Starting phenix.real_space_refine on Thu Dec 14 03:22:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/12_2023/7ole_12979_neut_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 88 5.16 5 C 16678 2.51 5 N 4879 2.21 5 O 5340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 271": "OD1" <-> "OD2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 312": "OD1" <-> "OD2" Residue "A ASP 325": "OD1" <-> "OD2" Residue "A ASP 340": "OD1" <-> "OD2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 486": "OE1" <-> "OE2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A TYR 536": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 550": "OD1" <-> "OD2" Residue "B ASP 35": "OD1" <-> "OD2" Residue "B GLU 107": "OE1" <-> "OE2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ASP 185": "OD1" <-> "OD2" Residue "B ASP 214": "OD1" <-> "OD2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 231": "OE1" <-> "OE2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ASP 385": "OD1" <-> "OD2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 105": "OE1" <-> "OE2" Residue "C ASP 173": "OD1" <-> "OD2" Residue "C GLU 178": "OE1" <-> "OE2" Residue "C GLU 212": "OE1" <-> "OE2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 214": "OD1" <-> "OD2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C ASP 356": "OD1" <-> "OD2" Residue "C PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Residue "D GLU 112": "OE1" <-> "OE2" Residue "D PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 273": "NH1" <-> "NH2" Residue "D GLU 300": "OE1" <-> "OE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 352": "OD1" <-> "OD2" Residue "D ARG 353": "NH1" <-> "NH2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "E PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 117": "NH1" <-> "NH2" Residue "E GLU 186": "OE1" <-> "OE2" Residue "E ASP 227": "OD1" <-> "OD2" Residue "E PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 333": "NH1" <-> "NH2" Residue "E GLU 396": "OE1" <-> "OE2" Residue "F ARG 124": "NH1" <-> "NH2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F ASP 148": "OD1" <-> "OD2" Residue "F ASP 185": "OD1" <-> "OD2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ASP 229": "OD1" <-> "OD2" Residue "F ARG 253": "NH1" <-> "NH2" Residue "F GLU 271": "OE1" <-> "OE2" Residue "F ARG 400": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 26995 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 3328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3328 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 417} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3209 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3281 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 3224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3224 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3156 Classifications: {'peptide': 413} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3232 Classifications: {'peptide': 419} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 3208 Classifications: {'peptide': 644} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 632} Link IDs: {'CIS': 1, 'TRANS': 642} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 1282 Unresolved non-hydrogen angles: 1924 Unresolved non-hydrogen dihedrals: 638 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'UNK:plan-1': 638} Unresolved non-hydrogen planarities: 640 Chain: "J" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 2273 Classifications: {'peptide': 456} Incomplete info: {'truncation_to_alanine': 449} Link IDs: {'CIS': 2, 'TRANS': 453} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 901 Unresolved non-hydrogen angles: 1351 Unresolved non-hydrogen dihedrals: 450 Planarities with less than four sites: {'UNK:plan-1': 450} Unresolved non-hydrogen planarities: 451 Chain: "K" Number of atoms: 1949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 1949 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 339} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 376} Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 1123 Unresolved non-hydrogen angles: 1443 Unresolved non-hydrogen dihedrals: 884 Unresolved non-hydrogen chiralities: 116 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 7, 'ASN:plan1': 5, 'TYR:plan': 3, 'UNK:plan-1': 36, 'TRP:plan': 3, 'ASP:plan': 9, 'PHE:plan': 11, 'GLU:plan': 24, 'ARG:plan': 30} Unresolved non-hydrogen planarities: 573 Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 15.41, per 1000 atoms: 0.57 Number of scatterers: 26995 At special positions: 0 Unit cell: (199.02, 190.46, 154.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 10 15.00 O 5340 8.00 N 4879 7.00 C 16678 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM26882 O3A ADP B 501 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.53 Conformation dependent library (CDL) restraints added in 4.4 seconds 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 176 helices and 23 sheets defined 71.9% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.67 Creating SS restraints... Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 183 through 186 No H-bonds generated for 'chain 'A' and resid 183 through 186' Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 338 through 346 removed outlier: 3.911A pdb=" N ALA A 346 " --> pdb=" O ASP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.625A pdb=" N LYS A 379 " --> pdb=" O GLY A 375 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A 382 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 416 removed outlier: 4.688A pdb=" N HIS A 414 " --> pdb=" O PHE A 410 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ARG A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 447 No H-bonds generated for 'chain 'A' and resid 445 through 447' Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 486 through 498 removed outlier: 4.426A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 518 removed outlier: 4.798A pdb=" N GLN A 506 " --> pdb=" O ARG A 502 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N THR A 509 " --> pdb=" O VAL