Starting phenix.real_space_refine (version: dev) on Thu Dec 15 01:48:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7njm_12387/12_2022/7njm_12387_trim_updated.pdb" } resolution = 2.84 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 488": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "D ASP 357": "OD1" <-> "OD2" Residue "D GLU 469": "OE1" <-> "OE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 332": "OE1" <-> "OE2" Residue "F PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ASP 357": "OD1" <-> "OD2" Residue "G TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "L GLU 65": "OE1" <-> "OE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T GLU 65": "OE1" <-> "OE2" Residue "T PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "a PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "b GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 74611 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 7659 Classifications: {'peptide': 506} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 484} Chain breaks: 2 Chain: "B" Number of atoms: 7649 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 504, 7628 Classifications: {'peptide': 504} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 482} Chain breaks: 2 bond proxies already assigned to first conformer: 7662 Chain: "C" Number of atoms: 8004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 8004 Classifications: {'peptide': 528} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 503} Chain breaks: 2 Chain: "D" Number of atoms: 7144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7144 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "E" Number of atoms: 7087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 464, 7087 Classifications: {'peptide': 464} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain: "F" Number of atoms: 7147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 7147 Classifications: {'peptide': 468} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 443} Chain: "G" Number of atoms: 4596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 4596 Classifications: {'peptide': 299} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 288} Chain breaks: 1 Chain: "H" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 1802 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "M" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "N" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "O" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "P" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "Q" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1204 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "R" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "S" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "T" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 1192 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 4, 'TRANS': 79} Chain: "a" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 3767 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 10, 'TRANS': 227} Chain: "b" Number of atoms: 2161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2161 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "d" Number of atoms: 6656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 6656 Classifications: {'peptide': 438} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 425} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 354 " occ=0.40 ... (38 atoms not shown) pdb=" HZ BPHE B 354 " occ=0.40 Time building chain proxies: 27.56, per 1000 atoms: 0.37 Number of scatterers: 74611 At special positions: 0 Unit cell: (131.97, 129.48, 251.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 107 16.00 P 16 15.00 Mg 5 11.99 O 7181 8.00 N 6404 7.00 C 23570 6.00 H 37328 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 52.06 Conformation dependent library (CDL) restraints added in 5.6 seconds 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 177 helices and 28 sheets defined 55.4% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 9 through 21 removed outlier: 3.754A pdb=" N ILE A 15 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER A 20 " --> pdb=" O ASP A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 139 through 141 No H-bonds generated for 'chain 'A' and resid 139 through 141' Processing helix chain 'A' and resid 154 through 159 Processing helix chain 'A' and resid 178 through 194 removed outlier: 3.761A pdb=" N GLN A 189 " --> pdb=" O THR A 185 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N GLU A 191 " --> pdb=" O LEU A 187 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N ALA A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 243 through 263 Proline residue: A 250 - end of helix removed outlier: 3.669A pdb=" N TRP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 287 Processing helix chain 'A' and resid 294 through 296 No H-bonds generated for 'chain 'A' and resid 294 through 296' Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 340 through 348 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 378 through 381 Processing helix chain 'A' and resid 384 through 403 removed outlier: 5.088A pdb=" N SER A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N LEU A 393 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ARG A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 431 Processing helix chain 'A' and resid 441 through 452 Processing helix chain 'A' and resid 461 through 478 removed outlier: 4.941A pdb=" N GLN A 465 " --> pdb=" O GLU A 462 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER A 478 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 489 Processing helix chain 'A' and resid 494 through 510 Processing helix chain 'B' and resid 10 through 21 Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 154 through 159 Processing helix chain 'B' and resid 178 through 195 removed outlier: 3.894A pdb=" N GLN B 189 " --> pdb=" O THR B 185 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N ARG B 190 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N GLU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N ALA B 192 " --> pdb=" O ASN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing helix chain 'B' and resid 243 through 263 Proline residue: B 250 - end of helix removed outlier: 3.753A pdb=" N TRP B 260 " --> pdb=" O ILE B 256 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 263 " --> pdb=" O HIS B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 287 Processing helix chain 'B' and resid 294 through 296 No H-bonds generated for 'chain 'B' and resid 294 through 296' Processing helix chain 'B' and resid 301 through 311 removed outlier: 3.685A pdb=" N LEU B 308 