53.17: 353 53.17 - 70.89: 59 70.89 - 88.61: 16 Dihedral angle restraints: 11327 sinusoidal: 4987 harmonic: 6340 Sorted by residual: dihedral pdb=" C ASN N 129 " pdb=" N ASN N 129 " pdb=" CA ASN N 129 " pdb=" CB ASN N 129 " ideal model delta harmonic sigma weight residual -122.60 -133.08 10.48 0 2.50e+00 1.60e-01 1.76e+01 dihedral pdb=" CA ARG H 105 " pdb=" C ARG H 105 " pdb=" N MET H 106 " pdb=" CA MET H 106 " ideal model delta harmonic sigma weight residual 180.00 159.32 20.68 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" N ASN N 129 " pdb=" C ASN N 129 " pdb=" CA ASN N 129 " pdb=" CB ASN N 129 " ideal model delta harmonic sigma weight residual 122.80 131.94 -9.14 0 2.50e+00 1.60e-01 1.34e+01 ... (remaining 11324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2656 0.063 - 0.125: 308 0.125 - 0.188: 23 0.188 - 0.250: 3 0.250 - 0.313: 1 Chirality restraints: 2991 Sorted by residual: chirality pdb=" CA ASN N 129 " pdb=" N ASN N 129 " pdb=" C ASN N 129 " pdb=" CB ASN N 129 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.45e+00 chirality pdb=" CA ILE H 98 " pdb=" N ILE H 98 " pdb=" C ILE H 98 " pdb=" CB ILE H 98 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA LEU N 193 " pdb=" N LEU N 193 " pdb=" C LEU N 193 " pdb=" CB LEU N 193 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.73e-01 ... (remaining 2988 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 225 " 0.029 2.00e-02 2.50e+03 2.86e-02 2.04e+01 pdb=" CG TRP L 225 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP L 225 " 0.036 2.00e-02 2.50e+03 pdb=" CD2 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 225 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 225 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 225 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 225 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP L 225 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 105 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ARG H 105 " 0.042 2.00e-02 2.50e+03 pdb=" O ARG H 105 " -0.015 2.00e-02 2.50e+03 pdb=" N MET H 106 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 163 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.30e+00 pdb=" C ASP Q 163 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP Q 163 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS Q 164 " -0.012 2.00e-02 2.50e+03 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 754 2.71 - 3.26: 19524 3.26 - 3.81: 32280 3.81 - 4.35: 37551 4.35 - 4.90: 60219 Nonbonded interactions: 150328 Sorted by model distance: nonbonded pdb=" OD1 ASN M 71 " pdb=" OG1 THR M 102 " model vdw 2.168 2.440 nonbonded pdb=" OG1 THR O 128 " pdb=" O ASP O 136 " model vdw 2.182 2.440 nonbonded pdb=" OD2 ASP I 596 " pdb=" OG SER I 598 " model vdw 2.189 2.440 nonbonded pdb=" O ARG O 23 " pdb=" OG1 THR O 26 " model vdw 2.191 2.440 nonbonded pdb=" CD1 ILE O 173 " pdb=" CB SER R 168 " model vdw 2.193 3.860 ... (remaining 150323 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 12.590 Check model and map are aligned: 0.280 Set scattering table: 0.160 Process input model: 53.170 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 : 0.003 0.036 18986 Z= 0.197 Angle : 0.678 11.285 25910 Z= 0.406 Chirality : 0.040 0.313 2991 Planarity : 0.004 0.043 3026 Dihedral : 16.456 88.614 7157 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.21 % Allowed : 0.73 % Favored : 99.07 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.19), residues: 2078 helix: 1.34 (0.15), residues: 1263 sheet: 0.64 (0.32), residues: 251 loop : -0.48 (0.28), residues: 564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 214 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 217 average time/residue: 0.3000 time to fit residues: 99.8583 Evaluate side-chains 151 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 167 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18986 Z= 0.230 Angle : 0.581 8.856 25910 Z= 0.314 Chirality : 0.037 0.176 2991 