A 505 " (cutoff:3.500A) Proline residue: A 510 - end of helix Processing helix chain 'A' and resid 525 through 531 removed outlier: 3.714A pdb=" N GLU A 529 " --> pdb=" O LYS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 551 removed outlier: 5.660A pdb=" N LYS A 551 " --> pdb=" O ASP A 547 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 26 No H-bonds generated for 'chain 'B' and resid 24 through 26' Processing helix chain 'B' and resid 50 through 65 removed outlier: 3.518A pdb=" N GLU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 105 through 108 removed outlier: 3.868A pdb=" N ILE B 108 " --> pdb=" O GLY B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 115 through 126 Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.739A pdb=" N GLU B 180 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N THR B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 270 through 283 removed outlier: 3.950A pdb=" N ALA B 281 " --> pdb=" O ASN B 277 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 303 No H-bonds generated for 'chain 'B' and resid 301 through 303' Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'B' and resid 348 through 351 No H-bonds generated for 'chain 'B' and resid 348 through 351' Processing helix chain 'B' and resid 364 through 375 removed outlier: 4.287A pdb=" N ILE B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B 374 " --> pdb=" O ILE B 370 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N CYS B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 396 removed outlier: 3.572A pdb=" N ILE B 393 " --> pdb=" O VAL B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 415 No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.571A pdb=" N GLN B 441 " --> pdb=" O SER B 437 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N MET B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N TYR B 446 " --> pdb=" O TYR B 442 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE B 450 " --> pdb=" O TYR B 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 55 Processing helix chain 'C' and resid 77 through 86 Processing helix chain 'C' and resid 98 through 101 removed outlier: 3.743A pdb=" N VAL C 101 " --> pdb=" O GLY C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 101' Processing helix chain 'C' and resid 108 through 118 Processing helix chain 'C' and resid 177 through 182 removed outlier: 5.356A pdb=" N LYS C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 273 through 289 removed outlier: 4.996A pdb=" N LYS C 281 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN C 284 " --> pdb=" O ASN C 280 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP C 288 " --> pdb=" O ASN C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 306 No H-bonds generated for 'chain 'C' and resid 304 through 306' Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 317 through 320 No H-bonds generated for 'chain 'C' and resid 317 through 320' Processing helix chain 'C' and resid 347 through 349 No H-bonds generated for 'chain 'C' and resid 347 through 349' Processing helix chain 'C' and resid 368 through 382 removed outlier: 4.160A pdb=" N GLN C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN C 380 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 400 removed outlier: 3.907A pdb=" N HIS C 393 " --> pdb=" O GLU C 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU C 394 " --> pdb=" O ALA C 390 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 396 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE C 397 " --> pdb=" O HIS C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 420 removed outlier: 4.026A pdb=" N GLN C 408 " --> pdb=" O ARG C 404 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 409 " --> pdb=" O TYR C 405 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 410 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N THR C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Proline residue: C 412 - end of helix removed outlier: 3.601A pdb=" N ASN C 420 " --> pdb=" O LEU C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 435 removed outlier: 3.951A pdb=" N GLU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'D' and resid 43 through 45 No H-bonds generated for 'chain 'D' and resid 43 through 45' Processing helix chain 'D' and resid 50 through 65 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 105 through 108 removed outlier: 3.670A pdb=" N ILE D 108 " --> pdb=" O GLY D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 115 through 125 Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.950A pdb=" N LEU D 182 " --> pdb=" O MET D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 removed outlier: 3.898A pdb=" N ASP D 248 " --> pdb=" O LEU D 244 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL D 249 " --> pdb=" O HIS D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 283 removed outlier: 3.595A pdb=" N GLU D 282 " --> pdb=" O ALA D 278 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.585A pdb=" N PHE D 311 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 345 No H-bonds generated for 'chain 'D' and resid 343 through 345' Processing helix chain 'D' and resid 348 through 352 Processing helix chain 'D' and resid 364 through 378 Processing helix chain 'D' and resid 386 through 389 No H-bonds generated for 'chain 'D' and resid 386 through 389' Processing helix chain 'D' and resid 391 through 394 No H-bonds generated for 'chain 'D' and resid 391 through 394' Processing helix chain 'D' and resid 399 through 416 removed outlier: 3.894A pdb=" N GLN D 404 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR D 407 " --> pdb=" O ILE D 403 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 411 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N VAL D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 429 removed outlier: 3.628A pdb=" N ARG D 428 " --> pdb=" O ASP D 424 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 441 through 450 Processing helix chain 'E' and resid 12 through 14 No H-bonds generated for 'chain 'E' and resid 12 through 14' Processing helix chain 'E' and