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG B 311 " --> pdb=" O ARG B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 340 through 348 Processing helix chain 'B' and resid 357 through 362 Processing helix chain 'B' and resid 384 through 405 removed outlier: 5.156A pdb=" N SER B 392 " --> pdb=" O GLU B 388 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 455 through 457 No H-bonds generated for 'chain 'B' and resid 455 through 457' Processing helix chain 'B' and resid 461 through 477 removed outlier: 5.271A pdb=" N GLN B 465 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 489 Processing helix chain 'B' and resid 494 through 510 removed outlier: 3.696A pdb=" N LYS B 509 " --> pdb=" O ASN B 505 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY B 510 " --> pdb=" O GLU B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 21 removed outlier: 3.868A pdb=" N TYR C 18 " --> pdb=" O ALA C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 106 No H-bonds generated for 'chain 'C' and resid 104 through 106' Processing helix chain 'C' and resid 139 through 141 No H-bonds generated for 'chain 'C' and resid 139 through 141' Processing helix chain 'C' and resid 154 through 159 Processing helix chain 'C' and resid 178 through 194 removed outlier: 3.680A pdb=" N GLN C 189 " --> pdb=" O THR C 185 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ARG C 190 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLU C 191 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ALA C 192 " --> pdb=" O ASN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 243 through 263 Proline residue: C 250 - end of helix removed outlier: 3.759A pdb=" N TRP C 260 " --> pdb=" O ILE C 256 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN C 263 " --> pdb=" O HIS C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 Processing helix chain 'C' and resid 294 through 296 No H-bonds generated for 'chain 'C' and resid 294 through 296' Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 340 through 348 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 384 through 406 removed outlier: 5.310A pdb=" N SER C 392 " --> pdb=" O GLU C 388 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU C 393 " --> pdb=" O VAL C 389 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 430 Processing helix chain 'C' and resid 441 through 452 Processing helix chain 'C' and resid 461 through 477 removed outlier: 5.137A pdb=" N GLN C 465 " --> pdb=" O GLU C 462 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 470 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU C 471 " --> pdb=" O GLU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 489 removed outlier: 4.117A pdb=" N THR C 489 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 510 removed outlier: 3.685A pdb=" N LYS C 509 " --> pdb=" O ASN C 505 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY C 510 " --> pdb=" O GLU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 142 through 147 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'D' and resid 194 through 207 Processing helix chain 'D' and resid 210 through 212 No H-bonds generated for 'chain 'D' and resid 210 through 212' Processing helix chain 'D' and resid 224 through 243 removed outlier: 5.046A pdb=" N ALA D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU D 232 " --> pdb=" O MET D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 267 removed outlier: 3.744A pdb=" N THR D 260 " --> pdb=" O ILE D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 278 No H-bonds generated for 'chain 'D' and resid 276 through 278' Processing helix chain 'D' and resid 283 through 293 Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 318 through 326 removed outlier: 4.278A pdb=" N ALA D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS D 326 " --> pdb=" O THR D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 363 through 389 removed outlier: 4.687A pdb=" N ASP D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N ILE D 385 " --> pdb=" O ASP D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 393 No H-bonds generated for 'chain 'D' and resid 391 through 393' Processing helix chain 'D' and resid 396 through 412 Processing helix chain 'D' and resid 417 through 423 removed outlier: 4.230A pdb=" N GLN D 421 " --> pdb=" O ALA D 418 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 423 " --> pdb=" O GLU D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 444 Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 127 through 129 No H-bonds generated for 'chain 'E' and resid 127 through 129' Processing helix chain 'E' and resid 142 through 147 Processing helix chain 'E' and resid 166 through 180 Processing helix chain 'E' and resid 194 through 207 Processing helix chain 'E' and resid 210 through 212 No H-bonds generated for 'chain 'E' and resid 210 through 212' Processing helix chain 'E' and resid 224 through 243 removed outlier: 5.101A pdb=" N ALA E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LEU E 232 " --> pdb=" O MET E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 269 Processing helix chain 'E' and resid 276 through 278 No H-bonds generated for 'chain 'E' and resid 276 through 278' Processing helix chain 'E' and resid 283 through 291 Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 318 through 325 removed outlier: 3.574A pdb=" N ALA E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 363 through 388 removed outlier: 4.615A pdb=" N ASP E 384 " --> pdb=" O LYS E 380 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE E 385 " --> pdb=" O ASP E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 411 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'E' and resid 432 through 444 Processing helix chain 'E' and resid 452 through 454 No H-bonds generated for 'chain 'E' and resid 452 through 454' Processing helix chain 'E' and resid 461 through 470 Processing helix chain 'F' and resid 43 through 45 No H-bonds generated for 'chain 'F' and resid 43 through 45' Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 147 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'F' and resid 194 through 207 Processing helix chain 'F' and resid 210 through 212 No H-bonds generated for 'chain 'F' and resid 210 through 212' Processing helix chain 'F' and resid 224 through 245 removed outlier: 4.886A pdb=" N ALA F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU F 232 " --> pdb=" O MET F 228 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN F 245 " --> pdb=" O PHE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 269 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 283 through 293 Processing helix chain 'F' and resid 311 through 313 No H-bonds generated for 