Starting phenix.real_space_refine (version: dev) on Sun Feb 26 03:39:00 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/02_2023/7ole_12979_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/02_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_12979/02_2023/7ole_12979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/02_2023/7ole_12979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/02_2023/7ole_12979_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ole_12979/02_2023/7ole_12979_neut_updated.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 14.86, per 1000 atoms: 0.55 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: 13.40 Conformation dependent library (CDL) restraints added in 3.3 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: 4.26 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: 9.33 Time building geometry restraints manager: 14.00 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 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. 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.150 Check model and map are aligned: 0.400 Process input model: 69.570 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.290 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2615 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 : 1.741 43.583 37098 Z= 0.968 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 % 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 *********************** 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 : 2.654 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: 225.3960 Evaluate side-chains 212 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 211 time to evaluate : 2.594 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2109 time to fit residues: 3.7107 ------------------------------------------------------------------------------- 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 339 HIS A 382 ASN A 467 GLN ** A 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2772 moved from start: 0.3174 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= 0.265 Angle : 0.879 14.491 37098 Z= 0.431 Chirality : 0.044 0.267 4610 Planarity : 0.005 0.088 4906 Dihedral : 8.758 150.873 4258 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 24.52 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.39 % Favored : 88.15 % Rotamer Outliers : 3.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % Twisted General : 0.43 % 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: -3.80 (0.14), residues: 2853 helix: -1.52 (0.13), residues: 1208 sheet: -2.10 (0.30), residues: 262 loop : -3.63 (0.14), residues: 1383 *********************** 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 295 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 226 time to evaluate : 3.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 28 residues processed: 280 average time/residue: 0.3794 time to fit residues: 172.5601 Evaluate side-chains 214 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 2.753 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.2493 time to fit residues: 16.6723 ------------------------------------------------------------------------------- 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: 0.9990 chunk 217 optimal weight: 3.9990 chunk 178 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 262 optimal weight: 40.0000 chunk 283 optimal weight: 40.0000 chunk 233 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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** ** B 302 HIS ** 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 348 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3300 moved from start: 0.8075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.115 27233 Z= 0.385 Angle : 0.979 16.379 37098 Z= 0.486 Chirality : 0.048 0.358 4610 Planarity : 0.006 0.075 4906 Dihedral : 8.317 168.577 4258 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 30.23 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.48 % Favored : 87.07 % Rotamer Outliers : 5.18 % 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: -3.54 (0.14), residues: 2853 helix: -1.32 (0.13), residues: 1188 sheet: -2.16 (0.28), residues: 289 loop : -3.42 (0.15), residues: 1376 *********************** 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 295 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 186 time to evaluate : 2.817 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: 109 outliers final: 41 residues processed: 275 average time/residue: 0.3438 time to fit residues: 157.1564 Evaluate side-chains 173 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 132 time to evaluate : 2.751 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2331 time to fit residues: 21.2874 ------------------------------------------------------------------------------- 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: 10.0000 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 175 optimal weight: 0.0470 chunk 262 optimal weight: 40.0000 chunk 278 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 249 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- 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** ** 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** ** 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** D 441 GLN D 447 GLN ** 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: 0.3333 moved from start: 0.8875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 27233 Z= 0.230 Angle : 0.765 13.503 37098 Z= 0.370 Chirality : 0.042 0.263 4610 Planarity : 0.004 0.081 4906 Dihedral : 7.178 151.595 4258 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 21.92 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.20 % Favored : 89.52 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 2.17 % 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: -2.68 (0.15), residues: 2853 helix: -0.40 (0.15), residues: 1208 sheet: -1.73 (0.30), residues: 281 loop : -3.18 (0.15), residues: 1364 *********************** 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 190 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 139 time to evaluate : 2.832 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 outliers start: 51 outliers final: 22 residues processed: 187 average time/residue: 0.3727 time to fit residues: 114.8016 Evaluate side-chains 139 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 3.245 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3741 time to fit residues: 19.1665 ------------------------------------------------------------------------------- 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: 2.9990 chunk 207 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 7.9990 chunk 249 optimal weight: 30.0000 chunk 70 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 483 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 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3439 moved from start: 1.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 27233 Z= 0.279 Angle : 0.801 15.656 37098 Z= 0.394 Chirality : 0.044 0.311 4610 Planarity : 0.005 0.088 4906 Dihedral : 7.143 151.973 4258 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 24.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 11.53 % Favored : 88.19 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.04 % Twisted Proline : 1.09 % Twisted General : 0.29 % 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: -2.42 (0.15), residues: 2853 helix: -0.24 (0.15), residues: 1221 sheet: -1.59 (0.31), residues: 277 loop : -3.00 (0.16), residues: 1355 *********************** 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 192 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 124 time to evaluate : 2.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 24 residues processed: 185 average time/residue: 0.3739 time to fit residues: 114.7916 Evaluate side-chains 135 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 2.812 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2635 time to fit residues: 15.4755 ------------------------------------------------------------------------------- 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: 4.9990 chunk 250 optimal weight: 40.0000 chunk 55 optimal weight: 7.9990 chunk 163 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 278 optimal weight: 40.0000 chunk 231 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 146 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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** B 44 GLN B 49 GLN B 92 GLN ** B 121 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** B 369 GLN C 156 HIS ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 369 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: 0.3518 moved from start: 1.