resid 17 through 20 removed outlier: 4.123A pdb=" N HIS E 20 " --> pdb=" O SER E 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 43 through 58 Processing helix chain 'E' and resid 76 through 87 Processing helix chain 'E' and resid 98 through 101 Processing helix chain 'E' and resid 108 through 120 Processing helix chain 'E' and resid 181 through 183 No H-bonds generated for 'chain 'E' and resid 181 through 183' Processing helix chain 'E' and resid 240 through 246 Processing helix chain 'E' and resid 273 through 289 removed outlier: 3.585A pdb=" N ILE E 279 " --> pdb=" O LEU E 275 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN E 280 " --> pdb=" O ARG E 276 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS E 281 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR E 286 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 306 No H-bonds generated for 'chain 'E' and resid 304 through 306' Processing helix chain 'E' and resid 309 through 319 Processing helix chain 'E' and resid 347 through 349 No H-bonds generated for 'chain 'E' and resid 347 through 349' Processing helix chain 'E' and resid 352 through 357 removed outlier: 4.091A pdb=" N ARG E 357 " --> pdb=" O ASP E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 382 removed outlier: 4.522A pdb=" N GLN E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN E 380 " --> pdb=" O LYS E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 400 removed outlier: 4.129A pdb=" N GLU E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 397 " --> pdb=" O HIS E 393 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY E 398 " --> pdb=" O LEU E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 406 No H-bonds generated for 'chain 'E' and resid 403 through 406' Processing helix chain 'E' and resid 408 through 419 Proline residue: E 412 - end of helix removed outlier: 3.956A pdb=" N LEU E 416 " --> pdb=" O PRO E 412 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 436 removed outlier: 3.667A pdb=" N ILE E 433 " --> pdb=" O HIS E 429 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 450 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 105 through 108 removed outlier: 3.583A pdb=" N ILE F 108 " --> pdb=" O GLY F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 115 through 126 Processing helix chain 'F' and resid 179 through 184 Processing helix chain 'F' and resid 244 through 250 Processing helix chain 'F' and resid 270 through 286 removed outlier: 4.532A pdb=" N ALA F 281 " --> pdb=" O ASN F 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU F 282 " --> pdb=" O ALA F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 343 through 345 No H-bonds generated for 'chain 'F' and resid 343 through 345' Processing helix chain 'F' and resid 348 through 351 No H-bonds generated for 'chain 'F' and resid 348 through 351' Processing helix chain 'F' and resid 364 through 378 removed outlier: 3.572A pdb=" N GLU F 376 " --> pdb=" O ARG F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 396 removed outlier: 3.544A pdb=" N ILE F 393 " --> pdb=" O VAL F 389 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU F 396 " --> pdb=" O ARG F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 415 removed outlier: 4.031A pdb=" N ILE F 406 " --> pdb=" O ALA F 402 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA F 408 " --> pdb=" O GLN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 423 through 432 Processing helix chain 'F' and resid 436 through 451 Processing helix chain 'H' and resid 40 through 54 Processing helix chain 'H' and resid 64 through 81 Processing helix chain 'H' and resid 88 through 110 Processing helix chain 'H' and resid 114 through 134 removed outlier: 3.768A pdb=" N UNK H 133 " --> pdb=" O UNK H 129 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 155 Processing helix chain 'H' and resid 157 through 160 No H-bonds generated for 'chain 'H' and resid 157 through 160' Processing helix chain 'H' and resid 162 through 175 removed outlier: 4.160A pdb=" N UNK H 166 " --> pdb=" O UNK H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 190 Processing helix chain 'H' and resid 192 through 218 removed outlier: 6.771A pdb=" N UNK H 200 " --> pdb=" O UNK H 197 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N UNK H 218 " --> pdb=" O UNK H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 238 Processing helix chain 'H' and resid 241 through 244 No H-bonds generated for 'chain 'H' and resid 241 through 244' Processing helix chain 'H' and resid 246 through 255 Processing helix chain 'H' and resid 264 through 276 Processing helix chain 'H' and resid 282 through 292 Processing helix chain 'H' and resid 297 through 309 Processing helix chain 'H' and resid 314 through 334 Processing helix chain 'H' and resid 340 through 359 Processing helix chain 'H' and resid 363 through 375 Processing helix chain 'H' and resid 379 through 389 Processing helix chain 'H' and resid 392 through 399 Processing helix chain 'H' and resid 402 through 413 Processing helix chain 'H' and resid 417 through 428 Processing helix chain 'H' and resid 435 through 449 Processing helix chain 'H' and resid 453 through 474 removed outlier: 3.509A pdb=" N UNK H 457 " --> pdb=" O UNK H 454 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N UNK H 472 " --> pdb=" O UNK H 469 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N UNK H 474 " --> pdb=" O UNK H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 477 through 494 Processing helix chain 'H' and resid 498 through 515 removed outlier: 3.827A pdb=" N UNK H 502 " --> pdb=" O UNK H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 521 through 539 Processing helix chain 'H' and resid 542 through 553 Processing helix chain 'H' and resid 561 through 572 Processing helix chain 'H' and resid 583 through 597 removed outlier: 4.388A pdb=" N UNK H 593 " --> pdb=" O UNK H 589 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N UNK H 594 " --> pdb=" O UNK H 590 " (cutoff:3.500A) Processing helix chain 'H' and resid 602 through 617 Processing helix chain 'H' and resid 622 through 