'chain 'F' and resid 311 through 313' Processing helix chain 'F' and resid 318 through 326 removed outlier: 4.403A pdb=" N ALA F 325 " --> pdb=" O ALA F 321 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N HIS F 326 " --> pdb=" O THR F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 340 removed outlier: 3.570A pdb=" N LYS F 340 " --> pdb=" O ALA F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 363 through 389 removed outlier: 3.602A pdb=" N GLN F 383 " --> pdb=" O TYR F 379 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP F 384 " --> pdb=" O LYS F 380 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ILE F 385 " --> pdb=" O ASP F 381 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE F 388 " --> pdb=" O ASP F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 396 through 411 Processing helix chain 'F' and resid 420 through 423 No H-bonds generated for 'chain 'F' and resid 420 through 423' Processing helix chain 'F' and resid 432 through 443 Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 461 through 471 Processing helix chain 'G' and resid 4 through 60 Proline residue: G 45 - end of helix Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'G' and resid 147 through 164 removed outlier: 3.684A pdb=" N GLY G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 302 Proline residue: G 237 - end of helix Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 92 through 98 Processing helix chain 'H' and resid 104 through 117 Processing helix chain 'L' and resid 5 through 45 Processing helix chain 'L' and resid 47 through 79 removed outlier: 4.418A pdb=" N GLY L 51 " --> pdb=" O GLU L 48 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR L 55 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Proline residue: L 56 - end of helix removed outlier: 3.796A pdb=" N VAL L 61 " --> pdb=" O PHE L 58 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU L 65 " --> pdb=" O GLY L 62 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA L 66 " --> pdb=" O LEU L 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 45 Processing helix chain 'M' and resid 47 through 80 removed outlier: 3.750A pdb=" N GLY M 51 " --> pdb=" O GLU M 48 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE M 54 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR M 55 " --> pdb=" O ARG M 52 " (cutoff:3.500A) Proline residue: M 56 - end of helix removed outlier: 3.899A pdb=" N VAL M 61 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU M 65 " --> pdb=" O GLY M 62 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA M 67 " --> pdb=" O VAL M 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL M 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 45 Processing helix chain 'N' and resid 47 through 79 removed outlier: 4.441A pdb=" N GLY N 51 " --> pdb=" O GLU N 48 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N PHE N 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR N 55 " --> pdb=" O ARG N 52 " (cutoff:3.500A) Proline residue: N 56 - end of helix removed outlier: 3.807A pdb=" N VAL N 61 " --> pdb=" O PHE N 58 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLU N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET N 75 " --> pdb=" O LEU N 72 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 45 Processing helix chain 'O' and resid 48 through 79 removed outlier: 4.385A pdb=" N PHE O 54 " --> pdb=" O GLY O 51 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR O 55 " --> pdb=" O ARG O 52 " (cutoff:3.500A) Proline residue: O 56 - end of helix removed outlier: 4.219A pdb=" N GLU O 65 " --> pdb=" O GLY O 62 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA O 66 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ILE O 70 " --> pdb=" O ALA O 67 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 45 Processing helix chain 'P' and resid 50 through 80 removed outlier: 3.892A pdb=" N THR P 55 " --> pdb=" O GLY P 51 " (cutoff:3.500A) Proline residue: P 56 - end of helix Processing helix chain 'Q' and resid 5 through 45 Processing helix chain 'Q' and resid 47 through 79 removed outlier: 4.051A pdb=" N GLN Q 50 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY Q 51 " --> pdb=" O GLU Q 48 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR Q 55 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) Proline residue: Q 56 - end of helix removed outlier: 4.048A pdb=" N VAL Q 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 5 through 45 Processing helix chain 'R' and resid 48 through 79 removed outlier: 4.098A pdb=" N PHE R 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) Proline residue: R 56 - end of helix removed outlier: 4.608A pdb=" N ALA R 66 " --> pdb=" O LEU R 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 45 Processing helix chain 'S' and resid 50 through 80 removed outlier: 4.531A pdb=" N THR S 55 " --> pdb=" O GLY S 51 " (cutoff:3.500A) Proline residue: S 56 - end of helix Processing helix chain 'T' and resid 5 through 45 Processing helix chain 'T' and resid 47 through 79 removed outlier: 4.539A pdb=" N GLY T 51 " --> pdb=" O GLU T 48 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE T 54 " --> pdb=" O GLY T 51 " (cutoff:3.500A) Proline residue: T 56 - end of helix removed outlier: 3.803A pdb=" N VAL T 61 " --> pdb=" O PHE T 58 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLU T 65 " --> pdb=" O GLY T 62 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA T 66 " --> pdb=" O LEU T 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 29 through 51 Processing helix chain 'a' and resid 61 through 80 Processing helix chain 'a' and resid 87 through 108 Proline residue: a 91 - end of helix removed outlier: 4.773A pdb=" N LEU a 106 " --> pdb=" O SER a 103 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 129 No H-bonds generated for 'chain 'a' and resid 127 through 129' Processing helix chain 'a' and resid 131 through 153 Processing helix chain 'a' and resid 155 through 164 Proline residue: a 159 - end of helix Processing helix chain 'a' and resid 168 through 205 Proline residue: a 172 - end of helix Proline residue: a 182 - end of helix removed outlier: 4.057A pdb=" N LEU a 187 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ARG a 188 " --> pdb=" O LEU a 185 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA a 195 " --> pdb=" O ASN a 192 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL a 200 " --> pdb=" O GLY a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 208 through 244 removed outlier: 5.601A pdb=" N PHE a 213 " --> pdb=" O TYR a 209 " (cutoff:3.500A) Proline residue: a 214 - end of helix removed outlier: 3.972A pdb=" N PHE a 224 " --> pdb=" O THR a 220 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 