Starting phenix.real_space_refine on Wed Apr 10 04:01:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7koe_22973/04_2024/7koe_22973_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 16 7.16 5 P 12 5.49 5 S 102 5.16 5 C 11690 2.51 5 N 3116 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ASP 155": "OD1" <-> "OD2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A ASP 186": "OD1" <-> "OD2" Residue "A ARG 192": "NH1" <-> "NH2" Residue "A ASP 218": "OD1" <-> "OD2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 511": "OE1" <-> "OE2" Residue "B GLU 518": "OE1" <-> "OE2" Residue "B GLU 576": "OE1" <-> "OE2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ARG 613": "NH1" <-> "NH2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C ASP 6": "OD1" <-> "OD2" Residue "C TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 60": "OD1" <-> "OD2" Residue "C ARG 94": "NH1" <-> "NH2" Residue "C ARG 109": "NH1" <-> "NH2" Residue "C ARG 151": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 251": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 345": "OD1" <-> "OD2" Residue "C GLU 348": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C ASP 408": "OD1" <-> "OD2" Residue "C ARG 420": "NH1" <-> "NH2" Residue "C ARG 435": "NH1" <-> "NH2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ARG 175": "NH1" <-> "NH2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "F GLU 297": "OE1" <-> "OE2" Residue "F GLU 309": "OE1" <-> "OE2" Residue "F GLU 325": "OE1" <-> "OE2" Residue "F GLU 333": "OE1" <-> "OE2" Residue "F PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 484": "OE1" <-> "OE2" Residue "F GLU 511": "OE1" <-> "OE2" Residue "F GLU 518": "OE1" <-> "OE2" Residue "F GLU 576": "OE1" <-> "OE2" Residue "F GLU 585": "OE1" <-> "OE2" Residue "F ARG 613": "NH1" <-> "NH2" Residue "G GLU 4": "OE1" <-> "OE2" Residue "G ASP 6": "OD1" <-> "OD2" Residue "G TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 60": "OD1" <-> "OD2" Residue "G ARG 94": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 151": "NH1" <-> "NH2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "G PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 251": "NH1" <-> "NH2" Residue "G ARG 278": "NH1" <-> "NH2" Residue "G GLU 291": "OE1" <-> "OE2" Residue "G GLU 339": "OE1" <-> "OE2" Residue "G PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 345": "OD1" <-> "OD2" Residue "G GLU 348": "OE1" <-> "OE2" Residue "G GLU 360": "OE1" <-> "OE2" Residue "G GLU 378": "OE1" <-> "OE2" Residue "G ASP 408": "OD1" <-> "OD2" Residue "G ARG 420": "NH1" <-> "NH2" Residue "G ARG 435": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 18348 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2195 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain: "C" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3445 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "E" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2195 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "F" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain: "G" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3445 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'FAD': 1, 'MQ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'FAD': 1, 'MQ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8700 SG CYS D 499 45.139 36.362 75.677 1.00 11.68 S ATOM 8723 SG CYS D 502 45.392 41.036 79.247 1.00 10.40 S ATOM 8740 SG CYS D 505 43.304 35.777 80.898 1.00 9.39 S ATOM 8549 SG CYS D 480 40.012 39.136 78.064 1.00 15.00 S ATOM 8457 SG CYS D 467 34.934 28.963 84.782 1.00 26.26 S ATOM 8486 SG CYS D 471 33.932 32.906 88.987 1.00 31.72 S ATOM 8524 SG CYS D 476 36.015 34.470 83.600 1.00 18.30 S ATOM 8772 SG CYS D 509 39.086 32.287 87.448 1.00 17.45 S ATOM 17651 SG CYS H 499 53.645 111.815 75.677 1.00 11.68 S ATOM 17674 SG CYS H 502 53.392 107.141 79.247 1.00 10.40 S ATOM 17691 SG CYS H 505 55.480 112.400 80.898 1.00 9.39 S ATOM 17500 SG CYS H 480 58.772 109.041 78.064 1.00 15.00 S ATOM 17408 SG CYS H 467 63.850 119.214 84.782 1.00 26.26 S ATOM 17437 SG CYS H 471 64.852 115.271 88.987 1.00 31.72 S ATOM 17475 SG CYS H 476 62.769 113.707 83.600 1.00 18.30 S ATOM 17723 SG CYS H 509 59.698 115.890 87.448 1.00 17.45 S Time building chain proxies: 10.79, per 1000 atoms: 0.59 Number of scatterers: 18348 At special positions: 0 Unit cell: (99.813, 149.205, 117.306, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 16 26.01 S 102 16.00 P 12 15.00 O 3412 8.00 N 3116 7.00 C 11690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.87 Conformation dependent library (CDL) restraints added in 3.9 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 601 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 480 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 499 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 502 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 505 " pdb=" SF4 D 602 " pdb="FE4 SF4 D 602 " - pdb=" SG CYS D 509 " pdb="FE1 SF4 D 602 " - pdb=" SG CYS D 467 " pdb="FE2 SF4 D 602 " - pdb=" SG CYS D 471 " pdb="FE3 SF4 D 602 " - pdb=" SG CYS D 476 " pdb=" SF4 H 601 " pdb="FE4 SF4 H 601 " - pdb=" SG CYS H 480 " pdb="FE1 SF4 H 601 " - pdb=" SG CYS H 499 " pdb="FE2 SF4 H 601 " - pdb=" SG CYS H 502 " pdb="FE3 SF4 H 601 " - pdb=" SG CYS H 505 " pdb=" SF4 H 602 " pdb="FE4 SF4 H 602 " - pdb=" SG CYS H 509 " pdb="FE1 SF4 H 602 " - pdb=" SG CYS H 467 " pdb="FE2 SF4 H 602 " - pdb=" SG CYS H 471 " pdb="FE3 SF4 H 602 " - pdb=" SG CYS H 476 " Number of angles