635 removed outlier: 3.557A pdb=" N UNK H 635 " --> pdb=" O UNK H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 638 through 646 Processing helix chain 'H' and resid 651 through 659 Processing helix chain 'H' and resid 670 through 681 Processing helix chain 'J' and resid 45 through 59 Processing helix chain 'J' and resid 71 through 82 Processing helix chain 'J' and resid 88 through 100 Processing helix chain 'J' and resid 102 through 121 Processing helix chain 'J' and resid 127 through 146 Processing helix chain 'J' and resid 153 through 170 WARNING: missing atoms! removed outlier: 4.277A pdb=" N UNK J 170 " --> pdb=" O GLY J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 189 Processing helix chain 'J' and resid 195 through 210 removed outlier: 3.672A pdb=" N UNK J 200 " --> pdb=" O UNK J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 214 through 230 Processing helix chain 'J' and resid 234 through 238 Processing helix chain 'J' and resid 244 through 262 Processing helix chain 'J' and resid 266 through 279 Processing helix chain 'J' and resid 288 through 303 removed outlier: 3.820A pdb=" N UNK J 295 " --> pdb=" O UNK J 291 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 328 Processing helix chain 'J' and resid 332 through 348 Processing helix chain 'J' and resid 352 through 375 removed outlier: 4.016A pdb=" N UNK J 371 " --> pdb=" O UNK J 367 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK J 374 " --> pdb=" O UNK J 370 " (cutoff:3.500A) Processing helix chain 'J' and resid 378 through 419 removed outlier: 7.472A pdb=" N UNK J 398 " --> pdb=" O UNK J 394 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N UNK J 399 " --> pdb=" O UNK J 395 " (cutoff:3.500A) Processing helix chain 'J' and resid 425 through 444 removed outlier: 4.103A pdb=" N UNK J 429 " --> pdb=" O UNK J 425 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N UNK J 430 " --> pdb=" O UNK J 426 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N UNK J 433 " --> pdb=" O UNK J 429 " (cutoff:3.500A) Processing helix chain 'J' and resid 447 through 450 No H-bonds generated for 'chain 'J' and resid 447 through 450' Processing helix chain 'J' and resid 457 through 474 Processing helix chain 'J' and resid 480 through 493 Processing helix chain 'J' and resid 497 through 507 Processing helix chain 'K' and resid 12 through 21 Processing helix chain 'K' and resid 25 through 37 removed outlier: 4.054A pdb=" N LEU K 35 " --> pdb=" O THR K 31 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS K 36 " --> pdb=" O LEU K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 41 through 66 removed outlier: 3.970A pdb=" N UNK K 45 " --> pdb=" O UNK K 41 " (cutoff:3.500A) Proline residue: K 50 - end of helix Proline residue: K 61 - end of helix removed outlier: 3.823A pdb=" N LEU K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 87 removed outlier: 3.813A pdb=" N ALA K 79 " --> pdb=" O PRO K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 102 Processing helix chain 'K' and resid 106 through 136 Proline residue: K 127 - end of helix Processing helix chain 'K' and resid 143 through 162 removed outlier: 4.388A pdb=" N UNK K 156 " --> pdb=" O UNK K 152 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY K 157 " --> pdb=" O UNK K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 170 through 189 Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 216 through 232 Proline residue: K 225 - end of helix Processing helix chain 'K' and resid 236 through 244 Processing helix chain 'K' and resid 249 through 263 Processing helix chain 'K' and resid 265 through 276 Processing helix chain 'K' and resid 283 through 294 Processing helix chain 'K' and resid 300 through 316 Processing helix chain 'K' and resid 318 through 332 removed outlier: 3.913A pdb=" N LEU K 321 " --> pdb=" O ARG K 318 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 339 No H-bonds generated for 'chain 'K' and resid 336 through 339' Processing helix chain 'K' and resid 344 through 358 Processing helix chain 'K' and resid 364 through 385 Processing helix chain 'K' and resid 389 through 402 Processing sheet with id= A, first strand: chain 'A' and resid 222 through 229 Processing sheet with id= B, first strand: chain 'A' and resid 257 through 259 Processing sheet with id= C, first strand: chain 'B' and resid 72 through 76 Processing sheet with id= D, first strand: chain 'B' and resid 100 through 102 removed outlier: 7.131A pdb=" N VAL B 295 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 323 " --> pdb=" O LEU B 296 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 132 through 138 Processing sheet with id= F, first strand: chain 'B' and resid 161 through 163 Processing sheet with id= G, first strand: chain 'B' and resid 332 through 334 Processing sheet with id= H, first strand: chain 'C' and resid 94 through 97 removed outlier: 3.704A pdb=" N CYS C 94 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N PHE C 300 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE C 326 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL C 301 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ILE C 328 " --> pdb=" O VAL C 301 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 236 through 239 Processing sheet with id= J, first strand: chain 'C' and resid 127 through 130 Processing sheet with id= K, first strand: chain 'C' and resid 131 through 133 Processing sheet with id= L, first strand: chain 'C' and resid 157 through 162 Processing sheet with id= M, first strand: chain 'C' and resid 335 through 337 Processing sheet with id= N, first strand: chain 'D' and resid 354 through 357 removed outlier: 6.860A pdb=" N ALA D 72 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N VAL D 357 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU D 74 " --> pdb=" O VAL D 357 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 299 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 332 through 334 Processing sheet with id= P, first strand: chain 'E' and resid 358 through 363 removed outlier: 6.536A pdb=" N ALA E 65 " --> pdb=" O