Planarity : 0.004 0.044 3026 Dihedral : 16.494 68.302 2879 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.10 % Allowed : 5.66 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.19), residues: 2078 helix: 1.80 (0.14), residues: 1275 sheet: 0.62 (0.32), residues: 252 loop : -0.43 (0.28), residues: 551 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 190 average time/residue: 0.2917 time to fit residues: 88.5120 Evaluate side-chains 139 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.214 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 chunk 53 optimal weight: 20.0000 chunk 194 optimal weight: 30.0000 chunk 210 optimal weight: 10.0000 chunk 173 optimal weight: 4.9990 chunk 193 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 602 GLN ** K 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 298 HIS ** M 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 153 HIS ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 216 GLN Q 234 ASN U 360 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18986 Z= 0.286 Angle : 0.621 8.864 25910 Z= 0.332 Chirality : 0.038 0.172 2991 Planarity : 0.004 0.047 3026 Dihedral : 16.696 64.144 2879 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.43 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 2078 helix: 1.63 (0.14), residues: 1278 sheet: 0.51 (0.32), residues: 257 loop : -0.53 (0.28), residues: 543 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4156 Ramachandran restraints generated. 2078 Oldfield, 0 Emsley, 2078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 180 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 181 average time/residue: 0.2977 time to fit residues: 85.6326 Evaluate side-chains 143 residues out of total 1973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 142 time to evaluate : 2.176 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1917 time to fit residues: 3.3449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.1205 > 50: distance: 3 - 27: 12.958 distance: 14 - 38: 28.508 distance: 18 - 46: 24.731 distance: 21 - 27: 13.354 distance: 22 - 55: 25.768 distance: 27 - 28: 26.390 distance: 28 - 29: 29.107 distance: 28 - 31: 30.407 distance: 29 - 30: 35.542 distance: 29 - 38: 37.111 distance: 30 - 61: 30.155 distance: 31 - 32: 40.802 distance: 32 - 33: 51.601 distance: 33 - 34: 29.268 distance: 34 - 35: 8.014 distance: 35 - 36: 27.159 distance: 35 - 37: 16.105 distance: 38 - 39: 42.077 distance: 39 - 40: 40.745 distance: 39 - 42: 46.250 distance: 40 - 41: 19.008 distance: 40 - 46: 12.589 distance: 42 - 43: 5.261 distance: 43 - 44: 27.620 distance: 43 - 45: 30.969 distance: 46 - 47: 19.305 distance: 47 - 48: 28.229 distance: 47 - 50: 29.088 distance: 48 - 49: 12.379 distance: 48 - 55: 33.339 distance: 50 - 51: 19.696 distance: 51 - 52: 36.202 distance: 52 - 54: 28.794 distance: 55 - 56: 18.730 distance: 56 - 57: 17.130 distance: 56 - 59: 7.786 distance: 57 - 58: 23.906 distance: 57 - 61: 31.671 distance: 59 - 60: 3.961 distance: 61 - 62: 12.902 distance: 62 - 65: 4.430 distance: 63 - 69: 57.318 distance: 65 - 66: 9.768 distance: 66 - 67: 34.178 distance: 66 - 68: 11.196 distance: 69 - 70: 17.175 distance: 70 - 71: 30.823 distance: 70 - 73: 21.981 distance: 71 - 72: 23.133 distance: 71 - 80: 4.843 distance: 73 - 74: 6.688 distance: 74 - 75: 5.728 distance: 74 - 76: 32.935 distance: 75 - 77: 42.254 distance: 76 - 78: 16.911 distance: 77 - 79: 18.983 distance: 78 - 79: 23.425 distance: 80 - 81: 39.877 distance: 81 - 84: 14.209 distance: 82 - 83: 40.460 distance: 82 - 85: 39.944 distance: 85 - 86: 30.713 distance: 86 - 87: 27.787 distance: 86 - 89: 37.428 distance: 87 - 88: 13.045 distance: 87 - 90: 36.901 distance: 90 - 91: 53.242 distance: 91 - 94: 40.917 distance: 92 - 93: 40.293 distance: 92 - 98: 17.671 distance: 94 - 95: 24.439 distance: 95 - 96: 25.117 distance: 95 - 97: 47.530 distance: 98 - 99: 43.525 distance: 100 - 106: 34.394 distance: 103 - 104: 54.494 distance: 103 - 105: 39.829