47 removed outlier: 4.035A pdb=" N VAL b 34 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER b 46 " --> pdb=" O GLY b 43 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS b 47 " --> pdb=" O VAL b 44 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 145 removed outlier: 3.791A pdb=" N SER b 142 " --> pdb=" O ASP b 138 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY b 143 " --> pdb=" O GLN b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 147 through 160 removed outlier: 3.546A pdb=" N LEU b 160 " --> pdb=" O SER b 157 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 138 removed outlier: 4.575A pdb=" N VAL d 23 " --> pdb=" O VAL d 19 " (cutoff:3.500A) Proline residue: d 24 - end of helix removed outlier: 3.785A pdb=" N ALA d 138 " --> pdb=" O ARG d 134 " (cutoff:3.500A) Processing helix chain 'd' and resid 140 through 156 Processing helix chain 'd' and resid 174 through 193 removed outlier: 3.637A pdb=" N GLY d 192 " --> pdb=" O ASP d 188 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N GLY d 193 " --> pdb=" O SER d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 215 Processing helix chain 'd' and resid 217 through 224 Processing helix chain 'd' and resid 231 through 241 Processing helix chain 'd' and resid 247 through 258 Processing helix chain 'd' and resid 264 through 286 removed outlier: 3.793A pdb=" N ILE d 268 " --> pdb=" O GLU d 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 307 through 314 Processing helix chain 'd' and resid 320 through 330 Processing helix chain 'd' and resid 339 through 351 Processing helix chain 'd' and resid 357 through 371 Processing helix chain 'd' and resid 387 through 401 Processing helix chain 'd' and resid 413 through 415 No H-bonds generated for 'chain 'd' and resid 413 through 415' Processing helix chain 'd' and resid 432 through 441 Processing sheet with id= A, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.329A pdb=" N GLY A 75 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N GLU A 45 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N VAL A 34 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 102 Processing sheet with id= C, first strand: chain 'A' and resid 351 through 355 Processing sheet with id= D, first strand: chain 'A' and resid 232 through 237 removed outlier: 6.480A pdb=" N CYS A 204 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL A 235 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N TYR A 206 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ALA A 237 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA A 208 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N SER A 323 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE A 269 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 325 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N PHE A 271 " --> pdb=" O THR A 325 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LEU A 327 " --> pdb=" O PHE A 271 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 31 through 33 removed outlier: 4.074A pdb=" N LEU B 63 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLY B 75 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N LEU B 69 " --> pdb=" O SER B 73 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N SER B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP B 36 " --> pdb=" O HIS B 43 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N GLU B 45 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL B 34 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 102 Processing sheet with id= G, first strand: chain 'B' and resid 352 through 355 removed outlier: 6.448A pdb=" N LEU B 169 " --> pdb=" O CYS B 353 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU B 355 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE B 171 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 237 removed outlier: 6.660A pdb=" N CYS B 204 " --> pdb=" O THR B 233 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N VAL B 235 " --> pdb=" O CYS B 204 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR B 206 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ALA B 237 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 208 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER B 323 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ILE B 269 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N THR B 325 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE B 271 " --> pdb=" O THR B 325 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU B 327 " --> pdb=" O PHE B 271 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.114A pdb=" N LEU C 63 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N GLY C 75 " --> pdb=" O LEU C 67 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP C 36 " --> pdb=" O HIS C 43 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLU C 45 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N VAL C 34 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 99 through 102 Processing sheet with id= K, first strand: chain 'C' and resid 352 through 355 removed outlier: 6.530A pdb=" N LEU C 169 " --> pdb=" O CYS C 353 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU C 355 " --> pdb=" O LEU C 169 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 171 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 232 through 237 removed outlier: 8.741A pdb=" N THR C 233 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS C 204 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N VAL C 235 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR C 206 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ALA C 237 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ALA C 208 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N HIS C 266 " --> pdb=" O ARG C 203 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL C 205 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU C 268 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 207 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL C 270 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE C 209 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ASP C 272 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N SER C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ILE C 269 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N THR C 325 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE C 271 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU C 327 " --> pdb=" O PHE C 271 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 10 through 16 removed outlier: 6.563A pdb=" N ASP D 21 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE D 15 " --> pdb=" O VAL D 19 