MET E 359 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE E 361 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 67 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR E 363 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ALA E 69 " --> pdb=" O THR E 363 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 292 through 294 Processing sheet with id= R, first strand: chain 'E' and resid 157 through 159 Processing sheet with id= S, first strand: chain 'E' and resid 335 through 337 Processing sheet with id= T, first strand: chain 'F' and resid 354 through 358 removed outlier: 6.715A pdb=" N ALA F 72 " --> pdb=" O LEU F 355 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL F 357 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU F 74 " --> pdb=" O VAL F 357 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 290 through 293 Processing sheet with id= V, first strand: chain 'F' and resid 160 through 163 Processing sheet with id= W, first strand: chain 'F' and resid 332 through 334 1397 hydrogen bonds defined for protein. 3849 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: 8.97 Time building geometry restraints manager: 13.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4832 1.26 - 1.40: 5698 1.40 - 1.54: 16338 1.54 - 1.68: 214 1.68 - 1.83: 151 Bond restraints: 27233 Sorted by residual: bond pdb=" C GLU K 268 " pdb=" O GLU K 268 " ideal model delta sigma weight residual 1.236 1.126 0.110 1.15e-02 7.56e+03 9.17e+01 bond pdb=" C GLN K 120 " pdb=" O GLN K 120 " ideal model delta sigma weight residual 1.236 1.118 0.118 1.29e-02 6.01e+03 8.33e+01 bond pdb=" CA VAL K 380 " pdb=" C VAL K 380 " ideal model delta sigma weight residual 1.524 1.421 0.103 1.16e-02 7.43e+03 7.92e+01 bond pdb=" C LYS K 280 " pdb=" O LYS K 280 " ideal model delta sigma weight residual 1.232 1.351 -0.118 1.38e-02 5.25e+03 7.33e+01 bond pdb=" C VAL K 380 " pdb=" O VAL K 380 " ideal model delta sigma weight residual 1.237 1.142 0.095 1.12e-02 7.97e+03 7.20e+01 ... (remaining 27228 not shown) Histogram of bond angle deviations from ideal: 81.57 - 96.12: 16 96.12 - 110.67: 9943 110.67 - 125.22: 26610 125.22 - 139.77: 526 139.77 - 154.32: 3 Bond angle restraints: 37098 Sorted by residual: angle pdb=" C ARG K 318 " pdb=" N PRO K 319 " pdb=" CA PRO K 319 " ideal model delta sigma weight residual 119.84 154.17 -34.33 1.25e+00 6.40e-01 7.54e+02 angle pdb=" N LEU K 273 " pdb=" CA LEU K 273 " pdb=" C LEU K 273 " ideal model delta sigma weight residual 111.03 91.22 19.81 1.11e+00 8.12e-01 3.18e+02 angle pdb=" C PHE K 169 " pdb=" N PRO K 170 " pdb=" CA PRO K 170 " ideal model delta sigma weight residual 119.19 134.97 -15.78 1.06e+00 8.90e-01 2.22e+02 angle pdb=" N VAL K 279 " pdb=" CA VAL K 279 " pdb=" C VAL K 279 " ideal model delta sigma weight residual 108.27 128.46 -20.19 1.37e+00 5.33e-01 2.17e+02 angle pdb=" N UNK H 311 " pdb=" CA UNK H 311 " pdb=" C UNK H 311 " ideal model delta sigma weight residual 110.74 154.32 -43.58 3.00e+00 1.11e-01 2.11e+02 ... (remaining 37093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.01: 16318 35.01 - 70.03: 272 70.03 - 105.04: 30 105.04 - 140.05: 6 140.05 - 175.07: 2 Dihedral angle restraints: 16628 sinusoidal: 4978 harmonic: 11650 Sorted by residual: dihedral pdb=" CA UNK J 242 " pdb=" C UNK J 242 " pdb=" N UNK J 243 " pdb=" CA UNK J 243 " ideal model delta harmonic sigma weight residual 180.00 64.65 115.35 0 5.00e+00 4.00e-02 5.32e+02 dihedral pdb=" CA UNK J 349 " pdb=" C UNK J 349 " pdb=" N UNK J 350 " pdb=" CA UNK J 350 " ideal model delta harmonic sigma weight residual 180.00 87.76 92.24 0 5.00e+00 4.00e-02 3.40e+02 dihedral pdb=" CA UNK H 177 " pdb=" C UNK H 177 " pdb=" N UNK H 178 " pdb=" CA UNK H 178 " ideal model delta harmonic sigma weight residual 180.00 89.23 90.77 0 5.00e+00 4.00e-02 3.30e+02 ... (remaining 16625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.337: 4556 0.337 - 0.675: 40 0.675 - 1.012: 12 1.012 - 1.350: 1 1.350 - 1.687: 1 Chirality restraints: 4610 Sorted by residual: chirality pdb=" CA UNK J 241 " pdb=" N UNK J 241 " pdb=" C UNK J 241 " pdb=" CB UNK J 241 " both_signs ideal model delta sigma weight residual False 2.52 0.83 1.69 2.00e-01 2.50e+01 7.12e+01 chirality pdb=" CA UNK H 311 " pdb=" N UNK H 311 " pdb=" C UNK H 311 " pdb=" CB UNK H 311 " both_signs ideal model delta sigma weight residual False 2.52 1.21 1.32 2.00e-01 2.50e+01 4.32e+01 chirality pdb=" CA UNK J 287 " pdb=" N UNK J 287 " pdb=" C UNK J 287 " pdb=" CB UNK J 287 " both_signs ideal model delta sigma weight residual False 2.52 1.54 0.98 2.00e-01 2.50e+01 2.40e+01 ... (remaining 4607 not shown) Planarity restraints: 4906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY K 214 " -0.075 2.00e-02 2.50e+03 1.39e-01 1.94e+02 pdb=" C GLY K 214 " 0.241 2.00e-02 2.50e+03 pdb=" O GLY K 214 " -0.089 2.00e-02 2.50e+03 pdb=" N ARG K 215 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK J 59 " -0.067 2.00e-02 2.50e+03 1.25e-01 1.56e+02 pdb=" C UNK J 59 " 0.216 2.00e-02 2.50e+03 pdb=" O UNK J 59 " -0.080 2.00e-02 2.50e+03 pdb=" N UNK J 60 " -0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA UNK H 497 " -0.063 2.00e-02 2.50e+03 1.11e-01 1.24e+02 pdb=" C UNK H 497 " 0.193 2.00e-02 2.50e+03 pdb=" O UNK H 497 " -0.067 2.00e-02 2.50e+03 pdb=" N UNK H 498 " -0.063 2.00e-02 2.50e+03 ... (remaining 4903 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 58 2.14 - 2.83: 10872 2.83 - 3.52: 46258 3.52 - 4.21: 64747 4.21 - 4.90: 104143 Nonbonded interactions: 226078 Sorted by model distance: nonbonded pdb=" O UNK H 376 " pdb=" CB UNK H 381 " model vdw 1.448 3.440 nonbonded pdb=" CB UNK J 393 " pdb=" O GLY J 400 " model vdw 1.456 3.440 nonbonded pdb=" O GLN K 171 " pdb=" CB PHE K 174 " model vdw 1.614 3.440 nonbonded pdb=" O ALA K 91 " pdb=" CB SER K 94 " model vdw 1.699 3.440 nonbonded pdb=" O LEU A 124 " pdb=" OG SER B 410 " model vdw 1.781 2.440 ... (remaining 226073 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 103 through 238 or resid 254 through 346 or (resid 369 thr \ ough 370 and (name N or name CA or name C or name O or name CB )) or resid 371 o \ r (resid 372 through 374 and (name N or name CA or name C or name O or name CB ) \ ) or resid 375 through 501 or (resid 502 and (name N or name CA or name C or nam \ e O or name CB )) or resid 503 through 550)) selection = (chain 'C' and (resid 5 through 140 or resid 156 through 248 or (resid 271 throu \ gh 272 and (name N or name CA or name C or name O or name CB )) or resid 273 or \ (resid 274 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 403 or (resid 404 and (name N or name CA or name C or name \ O or name CB )) or resid 405 through 452)) selection = (chain 'E' and (resid 5 through 248 or resid 271 through 452)) } ncs_group { reference = chain 'B' selection = (chain 'D' and (resid 23 through 253 or resid 267 through 269 or (resid 270 and \ (name N or name CA or name C or name O or name CB )) or resid 271 through 451 or \ (resid 452 through 453 and (name N or name CA or name C or name O or name CB )) \ or resid 501)) selection = (chain 'F' and (resid 23 through 252 or (resid 253 through 267 and (name N or na \ me CA or name C or name O or name CB )) or resid 268 through 451 or (resid 452 t \ hrough 453 and (name N or name CA or name C or name O or name CB )) or resid 501 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.030 Extract box with map and model: 6.940 Check model and map are aligned: 1.180 Set scattering table: 0.000 Process input model: 74.610 Find NCS groups from input model: 2.380 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2731 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 : 0.013 0.171 27233 Z= 0.783 Angle : 1.742 43.583 37098 Z= 0.969 Chirality : 0.099 1.687 4610 Planarity : 0.009 0.139 4906 Dihedral : 15.117 175.065 9044 Min Nonbonded Distance : 1.448 Molprobity Statistics. All-atom Clashscore : 42.05 Ramachandran Plot: Outliers : 0.84 % Allowed : 17.25 % Favored : 81.91 % Rotamer: Outliers : 0.38 % Allowed : 13.07 % Favored : 86.55 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.68 % 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: -5.68 (0.11), residues: 2853 helix: -3.72 (0.10), residues: 1119 sheet: -2.69 (0.28), residues: 258 loop : -4.12 (0.13), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 283 HIS 0.012 0.002 HIS B 27 PHE 0.033 0.002 PHE A 398 TYR 0.023 0.003 TYR E 209 ARG 0.009 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 349 time to evaluate : 2.529 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: 8 outliers final: 1 residues processed: 356 average time/residue: 0.4083 time to fit residues: 226.3394 Evaluate side-chains 212 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.951 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2315 time to fit residues: 4.1671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 3.9990 chunk 218 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 147 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN A 467 GLN A 548 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 422 GLN B 441 GLN C 18 HIS ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 284 ASN C 305 HIS ** C 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 302 HIS D 341 GLN D 369 GLN E 18 HIS E 42 GLN E 156 HIS E 181 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 GLN ** F 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN ** F 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 344 HIS F 447 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2903 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 27233 Z= 0.243 Angle : 0.865 13.920 37098 Z= 0.424 Chirality : 0.044 0.274 4610 Planarity : 0.005 0.085 4906 Dihedral : 8.645 148.271 4258 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.46 % Allowed : 10.62 % Favored : 88.92 % Rotamer: Outliers : 3.80 % Allowed : 18.63 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.40 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.14), residues: 2853 helix: -1.31 (0.14), residues: 1216 sheet: -1.98 (0.30), residues: 269 loop : -3.58 (0.14), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 283 HIS 0.012 0.002 HIS B 27 PHE 0.022 0.002 PHE E 300 TYR 0.022 0.002 TYR E 192 ARG 0.007 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 229 time to evaluate : 2.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 27 residues processed: 292 average time/residue: 0.3712 time to fit residues: 177.6139 Evaluate side-chains 215 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 2.642 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2382 time to fit residues: 15.6994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 40.0000 chunk 81 optimal weight: 9.9990 chunk 217 optimal weight: 0.0040 chunk 178 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 262 optimal weight: 40.0000 chunk 283 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 259 optimal weight: 50.0000 chunk 89 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 overall best weight: 5.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 121 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN E 169 GLN ** E 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 HIS F 226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3426 moved from start: 0.8420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 27233 Z= 0.402 Angle : 1.007 16.446 37098 Z= 0.500 Chirality : 0.049 0.359 4610 Planarity : 0.006 0.076 4906 Dihedral : 8.374 174.347 4258 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 31.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 12.72 % Favored : 86.79 % Rotamer: Outliers : 5.47 % Allowed : 22.29 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.47 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.14), residues: 2853 helix: -1.20 (0.14), residues: 1175 sheet: -2.18 (0.27), residues: 308 loop : -3.40 (0.15), residues: 1370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 283 HIS 0.014 0.003 HIS A 403 PHE 0.030 0.003 PHE A 535 TYR 0.046 0.003 TYR D 387 ARG 0.011 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 186 time to evaluate : 2.592 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 outliers start: 115 outliers final: 40 residues processed: 283 average time/residue: 0.3453 time to fit residues: 161.9360 Evaluate side-chains 169 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 2.681 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.2503 time to fit residues: 21.