added : 48 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4196 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 28 sheets defined 29.8% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'A' and resid 36 through 52 removed outlier: 3.931A pdb=" N ARG A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.650A pdb=" N LYS A 67 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 69 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 70 " --> pdb=" O LYS A 67 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 71 " --> pdb=" O GLU A 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A 73 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 75 " --> pdb=" O ASP A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 109 Processing helix chain 'A' and resid 131 through 139 removed outlier: 3.768A pdb=" N THR A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 203 Processing helix chain 'A' and resid 212 through 215 No H-bonds generated for 'chain 'A' and resid 212 through 215' Processing helix chain 'A' and resid 254 through 263 removed outlier: 3.583A pdb=" N LYS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 271 Processing helix chain 'B' and resid 305 through 318 removed outlier: 4.024A pdb=" N LEU B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE B 311 " --> pdb=" O TRP B 308 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 312 " --> pdb=" O GLU B 309 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA B 314 " --> pdb=" O ILE B 311 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 315 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 345 removed outlier: 4.266A pdb=" N GLU B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 363 through 369 removed outlier: 3.695A pdb=" N LYS B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 375 No H-bonds generated for 'chain 'B' and resid 372 through 375' Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.526A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 511 through 522 removed outlier: 3.978A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 534 No H-bonds generated for 'chain 'B' and resid 531 through 534' Processing helix chain 'B' and resid 541 through 543 No H-bonds generated for 'chain 'B' and resid 541 through 543' Processing helix chain 'B' and resid 566 through 569 No H-bonds generated for 'chain 'B' and resid 566 through 569' Processing helix chain 'B' and resid 605 through 616 removed outlier: 4.016A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 removed outlier: 3.517A pdb=" N VAL C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 57 removed outlier: 3.526A pdb=" N ILE C 57 " --> pdb=" O PRO C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 109 through 123 removed outlier: 3.629A pdb=" N ARG C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 175 removed outlier: 3.532A pdb=" N LYS C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 170 through 175' Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 247 through 251 Processing helix chain 'C' and resid 258 through 265 Processing helix chain 'C' and resid 270 through 273 No H-bonds generated for 'chain 'C' and resid 270 through 273' Processing helix chain 'C' and resid 293 through 295 No H-bonds generated for 'chain 'C' and resid 293 through 295' Processing helix chain 'C' and resid 323 through 343 removed outlier: 3.560A pdb=" N THR C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 360 removed outlier: 3.573A pdb=" N TYR C 354 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 358 " --> pdb=" O TYR C 355 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C 360 " --> pdb=" O ARG C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 387 through 399 Processing helix chain 'C' and resid 410 through 420 removed outlier: 3.649A pdb=" N ALA C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 432 removed outlier: 3.948A pdb=" N LEU C 428 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 437 No H-bonds generated for 'chain 'C' and resid 434 through 437' Processing helix chain 'D' and resid 440 through 445 removed outlier: 3.943A pdb=" N LYS D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 478 No H-bonds generated for 'chain 'D' and resid 475 through 478' Processing helix chain 'D' and resid 496 through 498 No H-bonds generated for 'chain 'D' and resid 496 through 498' Processing helix chain 'D' and resid 504 through 508 Processing helix chain 'E' and resid 36 through 52 removed outlier: 3.931A pdb=" N ARG E 40 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.650A pdb=" N LYS E 67 " --> pdb=" O PRO E 64 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 69 " --> pdb=" O ALA E 66 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU E 70 " --> pdb=" O LYS E 67 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS E 71 " --> pdb=" O GLU E 68 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA E 73 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA E 75 " --> pdb=" O ASP E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 109 Processing helix chain 'E' and resid 131 through 139 removed outlier: 3.768A pdb=" N THR E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 203 Processing helix chain 'E' and resid 212 through 215 No H-bonds generated for 'chain 'E' and resid 212 through 215' Processing helix chain 'E' and resid 254 through 263 removed outlier: 3.583A pdb=" N LYS E 258 " --> pdb=" O VAL E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 271 Processing helix chain 'F' and