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 19 " --> pdb=" O ILE D 15 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE D 65 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL D 53 " --> pdb=" O ILE D 65 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 87 through 89 Processing sheet with id= O, first strand: chain 'D' and resid 329 through 332 removed outlier: 7.535A pdb=" N ILE D 156 " --> pdb=" O ILE D 302 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N SER D 304 " --> pdb=" O ILE D 156 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N LEU D 158 " --> pdb=" O SER D 304 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN D 306 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY D 160 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL D 308 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N VAL D 249 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N MET D 305 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N LEU D 251 " --> pdb=" O MET D 305 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ALA D 307 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ILE D 253 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N TYR D 309 " --> pdb=" O ILE D 253 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR D 184 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N PHE D 252 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL D 186 " --> pdb=" O PHE D 252 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ASP D 254 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA D 188 " --> pdb=" O ASP D 254 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 11 through 16 removed outlier: 6.513A pdb=" N ASP E 21 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ILE E 15 " --> pdb=" O VAL E 19 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ILE E 65 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N VAL E 53 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 87 through 89 Processing sheet with id= R, first strand: chain 'E' and resid 329 through 332 removed outlier: 8.591A pdb=" N ILE E 156 " --> pdb=" O ILE E 302 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER E 304 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N LEU E 158 " --> pdb=" O SER E 304 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLN E 306 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL E 249 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N MET E 305 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 251 " --> pdb=" O MET E 305 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ALA E 307 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE E 253 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N THR E 184 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE E 252 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL E 186 " --> pdb=" O PHE E 252 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ASP E 254 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA E 188 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 11 through 16 removed outlier: 6.496A pdb=" N ASP F 21 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE F 15 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE F 65 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N VAL F 53 " --> pdb=" O ILE F 65 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 87 through 90 removed outlier: 3.873A pdb=" N GLU F 116 " --> pdb=" O VAL F 90 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 329 through 332 removed outlier: 7.568A pdb=" N ILE F 156 " --> pdb=" O ILE F 302 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N SER F 304 " --> pdb=" O ILE F 156 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU F 158 " --> pdb=" O SER F 304 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLN F 306 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY F 160 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL F 308 " --> pdb=" O GLY F 160 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL F 249 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET F 305 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU F 251 " --> pdb=" O MET F 305 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA F 307 " --> pdb=" O LEU F 251 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE F 253 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N TYR F 309 " --> pdb=" O ILE F 253 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR F 184 " --> pdb=" O LEU F 250 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE F 252 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL F 186 " --> pdb=" O PHE F 252 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASP F 254 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ALA F 188 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 196 through 204 removed outlier: 6.314A pdb=" N LEU G 183 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N HIS G 184 " --> pdb=" O ARG G 76 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY G 78 " --> pdb=" O HIS G 184 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL G 186 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU G 80 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N THR G 188 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N VAL G 82 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 10.962A pdb=" N PHE G 190 " --> pdb=" O VAL G 82 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ASP G 113 " --> pdb=" O ALA G 77 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL G 79 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N VAL G 115 " --> pdb=" O VAL G 79 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N VAL G 81 " --> pdb=" O VAL G 115 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR G 117 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N GLU G 136 " --> pdb=" O VAL G 118 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 41 through 44 removed outlier: 6.302A pdb=" N ASN H 5 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ILE H 79 " --> pdb=" O ASN H 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLU H 7 " --> pdb=" O ILE H 79 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N VAL H 81 " --> pdb=" O GLU H 7 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL H 9 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA H 10 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 31 through 34 removed outlier: 4.221A pdb=" N ARG H 26 " --> pdb=" O MET H 50 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N MET H 50 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'a' and resid 20 through 22 Processing sheet with id= Z, first strand: chain 'a' and resid 112 through 114 Processing sheet with id= AA, first strand: chain 'd' and resid 375 through 381 Processing sheet with id= AB, first strand: chain 'd' and resid 420 through 423 2122 hydrogen bonds defined for protein. 