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 30.0000 chunk 196 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 175 optimal weight: 0.3980 chunk 262 optimal weight: 40.0000 chunk 278 optimal weight: 9.9990 chunk 137 optimal weight: 30.0000 chunk 249 optimal weight: 30.0000 chunk 75 optimal weight: 0.9980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3460 moved from start: 0.9233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27233 Z= 0.251 Angle : 0.788 16.388 37098 Z= 0.382 Chirality : 0.042 0.244 4610 Planarity : 0.005 0.082 4906 Dihedral : 7.309 152.838 4258 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.35 % Allowed : 10.02 % Favored : 89.62 % Rotamer: Outliers : 3.14 % Allowed : 24.19 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.15), residues: 2853 helix: -0.58 (0.14), residues: 1226 sheet: -1.77 (0.29), residues: 280 loop : -3.21 (0.15), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 283 HIS 0.009 0.001 HIS A 118 PHE 0.019 0.002 PHE C 177 TYR 0.020 0.002 TYR B 442 ARG 0.008 0.001 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 142 time to evaluate : 2.814 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: 66 outliers final: 24 residues processed: 201 average time/residue: 0.3682 time to fit residues: 121.3276 Evaluate side-chains 147 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 123 time to evaluate : 2.822 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2577 time to fit residues: 14.6306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 20.0000 chunk 158 optimal weight: 20.0000 chunk 4 optimal weight: 0.2980 chunk 207 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 237 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 142 optimal weight: 50.0000 chunk 249 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN ** E 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3566 moved from start: 1.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 27233 Z= 0.314 Angle : 0.835 13.080 37098 Z= 0.409 Chirality : 0.044 0.348 4610 Planarity : 0.005 0.074 4906 Dihedral : 7.326 155.650 4258 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 26.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.60 % Favored : 88.05 % Rotamer: Outliers : 3.18 % Allowed : 25.33 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.15), residues: 2853 helix: -0.41 (0.15), residues: 1228 sheet: -1.63 (0.30), residues: 283 loop : -3.14 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 283 HIS 0.008 0.002 HIS A 339 PHE 0.026 0.002 PHE A 427 TYR 0.016 0.002 TYR B 362 ARG 0.010 0.001 ARG C 378 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 122 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 27 residues processed: 179 average time/residue: 0.3702 time to fit residues: 108.9381 Evaluate side-chains 134 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 2.744 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.2769 time to fit residues: 16.8497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 0.3980 chunk 250 optimal weight: 10.0000 chunk 55 optimal weight: 50.0000 chunk 163 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 129 optimal weight: 7.9990 chunk 23 optimal weight: 8.9990 chunk 92 optimal weight: 0.0970 chunk 146 optimal weight: 7.9990 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN B 44 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN C 145 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3549 moved from start: 1.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27233 Z= 0.221 Angle : 0.734 13.140 37098 Z= 0.356 Chirality : 0.041 0.238 4610 Planarity : 0.004 0.067 4906 Dihedral : 6.926 146.903 4258 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.41 % Favored : 89.34 % Rotamer: Outliers : 1.76 % Allowed : 25.67 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.15), residues: 2853 helix: -0.16 (0.15), residues: 1225 sheet: -1.34 (0.31), residues: 275 loop : -3.04 (0.16), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.007 0.001 HIS A 339 PHE 0.019 0.001 PHE F 100 TYR 0.014 0.001 TYR F 172 ARG 0.009 0.000 ARG B 374 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 2.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 18 residues processed: 156 average time/residue: 0.3914 time to fit residues: 99.2124 Evaluate side-chains 129 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 2.878 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3216 time to fit residues: 13.3029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 9.9990 chunk 31 optimal weight: 5.9990 chunk 158 optimal weight: 0.7980 chunk 203 optimal weight: 2.9990 chunk 157 optimal weight: 7.9990 chunk 234 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 277 optimal weight: 30.0000 chunk 173 optimal weight: 5.9990 chunk 169 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN B 121 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 369 GLN C 451 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3621 moved from start: 1.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27233 Z= 0.293 Angle : 0.803 14.088 37098 Z= 0.393 Chirality : 0.043 0.269 4610 Planarity : 0.005 0.093 4906 Dihedral : 7.064 142.083 4258 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 25.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.16 % Favored : 87.59 % Rotamer: Outliers : 2.04 % Allowed : 25.81 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.15), residues: 2853 helix: -0.14 (0.15), residues: 1224 sheet: -1.27 (0.30), residues: 282 loop : -3.07 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 283 HIS 0.012 0.002 HIS A 327 PHE 0.031 0.002 PHE F 100 TYR 0.018 0.002 TYR F 362 ARG 0.010 0.001 ARG D 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 122 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 14 residues processed: 157 average time/residue: 0.3967 time to fit residues: 102.0736 Evaluate side-chains 129 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 3.048 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3228 time to fit residues: 12.5056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 165 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 176 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 218 optimal weight: 9.