resid 305 through 318 removed outlier: 4.024A pdb=" N LEU F 310 " --> pdb=" O SER F 307 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE F 311 " --> pdb=" O TRP F 308 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY F 312 " --> pdb=" O GLU F 309 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 314 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG F 315 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 345 removed outlier: 4.266A pdb=" N GLU F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 363 through 369 removed outlier: 3.696A pdb=" N LYS F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 375 No H-bonds generated for 'chain 'F' and resid 372 through 375' Processing helix chain 'F' and resid 388 through 398 removed outlier: 3.526A pdb=" N MET F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 490 No H-bonds generated for 'chain 'F' and resid 488 through 490' Processing helix chain 'F' and resid 511 through 522 removed outlier: 3.978A pdb=" N LYS F 515 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 519 " --> pdb=" O LYS F 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 522 " --> pdb=" O GLU F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 534 No H-bonds generated for 'chain 'F' and resid 531 through 534' Processing helix chain 'F' and resid 541 through 543 No H-bonds generated for 'chain 'F' and resid 541 through 543' Processing helix chain 'F' and resid 566 through 569 No H-bonds generated for 'chain 'F' and resid 566 through 569' Processing helix chain 'F' and resid 605 through 616 removed outlier: 4.016A pdb=" N LYS F 611 " --> pdb=" O ALA F 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F 614 " --> pdb=" O ALA F 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 25 removed outlier: 3.517A pdb=" N VAL G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 57 removed outlier: 3.526A pdb=" N ILE G 57 " --> pdb=" O PRO G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 109 through 123 removed outlier: 3.629A pdb=" N ARG G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 170 through 175 removed outlier: 3.532A pdb=" N LYS G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 170 through 175' Processing helix chain 'G' and resid 201 through 206 Processing helix chain 'G' and resid 221 through 223 No H-bonds generated for 'chain 'G' and resid 221 through 223' Processing helix chain 'G' and resid 247 through 251 Processing helix chain 'G' and resid 258 through 265 Processing helix chain 'G' and resid 270 through 273 No H-bonds generated for 'chain 'G' and resid 270 through 273' Processing helix chain 'G' and resid 293 through 295 No H-bonds generated for 'chain 'G' and resid 293 through 295' Processing helix chain 'G' and resid 323 through 343 removed outlier: 3.560A pdb=" N THR G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 360 removed outlier: 3.573A pdb=" N TYR G 354 " --> pdb=" O LEU G 351 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 358 " --> pdb=" O TYR G 355 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU G 360 " --> pdb=" O ARG G 357 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 369 Processing helix chain 'G' and resid 374 through 378 Processing helix chain 'G' and resid 387 through 399 Processing helix chain 'G' and resid 410 through 420 removed outlier: 3.649A pdb=" N ALA G 414 " --> pdb=" O GLN G 410 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER G 419 " --> pdb=" O ASP G 415 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 420 " --> pdb=" O MET G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 423 through 432 removed outlier: 3.948A pdb=" N LEU G 428 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU G 431 " --> pdb=" O SER G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 437 No H-bonds generated for 'chain 'G' and resid 434 through 437' Processing helix chain 'H' and resid 440 through 445 removed outlier: 3.943A pdb=" N LYS H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 478 No H-bonds generated for 'chain 'H' and resid 475 through 478' Processing helix chain 'H' and resid 496 through 498 No H-bonds generated for 'chain 'H' and resid 496 through 498' Processing helix chain 'H' and resid 504 through 508 Processing sheet with id= A, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.548A pdb=" N GLY A 121 " --> pdb=" O CYS A 6 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N THR A 55 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL A 5 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR A 57 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU A 80 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR A 60 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL A 82 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE A 208 " --> pdb=" O HIS A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 9 through 11 Processing sheet with id= C, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.141A pdb=" N ARG A 17 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 171 through 177 removed outlier: 3.740A pdb=" N ARG A 150 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG A 166 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL A 148 " --> pdb=" O ARG A 166 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.339A pdb=" N LEU B 351 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU B 469 " --> pdb=" O TYR B 352 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 383 through 385 removed outlier: 6.302A pdb=" N ALA B 