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.087 27233 Z= 0.373 Angle : 0.852 15.734 37098 Z= 0.415 Chirality : 0.044 0.249 4610 Planarity : 0.005 0.088 4906 Dihedral : 7.422 152.403 4258 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.67 % Favored : 88.08 % Rotamer Outliers : 2.71 % 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: -2.71 (0.15), residues: 2853 helix: -0.52 (0.15), residues: 1228 sheet: -1.68 (0.31), residues: 271 loop : -3.15 (0.16), residues: 1354 *********************** 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 176 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 119 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 24 residues processed: 169 average time/residue: 0.3779 time to fit residues: 104.9993 Evaluate side-chains 132 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3454 time to fit residues: 17.1554 ------------------------------------------------------------------------------- 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: 10.0000 chunk 31 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 203 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 277 optimal weight: 20.0000 chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 ASN B 92 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3464 moved from start: 1.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 27233 Z= 0.182 Angle : 0.720 15.073 37098 Z= 0.347 Chirality : 0.041 0.260 4610 Planarity : 0.004 0.089 4906 Dihedral : 6.733 143.782 4258 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.30 % Favored : 89.48 % Rotamer Outliers : 1.33 % 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: -2.21 (0.16), residues: 2853 helix: -0.04 (0.15), residues: 1229 sheet: -1.34 (0.32), residues: 261 loop : -2.95 (0.16), residues: 1363 *********************** 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 145 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 2.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 7 residues processed: 141 average time/residue: 0.3707 time to fit residues: 88.4890 Evaluate side-chains 119 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 112 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2487 time to fit residues: 6.9400 ------------------------------------------------------------------------------- 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: 0.9990 chunk 110 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 176 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 GLN ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** B 121 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** B 369 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 GLN ** 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: 0.3514 moved from start: 1.2704 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= 0.256 Angle : 0.755 17.026 37098 Z= 0.365 Chirality : 0.042 0.220 4610 Planarity : 0.005 0.094 4906 Dihedral : 6.795 134.443 4258 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.95 Ramachandran Plot: Outliers : 0.18 % Allowed : 11.71 % Favored : 88.12 % Rotamer Outliers : 1.76 % 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: -2.19 (0.16), residues: 2853 helix: -0.02 (0.15), residues: 1229 sheet: -1.36 (0.31), residues: 277 loop : -2.95 (0.16), residues: 1347 *********************** 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 150 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 3.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 12 residues processed: 142 average time/residue: 0.3720 time to fit residues: 88.5953 Evaluate side-chains 121 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 2.634 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2607 time to fit residues: 9.2247 ------------------------------------------------------------------------------- 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: 40.0000 chunk 242 optimal weight: 9.9990 chunk 258 optimal weight: 40.0000 chunk 155 optimal weight: 6.9990 chunk 112 optimal weight: 0.6980 chunk 203 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 233 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 257 optimal weight: 5.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- 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** B 121 GLN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 348 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 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 34 GLN E 181 GLN ** E 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3534 moved from start: 1.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 27233 Z= 0.277 Angle : 0.764 16.377 37098 Z= 0.373 Chirality : 0.042 0.248 4610 Planarity : 0.005 0.146 4906 Dihedral : 6.872 136.230 4258 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 11.15 % Favored : 88.64 % Rotamer Outliers : 0.71 % 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: -2.18 (0.16), residues: 2853 helix: 0.04 (0.15), residues: 1217 sheet: -1.25 (0.32), residues: 274 loop : -3.00 (0.16), residues: 1362 *********************** 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 131 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 2.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 129 average time/residue: 0.3748 time to fit residues: 80.5192 Evaluate side-chains 112 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 107 time to evaluate : 2.755 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2370 time to fit residues: 5.8483 ------------------------------------------------------------------------------- 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: 0.0040 chunk 273 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 286 optimal weight: 10.0000 chunk 264 optimal weight: 20.0000 chunk 228 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 176 optimal weight: 5.9990 chunk 140 optimal weight: 30.0000 overall best weight: 2.7996 ------------------------------------------------------------------------------- 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 403 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 ASN ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 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 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3521 moved from start: 1.3531 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= 0.220 Angle : 0.743 17.658 37098 Z= 0.360 Chirality : 0.041 0.252 4610 Planarity : 0.005 0.134 4906 Dihedral : 6.664 125.728 4258 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 21.74 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.94 % Favored : 88.85 % Rotamer Outliers : 0.62 % 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: -2.06 (0.16), residues: 2853 helix: 0.14 (0.15), residues: 1219 sheet: -1.17 (0.32), residues: 267 loop : -2.94 (0.16), residues: 1367 ********************** 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 128 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 3.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.3913 time to fit residues: 82.3135 Evaluate side-chains 118 residues out of total 2440 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 112 time to evaluate : 2.748 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2524 time to fit residues: 6.6382 ------------------------------------------------------------------------------- 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: 2.9990 chunk 243 optimal weight: 2.9990 chunk 69 optimal weight: 0.1980 chunk 210 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 chunk 95 optimal weight: 0.9990 chunk 234 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.097053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.070925 restraints weight = 189786.796| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 7.59 r_work: 0.3518 rms_B_bonded: 7.58 restraints_weight: 2.0000 r_work: 0.3608 rms_B_bonded: 5.65 restraints_weight: 4.0000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4323 r_free = 0.4323 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4323 r_free = 0.4323 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 1.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 27233 Z= 0.184 Angle : 0.719 17.197 37098 Z= 0.346 Chirality : 0.041 0.260 4610 Planarity : 0.005 0.198 4906 Dihedral : 6.420 110.914 4258 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.99 % Favored : 89.80 % Rotamer Outliers : 0.24 % 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: -1.90 (0.16), residues: 2853 helix: 0.27 (0.15), residues: 1220 sheet: -1.00 (0.33), residues: 263 loop : -2.87 (0.16), residues: 1370 =============================================================================== Job complete usr+sys time: 6401.01 seconds wall clock time: 116 minutes 53.97 seconds (7013.97 seconds total)