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 447 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3565 moved from start: 1.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27233 Z= 0.178 Angle : 0.718 14.106 37098 Z= 0.346 Chirality : 0.041 0.282 4610 Planarity : 0.004 0.098 4906 Dihedral : 6.608 129.937 4258 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.67 % Favored : 90.15 % Rotamer: Outliers : 1.14 % Allowed : 25.95 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2853 helix: 0.13 (0.15), residues: 1228 sheet: -1.14 (0.31), residues: 273 loop : -2.92 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 283 HIS 0.006 0.001 HIS A 327 PHE 0.063 0.001 PHE F 309 TYR 0.018 0.001 TYR B 442 ARG 0.011 0.001 ARG D 414 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 2.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 140 average time/residue: 0.3823 time to fit residues: 88.8601 Evaluate side-chains 120 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 111 time to evaluate : 2.807 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.3307 time to fit residues: 8.4131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 40.0000 chunk 265 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 258 optimal weight: 50.0000 chunk 155 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 203 optimal weight: 0.0060 chunk 79 optimal weight: 6.9990 chunk 233 optimal weight: 0.9980 chunk 244 optimal weight: 7.9990 chunk 257 optimal weight: 20.0000 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3633 moved from start: 1.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27233 Z= 0.285 Angle : 0.774 12.351 37098 Z= 0.379 Chirality : 0.042 0.312 4610 Planarity : 0.005 0.098 4906 Dihedral : 6.807 130.460 4258 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 24.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.74 % Favored : 88.05 % Rotamer: Outliers : 0.62 % Allowed : 26.85 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.16), residues: 2853 helix: 0.14 (0.15), residues: 1210 sheet: -1.21 (0.30), residues: 295 loop : -2.87 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 283 HIS 0.013 0.002 HIS A 403 PHE 0.031 0.002 PHE A 427 TYR 0.019 0.002 TYR F 387 ARG 0.010 0.001 ARG A 476 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 2.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 123 average time/residue: 0.3933 time to fit residues: 80.0948 Evaluate side-chains 114 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 106 time to evaluate : 3.179 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2746 time to fit residues: 8.2233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 4.9990 chunk 273 optimal weight: 50.0000 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 286 optimal weight: 30.0000 chunk 264 optimal weight: 50.0000 chunk 228 optimal weight: 50.0000 chunk 23 optimal weight: 6.9990 chunk 176 optimal weight: 0.0670 chunk 140 optimal weight: 0.0270 overall best weight: 2.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3612 moved from start: 1.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 27233 Z= 0.217 Angle : 0.735 11.866 37098 Z= 0.357 Chirality : 0.041 0.325 4610 Planarity : 0.004 0.106 4906 Dihedral : 6.596 122.108 4258 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 21.49 Ramachandran Plot: Outliers : 0.18 % Allowed : 10.34 % Favored : 89.48 % Rotamer: Outliers : 0.14 % Allowed : 27.38 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.14 % 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: -1.89 (0.16), residues: 2853 helix: 0.27 (0.15), residues: 1216 sheet: -0.98 (0.32), residues: 261 loop : -2.85 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 283 HIS 0.008 0.001 HIS A 403 PHE 0.043 0.002 PHE D 452 TYR 0.017 0.001 TYR D 430 ARG 0.014 0.001 ARG B 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5706 Ramachandran restraints generated. 2853 Oldfield, 0 Emsley, 2853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 2.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 113 average time/residue: 0.4032 time to fit residues: 76.9049 Evaluate side-chains 109 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 2.880 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.2022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 228 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 4.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.095327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.072248 restraints weight = 188920.993| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 7.03 r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3641 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3641 r_free = 0.3641 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3641 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 1.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 27233 Z= 0.286 Angle : 0.776 11.438 37098 Z= 0.381 Chirality : 0.042 0.346 4610 Planarity : 0.005 0.100 4906 Dihedral : 6.750 123.446 4258 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 24.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.81 % Favored : 87.98 % Rotamer: Outliers : 0.52 % Allowed : 27.23 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.16), residues: 2853 helix: 0.15 (0.15), residues: 1219 sheet: -1.04 (0.31), residues: 293 loop : -2.92 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 283 HIS 0.015 0.002 HIS A 403 PHE 0.034 0.002 PHE A 427 TYR 0.020 0.002 TYR D 430 ARG 0.013 0.001 ARG A 476 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4958.90 seconds wall clock time: 91 minutes 57.52 seconds (5517.52 seconds total)