446 " --> pdb=" O ILE B 384 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 422 through 427 Processing sheet with id= H, first strand: chain 'B' and resid 526 through 529 removed outlier: 3.756A pdb=" N GLY B 503 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 556 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA B 502 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE B 558 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE B 595 " --> pdb=" O ALA B 580 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.267A pdb=" N ILE C 3 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 305 through 307 removed outlier: 6.401A pdb=" N VAL C 161 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU C 126 " --> pdb=" O VAL C 32 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 88 through 91 removed outlier: 7.688A pdb=" N THR C 215 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN C 78 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU C 217 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU C 80 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU C 219 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 82 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA C 214 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER C 196 " --> pdb=" O THR C 281 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR C 281 " --> pdb=" O SER C 196 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 71 through 74 Processing sheet with id= M, first strand: chain 'D' and resid 459 through 461 Processing sheet with id= N, first strand: chain 'D' and resid 485 through 488 removed outlier: 3.599A pdb=" N GLY D 491 " --> pdb=" O THR D 488 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 143 through 145 removed outlier: 4.548A pdb=" N GLY E 121 " --> pdb=" O CYS E 6 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N THR E 55 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL E 5 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR E 57 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLU E 80 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR E 60 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL E 82 " --> pdb=" O THR E 60 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ILE E 208 " --> pdb=" O HIS E 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 9 through 11 Processing sheet with id= Q, first strand: chain 'E' and resid 17 through 19 removed outlier: 4.141A pdb=" N ARG E 17 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 171 through 177 removed outlier: 3.740A pdb=" N ARG E 150 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG E 166 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL E 148 " --> pdb=" O ARG E 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 329 through 331 removed outlier: 6.338A pdb=" N LEU F 351 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU F 469 " --> pdb=" O TYR F 352 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 383 through 385 removed outlier: 6.302A pdb=" N ALA F 446 " --> pdb=" O ILE F 384 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 422 through 427 Processing sheet with id= V, first strand: chain 'F' and resid 526 through 529 removed outlier: 3.756A pdb=" N GLY F 503 " --> pdb=" O GLY F 528 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU F 556 " --> pdb=" O VAL F 500 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ALA F 502 " --> pdb=" O LEU F 556 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N PHE F 558 " --> pdb=" O ALA F 502 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 595 " --> pdb=" O ALA F 580 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 3 through 5 removed outlier: 4.267A pdb=" N ILE G 3 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 305 through 307 removed outlier: 6.401A pdb=" N VAL G 161 " --> pdb=" O LEU G 306 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU G 126 " --> pdb=" O VAL G 32 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 88 through 91 removed outlier: 7.688A pdb=" N THR G 215 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLN G 78 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLU G 217 " --> pdb=" O GLN G 78 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU G 80 " --> pdb=" O GLU G 217 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LEU G 219 " --> pdb=" O LEU G 80 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU G 82 " --> pdb=" O LEU G 219 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA G 214 " --> pdb=" O ALA G 234 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N SER G 196 " --> pdb=" O THR G 281 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N THR G 281 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 71 through 74 Processing sheet with id= AA, first strand: chain 'H' and resid 459 through 461 Processing sheet with id= AB, first strand: chain 'H' and resid 485 through 488 removed outlier: 3.599A pdb=" N GLY H 491 " --> pdb=" O THR H 488 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1224 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: 5.43 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 7296 1.40 - 1.58: 11236 1.58 - 1.77: 14 1.77 - 1.95: 136 1.95 - 2.14: 48 Bond restraints: 18730 Sorted by residual: bond pdb=" C17 MQ7 G 502 " pdb=" C18 MQ7 G 502 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C17 MQ7 C 502 " pdb=" C18 MQ7 C 502 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C12 MQ7 C 502 " pdb=" C13 MQ7 C 502 " ideal model delta sigma weight residual 1.335 1.552 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C12 MQ7 G 502 " pdb=" C13 MQ7 G 502 " ideal model delta sigma weight residual 1.335 1.552 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C32 MQ7 G 502 " pdb=" C33 MQ7 G 502 " ideal model delta sigma weight residual 1.336 1.553 -0.217 2.00e-02 2.50e+03 1.18e+02 ... (remaining 18725 not shown) Histogram of bond angle deviations from ideal: 89.97 - 98.82: 96 98.82 - 107.68: 936 107.68 - 116.53: 12012 116.53 - 125.38: 12024 125.38 - 134.24: 338 Bond angle restraints: 25406 Sorted by residual: angle pdb="FE2 SF4 D 601 " pdb=" S1 SF4 D 601 " pdb="FE4 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE2 SF4 H 601 " pdb=" S1 SF4 H 601 " pdb="FE4 SF4 H 601 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 D 601 " pdb=" S4 SF4 D 601 " pdb="FE3 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 H 601 " pdb=" S4 SF4 H 601 " pdb="FE3 SF4 H 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE2 SF4 D 601 " pdb=" S3 SF4 D 601 " pdb="FE4 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 ... (remaining 25401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 11034 35.02 - 70.03: 370 70.03 - 105.04: 22 105.04 - 140.06: 0 140.06 - 175.07: 4 Dihedral angle restraints: 11430 sinusoidal: 4876 harmonic: 6554 Sorted by residual: dihedral pdb=" CA VAL C 197 " pdb=" C VAL C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL G 197 " pdb=" C VAL G 197 " pdb=" N PRO G 198 " pdb=" CA PRO G 198 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PRO C 198 " pdb=" C PRO C 198 " pdb=" N GLU C 199 " pdb=" CA GLU C 199 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 11427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 2798 0.166 - 0.331: 28 0.331 - 0.497: 2 0.497 - 0.662: 0 0.662 - 0.828: 16 Chirality restraints: 2844 Sorted by residual: chirality pdb="FE1 SF4 D 602 " pdb=" S2 SF4 D 602 " pdb=" S3 SF4 D 602 " pdb=" S4 SF4 D 602 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE1 SF4 H 602 " pdb=" S2 SF4 H 602 " pdb=" S3 SF4 H 602 " pdb=" S4 SF4 H 602 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE3 SF4 D 601 " pdb=" S1 SF4 D 601 " pdb=" S2 SF4 D 601 " pdb=" S4 SF4 D 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 2841 not shown) Planarity restraints: 3200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 MQ7 G 502 " 0.248 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C12 MQ7 G 502 " -0.516 2.00e-02 2.50e+03 pdb=" C13 MQ7 G 502 " 0.293 2.00e-02 2.50e+03 pdb=" C14 MQ7 G 502 " 0.021 2.00e-02 2.50e+03 pdb=" C15 MQ7 G 502 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 MQ7 C 502 " -0.248 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C12 MQ7 C 502 " 0.516 2.00e-02 2.50e+03 pdb=" C13 MQ7 C 502 " -0.293 2.00e-02 2.50e+03 pdb=" C14 MQ7 C 502 " -0.021 2.00e-02 2.50e+03 pdb=" C15 MQ7 C 502 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 MQ7 G 502 " -0.149 2.00e-02 2.50e+03 2.27e-01 6.43e+02 pdb=" C32 MQ7 G 502 " 0.329 2.00e-02 2.50e+03 pdb=" C33 MQ7 G 502 " -0.327 2.00e-02 2.50e+03 pdb=" C34 MQ7 G 502 " 0.141 2.00e-02 2.50e+03 pdb=" C35 MQ7 G 502 " 0.005 2.00e-02 2.50e+03 ... (remaining 3197 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 198 2.57 - 3.15: 13610 3.15 - 3.73: 29706 3.73 - 4.32: 45284 4.32 - 4.90: 73248 Nonbonded interactions: 162046 Sorted by model distance: nonbonded pdb=" O CYS E 6 " pdb=" O2B FAD E 301 " model vdw 1.984 2.440 nonbonded pdb=" O CYS A 6 " pdb=" O2B FAD A 301 " model vdw 1.984 2.440 nonbonded pdb=" OG1 THR A 97 " pdb=" O4' FAD A 301 " model vdw 2.002 2.440 nonbonded pdb=" OG1 THR E 97 " pdb=" O4' FAD E 301 " model vdw 2.002 2.440 nonbonded pdb=" O GLY E 127 " pdb=" O1P FAD E 301 " model vdw 2.045 3.040 ... (remaining 162041 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.000 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: 0.000 Extract box with map and model: 7.400 Check model and map are aligned: 0.300 Set scattering table: 0.200 Process input model: 56.880 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 0.221 18730 Z= 0.806 Angle : 1.422 16.342 25406 Z= 0.832 Chirality : 0.085 0.828 2844 Planarity : 0.016 0.288 3200 Dihedral : 16.975 175.074 7234 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 2.18 % Allowed : 7.48 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.13), residues: 2280 helix: -4.48 (0.08), residues: 776 sheet: -2.25 (0.22), residues: 404 loop : -2.60 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 327 HIS 0.004 0.001 HIS C 267 PHE 0.018 0.002 PHE B 476 TYR 0.021 0.002 TYR B 352 ARG 0.008 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 358 time to evaluate : 2.209 Fit side-chains REVERT: A 142 TYR cc_start: 0.8560 (m-10) cc_final: 0.8355 (m-10) REVERT: A 152 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: A 245 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 291 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6732 (mt-10) REVERT: C 370 TYR cc_start: 0.8636 (m-80) cc_final: 0.8406 (m-80) REVERT: C 371 LYS cc_start: 0.8240 (ttpt) cc_final: 0.8007 (ttpp) REVERT: C 390 LEU cc_start: 0.8571 (tt) cc_final: 0.8350 (tp) REVERT: C 435 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7049 (ptm160) REVERT: D 465 SER cc_start: 0.8103 (p) cc_final: 0.7578 (p) REVERT: D 517 ASN cc_start: 0.8194 (m-40) cc_final: 0.7979 (m110) REVERT: E 142 TYR cc_start: 0.8560 (m-10) cc_final: 0.8353 (m-10) REVERT: E 152 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: E 245 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7418 (mm) REVERT: G 291 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6730 (mt-10) REVERT: G 370 TYR cc_start: 0.8634 (m-80) cc_final: 0.8404 (m-80) REVERT: G 371 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8005 (ttpp) REVERT: G 390 LEU cc_start: 0.8571 (tt) cc_final: 0.8351 (tp) REVERT: G 435 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: H 465 SER cc_start: 0.8101 (p) cc_final: 0.7581 (p) REVERT: H 517 ASN cc_start: 0.8187 (m-40) cc_final: 0.7977 (m110) outliers start: 42 outliers final: 14 residues processed: 392 average time/residue: 1.6124 time to fit residues: 695.9235 Evaluate side-chains 256 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 471 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 0.8980 chunk 171 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 177 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 131 optimal weight: 0.6980 chunk 205 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 235 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 79 ASN C 101 ASN C 118 GLN C 168 ASN C 203 ASN C 324 ASN C 382 GLN C 392 ASN C 412 GLN D 448 ASN E 15 ASN E 235 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN G 79 ASN G 101 ASN G 118 GLN G 168 ASN G 203 ASN G 324 ASN G 382 GLN G 392 ASN G 412 GLN H 448 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18730 Z= 0.238 Angle : 0.593 7.758 25406 Z= 0.301 Chirality : 0.046 0.150 2844 Planarity : 0.005 0.063 3200 Dihedral : 13.020 165.852 2846 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.43 % Allowed : 15.38 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.80 (0.15), residues: 2280 helix: -3.11 (0.14), residues: 766 sheet: -2.00 (0.22), residues: 428 loop : -2.17 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 103 HIS 0.003 0.001 HIS C 93 PHE 0.013 0.001 PHE G 112 TYR 0.011 0.002 TYR G 258 ARG 0.009 0.000 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 234 time to evaluate : 2.331 Fit side-chains REVERT: A 154 ILE cc_start: 0.7491 (OUTLIER) cc_final: 0.7220 (mt) REVERT: C 165 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7622 (pp20) REVERT: D 470 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8283 (ttpt) REVERT: E 154 ILE cc_start: 0.7494 (OUTLIER) cc_final: 0.7221 (mt) REVERT: G 165 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7626 (pp20) REVERT: G 291 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6710 (mt-10) REVERT: H 470 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8283 (ttpt) outliers start: 66 outliers final: 25 residues processed: 286 average time/residue: 1.3344 time to fit residues: 430.7294 Evaluate side-chains 249 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 2.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 249 ASN Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain H residue 490 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 170 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 203 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 85 ASN C 101 ASN C 118 GLN C 324 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN G 85 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18730 Z= 0.297 Angle : 0.589 8.376 25406 Z= 0.299 Chirality : 0.047 0.144 2844 Planarity : 0.005 0.056 3200 Dihedral : 12.127 154.578 2798 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.59 % Allowed : 17.78 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.15), residues: 2280 helix: -2.40 (0.16), residues: 780 sheet: -1.89 (0.21), residues: 428 loop : -1.99 (0.17), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 103 HIS 0.003 0.001 HIS C 93 PHE 0.015 0.002 PHE B 382 TYR 0.011 0.002 TYR C 50 ARG 0.006 0.000 ARG H 451 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 230 time to evaluate : 2.186 Fit side-chains REVERT: A 154 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7130 (mt) REVERT: B 557 TYR cc_start: 0.8236 (t80) cc_final: 0.7980 (t80) REVERT: C 273 MET cc_start: 0.8360 (mtp) cc_final: 0.8061 (mtm) REVERT: C 291 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6603 (mt-10) REVERT: C 372 ASP cc_start: 0.7565 (m-30) cc_final: 0.7296 (m-30) REVERT: D 454 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7234 (mp0) REVERT: E 154 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.7135 (mt) REVERT: F 557 TYR cc_start: 0.8235 (t80) cc_final: 0.7979 (t80) REVERT: G 273 MET cc_start: 0.8357 (mtp) cc_final: 0.8060 (mtm) REVERT: G 372 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: H 454 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7235 (mp0) outliers start: 69 outliers final: 30 residues processed: 280 average time/residue: 1.3663 time to fit residues: 430.4783 Evaluate side-chains 245 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 210 time to evaluate : 2.