5460 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: 27.94 Time building geometry restraints manager: 54.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 37308 1.03 - 1.23: 37 1.23 - 1.42: 15318 1.42 - 1.62: 22348 1.62 - 1.81: 194 Bond restraints: 75205 Sorted by residual: bond pdb=" C4 ADP D 600 " pdb=" C5 ADP D 600 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.61e+00 bond pdb=" CG LEU L 19 " pdb=" CD1 LEU L 19 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.53e+00 bond pdb=" CG LEU T 19 " pdb=" CD2 LEU T 19 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" C ALA C 390 " pdb=" O ALA C 390 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.31e-02 5.83e+03 1.35e+00 bond pdb=" C4 ADP E 600 " pdb=" C5 ADP E 600 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.26e+00 ... (remaining 75200 not shown) Histogram of bond angle deviations from ideal: 99.73 - 107.78: 6654 107.78 - 115.84: 91541 115.84 - 123.89: 32838 123.89 - 131.95: 5182 131.95 - 140.00: 43 Bond angle restraints: 136258 Sorted by residual: angle pdb=" N GLN b 82 " pdb=" CA GLN b 82 " pdb=" CB GLN b 82 " ideal model delta sigma weight residual 110.28 115.41 -5.13 1.55e+00 4.16e-01 1.10e+01 angle pdb=" N VAL A 519 " pdb=" CA VAL A 519 " pdb=" C VAL A 519 " ideal model delta sigma weight residual 112.29 109.37 2.92 9.40e-01 1.13e+00 9.66e+00 angle pdb=" N GLU F 289 " pdb=" CA GLU F 289 " pdb=" CB GLU F 289 " ideal model delta sigma weight residual 110.01 114.20 -4.19 1.45e+00 4.76e-01 8.36e+00 angle pdb=" C3' ATP F 600 " pdb=" C4' ATP F 600 " pdb=" O4' ATP F 600 " ideal model delta sigma weight residual 105.22 101.49 3.73 1.30e+00 5.94e-01 8.27e+00 angle pdb=" N GLY F 218 " pdb=" CA GLY F 218 " pdb=" C GLY F 218 " ideal model delta sigma weight residual 113.18 106.37 6.81 2.37e+00 1.78e-01 8.25e+00 ... (remaining 136253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.63: 28855 32.63 - 65.26: 560 65.26 - 97.88: 72 97.88 - 130.51: 1 130.51 - 163.14: 2 Dihedral angle restraints: 29490 sinusoidal: 13820 harmonic: 15670 Sorted by residual: dihedral pdb=" C5' ADP D 600 " pdb=" O5' ADP D 600 " pdb=" PA ADP D 600 " pdb=" O2A ADP D 600 " ideal model delta sinusoidal sigma weight residual -60.00 103.14 -163.14 1 2.00e+01 2.50e-03 4.70e+01 dihedral pdb=" C5' ADP E 600 " pdb=" O5' ADP E 600 " pdb=" PA ADP E 600 " pdb=" O2A ADP E 600 " ideal model delta sinusoidal sigma weight residual 300.00 168.92 131.08 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PB ADP E 600 " pdb=" PA ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 67.34 -127.35 1 2.00e+01 2.50e-03 3.86e+01 ... (remaining 29487 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 5194 0.059 - 0.118: 696 0.118 - 0.177: 59 0.177 - 0.237: 3 0.237 - 0.296: 9 Chirality restraints: 5961 Sorted by residual: chirality pdb=" C2' ATP B 600 " pdb=" C1' ATP B 600 " pdb=" C3' ATP B 600 " pdb=" O2' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C2' ATP F 600 " pdb=" C1' ATP F 600 " pdb=" C3' ATP F 600 " pdb=" O2' ATP F 600 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C3' ATP B 600 " pdb=" C2' ATP B 600 " pdb=" C4' ATP B 600 " pdb=" O3' ATP B 600 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 5958 not shown) Planarity restraints: 11423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU C 429 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" CD GLU C 429 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU C 429 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU C 429 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 99 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C PHE a 99 " -0.034 2.00e-02 2.50e+03 pdb=" O PHE a 99 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE a 100 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE a 97 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C PHE a 97 " 0.032 2.00e-02 2.50e+03 pdb=" O PHE a 97 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL a 98 " -0.011 2.00e-02 2.50e+03 ... (remaining 11420 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 2186 2.13 - 2.75: 141125 2.75 - 3.36: 228622 3.36 - 3.98: 293247 3.98 - 4.60: 463111 Nonbonded interactions: 1128291 Sorted by model distance: nonbonded pdb=" OE1 GLU d 216 " pdb=" H LEU d 219 " model vdw 1.509 1.850 nonbonded pdb=" O VAL R 61 " pdb=" H GLU R 65 " model vdw 1.542 1.850 nonbonded pdb=" OD1 ASN G 95 " pdb="HH21 ARG G 98 " model vdw 1.598 1.850 nonbonded pdb=" OE1 GLU E 239 " pdb="HH21 ARG E 293 " model vdw 1.600 1.850 nonbonded pdb=" O ALA a 126 " pdb=" HG SER a 129 " model vdw 1.611 1.850 ... (remaining 1128286 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 5 through 353 or resid 356 through 406 or resid 415 throug \ h 515 or resid 518 through 519 or resid 521 or resid 600 through 601)) selection = (chain 'B' and (resid 5 through 353 or resid 356 through 406 or resid 415 throug \ h 515 or resid 518 through 519 or resid 521 or resid 600 through 601)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 6 through 22 or (resid 29 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2 or name \ HA or name HB2 or name HB3 or name HG2 or name HG3)) or resid 30 through 353 or \ resid 356 through 406 or resid 415 through 515 or resid 537 through 538 or resi \ d 540 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 8 through 471) selection = (chain 'E' and (resid 8 through 166 or (resid 167 and (name N or name CA or name \ C or name O or name CB or name OG1 or name CG2 or name H or name HA or name HB \ or name HG21 or name HG22 or name HG23)) or resid 168 through 471)) selection = (chain 'F' and ((resid 8 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2 or name HA or name HB or name HG1 or name HG21 or name HG \ 22 or name HG23)) or resid 9 through 471)) } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = (chain 'Q' and ((resid 3 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD1 or name CD2 or name HA or name HB2 or name HB3 or name HG \ or name HD11 or name HD12 or name HD13 or name HD21 or name HD22 or name HD23)) \ or resid 4 through 86)) selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 16 5.49 5 Mg 5 5.21 5 S 107 5.16 5 C 23570 2.51 5 N 6404 2.21 5 O 7181 1.98 5 H 37328 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 7.390 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: 0.890 Extract box with map and model: 29.910 Check model and map are aligned: 0.810 Convert atoms to be neutral: 0.490 Process input model: 192.610 Find NCS groups from input model: 3.020 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 247.