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 372 ASP Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 472 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 0.9990 chunk 154 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 206 optimal weight: 0.2980 chunk 218 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 85 ASN C 101 ASN C 118 GLN C 324 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18730 Z= 0.256 Angle : 0.567 8.183 25406 Z= 0.286 Chirality : 0.046 0.151 2844 Planarity : 0.005 0.056 3200 Dihedral : 11.526 152.322 2798 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.74 % Allowed : 19.18 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.16), residues: 2280 helix: -1.87 (0.17), residues: 768 sheet: -1.69 (0.22), residues: 418 loop : -1.81 (0.17), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 103 HIS 0.003 0.001 HIS D 458 PHE 0.012 0.001 PHE G 112 TYR 0.011 0.001 TYR H 450 ARG 0.007 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 217 time to evaluate : 2.243 Fit side-chains REVERT: A 154 ILE cc_start: 0.7400 (OUTLIER) cc_final: 0.7146 (mt) REVERT: C 97 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7387 (tm-30) REVERT: C 273 MET cc_start: 0.8322 (mtp) cc_final: 0.8048 (mtm) REVERT: D 454 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: E 154 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7150 (mt) REVERT: G 97 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7384 (tm-30) REVERT: G 273 MET cc_start: 0.8318 (mtp) cc_final: 0.8048 (mtm) REVERT: H 454 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7163 (mp0) outliers start: 72 outliers final: 40 residues processed: 277 average time/residue: 1.4125 time to fit residues: 440.0296 Evaluate side-chains 260 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 214 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 162 optimal weight: 0.3980 chunk 90 optimal weight: 0.4980 chunk 186 optimal weight: 0.0670 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 111 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.5120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** B 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN C 85 ASN C 101 ASN C 118 GLN C 324 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN ** F 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 359 ASN G 85 ASN G 101 ASN G 118 GLN G 324 ASN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18730 Z= 0.190 Angle : 0.533 7.834 25406 Z= 0.267 Chirality : 0.045 0.153 2844 Planarity : 0.004 0.055 3200 Dihedral : 10.781 153.706 2798 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.31 % Allowed : 19.54 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.16), residues: 2280 helix: -1.43 (0.18), residues: 768 sheet: -1.45 (0.23), residues: 414 loop : -1.68 (0.17), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 103 HIS 0.002 0.001 HIS C 319 PHE 0.010 0.001 PHE C 112 TYR 0.012 0.001 TYR A 99 ARG 0.004 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 242 time to evaluate : 2.371 Fit side-chains REVERT: A 154 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.7047 (mt) REVERT: C 273 MET cc_start: 0.8281 (mtp) cc_final: 0.8035 (mtm) REVERT: C 431 LEU cc_start: 0.6048 (OUTLIER) cc_final: 0.5392 (pt) REVERT: E 154 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.7049 (mt) REVERT: G 273 MET cc_start: 0.8280 (mtp) cc_final: 0.8034 (mtm) REVERT: G 372 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7174 (m-30) REVERT: G 431 LEU cc_start: 0.6040 (OUTLIER) cc_final: 0.5393 (pt) outliers start: 83 outliers final: 39 residues processed: 309 average time/residue: 1.3191 time to fit residues: 459.5229 Evaluate side-chains 270 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 226 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 253 LYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 253 LYS Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 372 ASP Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 0.0770 chunk 196 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 128 optimal weight: 8.9990 chunk 53 optimal weight: 0.0040 chunk 218 optimal weight: 0.0060 chunk 181 optimal weight: 1.9990 chunk 101 optimal weight: 0.0270 chunk 18 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 overall best weight: 0.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN B 547 GLN C 101 ASN C 118 GLN C 324 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN F 547 GLN G 101 ASN G 118 GLN ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 18730 Z= 0.139 Angle : 0.504 6.971 25406 Z= 0.252 Chirality : 0.044 0.152 2844 Planarity : 0.004 0.048 3200 Dihedral : 9.720 157.676 2798 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.07 % Allowed : 21.41 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2280 helix: -0.93 (0.19), residues: 752 sheet: -1.21 (0.23), residues: 414 loop : -1.53 (0.18), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 327 HIS 0.003 0.001 HIS G 319 PHE 0.009 0.001 PHE C 231 TYR 0.013 0.001 TYR E 99 ARG 0.003 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 251 time to evaluate : 2.023 Fit side-chains REVERT: A 154 ILE cc_start: 0.7229 (OUTLIER) cc_final: 0.6980 (mt) REVERT: B 373 MET cc_start: 0.7273 (mmt) cc_final: 0.6962 (mpm) REVERT: C 273 MET cc_start: 0.8237 (mtp) cc_final: 0.8025 (mtm) REVERT: C 431 LEU cc_start: 0.5787 (OUTLIER) cc_final: 0.5424 (pt) REVERT: D 460 LYS cc_start: 0.7749 (mppt) cc_final: 0.7536 (mppt) REVERT: D 517 ASN cc_start: 0.8017 (m110) cc_final: 0.7817 (m110) REVERT: E 154 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6984 (mt) REVERT: G 273 MET cc_start: 0.8228 (mtp) cc_final: 0.8020 (mtm) REVERT: G 372 ASP cc_start: 0.7428 (OUTLIER) cc_final: 0.7206 (m-30) REVERT: G 431 LEU cc_start: 0.5793 (OUTLIER) cc_final: 0.5422 (pt) REVERT: H 460 LYS cc_start: 0.7752 (mppt) cc_final: 0.7534 (mppt) outliers start: 59 outliers final: 24 residues processed: 292 average time/residue: 1.3024 time to fit residues: 429.5019 Evaluate side-chains 245 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 216 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 372 