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 0.042 37877 Z= 0.185 Angle : 0.496 6.807 51371 Z= 0.263 Chirality : 0.041 0.296 5961 Planarity : 0.004 0.049 6723 Dihedral : 14.837 163.141 13747 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4879 helix: 1.72 (0.10), residues: 2637 sheet: -0.48 (0.21), residues: 577 loop : 0.34 (0.16), residues: 1665 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 410 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 4.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 2.4535 time to fit residues: 1249.0944 Evaluate side-chains 273 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 273 time to evaluate : 4.447 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 407 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 202 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 377 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 437 optimal weight: 0.9980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN T 86 GLN a 112 GLN ** a 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 339 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.0656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 37877 Z= 0.297 Angle : 0.516 8.175 51371 Z= 0.269 Chirality : 0.040 0.144 5961 Planarity : 0.004 0.073 6723 Dihedral : 5.474 132.378 5281 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.95 % Favored : 97.03 % Rotamer Outliers : 0.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.32 (0.12), residues: 4879 helix: 1.68 (0.10), residues: 2632 sheet: -0.44 (0.21), residues: 572 loop : 0.22 (0.16), residues: 1675 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 321 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 285 time to evaluate : 4.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 9 residues processed: 303 average time/residue: 2.3278 time to fit residues: 899.4779 Evaluate side-chains 276 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 267 time to evaluate : 4.482 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 1.1153 time to fit residues: 12.3437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 243 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 438 optimal weight: 4.9990 chunk 473 optimal weight: 7.9990 chunk 390 optimal weight: 3.9990 chunk 434 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN ** C 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 370 GLN a 15 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.0891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 37877 Z= 0.392 Angle : 0.549 8.657 51371 Z= 0.290 Chirality : 0.042 0.149 5961 Planarity : 0.004 0.072 6723 Dihedral : 5.679 134.925 5281 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.10 (0.12), residues: 4879 helix: 1.52 (0.10), residues: 2636 sheet: -0.50 (0.21), residues: 572 loop : 0.06 (0.16), residues: 1671 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 304 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 276 time to evaluate : 4.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 9 residues processed: 294 average time/residue: 2.2069 time to fit residues: 824.8436 Evaluate side-chains 268 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 259 time to evaluate : 4.432 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.9851 time to fit residues: 11.6038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 433 optimal weight: 0.4980 chunk 329 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 294 optimal weight: 0.9980 chunk 440 optimal weight: 6.9990 chunk 465 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 417 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 399 GLN E 370 GLN a 15 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 37877 Z= 0.267 Angle : 0.514 8.382 51371 Z= 0.267 Chirality : 0.040 0.148 5961 Planarity : 0.004 0.069 6723 Dihedral : 5.563 132.259 5281 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.21 (0.12), residues: 4879 helix: 1.64 (0.10), residues: 2609 sheet: -0.48 (0.21), residues: 572 loop : 0.09 (0.16), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 272 time to evaluate : 4.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 12 residues processed: 288 average time/residue: 2.2094 time to fit residues: 811.1203 Evaluate side-chains 276 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 264 time to evaluate : 4.455 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.7752 time to fit residues: 9.5340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 388 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 346 optimal weight: 0.3980 chunk 192 optimal weight: 1.9990 chunk 397 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 418 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 15 HIS ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 37877 Z= 0.262 Angle : 0.508 8.412 51371 Z= 0.264 Chirality : 0.040 0.146 5961 Planarity : 0.004 0.076 6723 Dihedral : 5.513 131.672 5281 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.93 % Favored : 97.05 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.28 (0.12), residues: 4879 helix: 1.67 (0.10), residues: 2615 sheet: -0.44 (0.21), residues: 559 loop : 0.16 (0.16), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 273 time to evaluate : 4.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 294 average time/residue: 2.2191 time to fit residues: 832.9022 Evaluate side-chains 275 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 260 time to evaluate : 4.530 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 10 residues processed: 5 average time/residue: 1.0727 time to fit residues: 13.9137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 156 optimal weight: 2.9990 chunk 419 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 273 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 466 optimal weight: 6.9990 chunk 387 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 15 HIS a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.082 37877 Z= 0.367 Angle : 0.540 8.754 51371 Z= 0.283 Chirality : 0.041 0.147 5961 Planarity : 0.004 0.083 6723 Dihedral : 5.624 135.067 5281 Min Nonbonded Distance : 1.650 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.10 % Favored : 96.88 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.13 (0.12), residues: 4879 helix: 1.56 (0.10), residues: 2618 sheet: -0.51 (0.21), residues: 563 loop : 0.05 (0.16), residues: 1698 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 296 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 5.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 16 residues processed: 287 average time/residue: 2.2612 time to fit residues: 823.4858 Evaluate side-chains 278 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 262 time to evaluate : 4.491 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.2267 time to fit residues: 14.6097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 449 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 265 optimal weight: 1.9990 chunk 340 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 392 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 464 optimal weight: 4.9990 chunk 290 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 15 HIS a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 37877 Z= 0.266 Angle : 0.514 8.419 51371 Z= 0.267 Chirality : 0.040 0.148 5961 Planarity : 0.004 0.086 6723 Dihedral : 5.539 132.659 5281 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.79 % Favored : 97.19 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.25 (0.12), residues: 4879 helix: 1.65 (0.10), residues: 2615 sheet: -0.47 (0.21), residues: 559 loop : 0.14 (0.16), residues: 1705 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 299 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 276 time to evaluate : 7.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 295 average time/residue: 2.2798 time to fit residues: 862.9544 Evaluate side-chains 283 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 268 time to evaluate : 4.469 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 1.3076 time to fit residues: 9.3805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 287 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 277 optimal weight: 0.0870 chunk 139 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 37877 Z= 0.210 Angle : 0.496 8.161 51371 Z= 0.255 Chirality : 0.039 0.145 5961 Planarity : 0.004 0.076 6723 Dihedral : 5.397 128.412 5281 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.67 % Favored : 97.29 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.42 (0.12), residues: 4879 helix: 1.77 (0.10), residues: 2617 sheet: -0.42 (0.21), residues: 561 loop : 0.25 (0.16), residues: 1701 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 309 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 280 time to evaluate : 4.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 301 average time/residue: 2.2250 time to fit residues: 851.3407 Evaluate side-chains 289 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 274 time to evaluate : 4.482 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 1.3195 time to fit residues: 9.2690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 422 optimal weight: 1.9990 chunk 445 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 432 optimal weight: 3.9990 chunk 444 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 339 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 391 optimal weight: 0.6980 chunk 409 optimal weight: 0.0980 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 37877 Z= 0.222 Angle : 0.502 8.357 51371 Z= 0.258 Chirality : 0.039 0.144 5961 Planarity : 0.004 0.080 6723 Dihedral : 5.372 127.100 5281 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.52 % Favored : 97.44 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.43 (0.12), residues: 4879 helix: 1.78 (0.10), residues: 2617 sheet: -0.43 (0.21), residues: 567 loop : 0.26 (0.16), residues: 1695 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 307 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 280 time to evaluate : 4.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 18 residues processed: 303 average time/residue: 2.2495 time to fit residues: 866.6950 Evaluate side-chains 289 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 271 time to evaluate : 4.436 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 16 residues processed: 3 average time/residue: 1.5652 time to fit residues: 11.8618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 431 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 457 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 318 optimal weight: 1.9990 chunk 480 optimal weight: 5.9990 chunk 441 optimal weight: 0.9990 chunk 382 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 295 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 37877 Z= 0.283 Angle : 0.521 9.147 51371 Z= 0.269 Chirality : 0.040 0.146 5961 Planarity : 0.004 0.087 6723 Dihedral : 5.448 128.653 5281 Min Nonbonded Distance : 1.699 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.38 (0.12), residues: 4879 helix: 1.69 (0.10), residues: 2649 sheet: -0.44 (0.21), residues: 567 loop : 0.31 (0.16), residues: 1663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9758 Ramachandran restraints generated. 4879 Oldfield, 0 Emsley, 4879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 179 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Residue THR 167 is missing expected H atoms. Skipping. Evaluate side-chains 291 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 4.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 15 residues processed: 287 average time/residue: 2.2579 time to fit residues: 824.9579 Evaluate side-chains 282 residues out of total 3841 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 267 time to evaluate : 4.586 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 14 residues processed: 2 average time/residue: 0.7915 time to fit residues: 8.2408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 482 random chunks: chunk 234 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 407 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 352 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 382 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 393 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 370 GLN a 229 GLN ** b 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.075758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.057479 restraints weight = 271136.760| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.63 r_work: 0.2852 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 37877 Z= 0.240 Angle : 0.512 8.941 51371 Z= 0.263 Chirality : 0.040 0.146 5961 Planarity : 0.004 0.081 6723 Dihedral : 5.413 127.577 5281 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.58 % Favored : 97.37 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.88 % Cis-general : 0.13 % 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: 1.43 (0.12), residues: 4879 helix: 1.72 (0.10), residues: 2651 sheet: -0.44 (0.21), residues: 567 loop : 0.35 (0.16), residues: 1661 =============================================================================== Job complete usr+sys time: 15922.77 seconds wall clock time: 275 minutes 11.26 seconds (16511.26 seconds total)