ASP Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 159 optimal weight: 8.9990 chunk 123 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 217 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 211 ASN C 324 ASN F 323 ASN F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 211 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18730 Z= 0.306 Angle : 0.593 7.514 25406 Z= 0.293 Chirality : 0.047 0.143 2844 Planarity : 0.004 0.054 3200 Dihedral : 9.669 151.870 2798 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.85 % Allowed : 21.99 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.17), residues: 2280 helix: -0.97 (0.18), residues: 778 sheet: -1.22 (0.24), residues: 414 loop : -1.50 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 103 HIS 0.003 0.001 HIS G 185 PHE 0.013 0.002 PHE B 382 TYR 0.012 0.002 TYR F 352 ARG 0.003 0.000 ARG C 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 227 time to evaluate : 2.276 Fit side-chains REVERT: A 154 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.7080 (mt) REVERT: B 373 MET cc_start: 0.7340 (mmt) cc_final: 0.7029 (mpm) REVERT: B 557 TYR cc_start: 0.8220 (t80) cc_final: 0.7892 (t80) REVERT: C 273 MET cc_start: 0.8328 (mtp) cc_final: 0.8125 (mtm) REVERT: C 431 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5397 (pt) REVERT: D 454 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: E 154 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7079 (mt) REVERT: F 373 MET cc_start: 0.7445 (mmt) cc_final: 0.7165 (mpm) REVERT: F 557 TYR cc_start: 0.8219 (t80) cc_final: 0.7892 (t80) REVERT: G 372 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.7176 (m-30) REVERT: G 431 LEU cc_start: 0.6043 (OUTLIER) cc_final: 0.5397 (pt) REVERT: H 454 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7133 (mp0) outliers start: 74 outliers final: 38 residues processed: 283 average time/residue: 1.3276 time to fit residues: 422.8721 Evaluate side-chains 256 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 2.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 295 LEU Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 372 ASP Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 0.3980 chunk 86 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 171 optimal weight: 0.0670 chunk 198 optimal weight: 1.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18730 Z= 0.192 Angle : 0.538 9.093 25406 Z= 0.267 Chirality : 0.045 0.149 2844 Planarity : 0.004 0.055 3200 Dihedral : 9.222 154.699 2798 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.86 % Allowed : 23.44 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.17), residues: 2280 helix: -0.81 (0.19), residues: 772 sheet: -1.14 (0.24), residues: 414 loop : -1.49 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 327 HIS 0.002 0.001 HIS G 185 PHE 0.011 0.001 PHE G 112 TYR 0.012 0.001 TYR C 295 ARG 0.003 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 229 time to evaluate : 2.133 Fit side-chains REVERT: A 154 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6999 (mt) REVERT: B 373 MET cc_start: 0.7283 (mmt) cc_final: 0.7001 (mpm) REVERT: B 557 TYR cc_start: 0.8190 (t80) cc_final: 0.7942 (t80) REVERT: C 431 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5392 (pt) REVERT: D 454 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: E 154 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6999 (mt) REVERT: F 373 MET cc_start: 0.7297 (mmt) cc_final: 0.6999 (mpm) REVERT: F 557 TYR cc_start: 0.8189 (t80) cc_final: 0.7946 (t80) REVERT: G 431 LEU cc_start: 0.5913 (OUTLIER) cc_final: 0.5391 (pt) REVERT: H 454 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7091 (mp0) outliers start: 55 outliers final: 35 residues processed: 269 average time/residue: 1.3147 time to fit residues: 399.0742 Evaluate side-chains 257 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 216 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 350 ILE Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.8980 chunk 190 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 122 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 133 optimal weight: 0.5980 chunk 214 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18730 Z= 0.222 Angle : 0.562 11.470 25406 Z= 0.277 Chirality : 0.046 0.143 2844 Planarity : 0.004 0.055 3200 Dihedral : 9.250 157.204 2798 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.01 % Allowed : 23.65 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2280 helix: -0.75 (0.19), residues: 774 sheet: -1.16 (0.23), residues: 422 loop : -1.41 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 327 HIS 0.002 0.001 HIS B 441 PHE 0.011 0.001 PHE C 112 TYR 0.014 0.001 TYR E 99 ARG 0.003 0.000 ARG D 451 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 2.220 Fit side-chains REVERT: A 154 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.7011 (mt) REVERT: A 273 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6260 (tt0) REVERT: B 373 MET cc_start: 0.7273 (mmt) cc_final: 0.7002 (mpm) REVERT: B 557 TYR cc_start: 0.8228 (t80) cc_final: 0.7913 (t80) REVERT: C 431 LEU cc_start: 0.5974 (OUTLIER) cc_final: 0.5395 (pt) REVERT: D 454 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: E 154 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.7012 (mt) REVERT: E 273 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6260 (tt0) REVERT: F 373 MET cc_start: 0.7296 (mmt) cc_final: 0.7021 (mpm) REVERT: F 489 GLN cc_start: 0.7735 (pm20) cc_final: 0.7376 (pm20) REVERT: F 557 TYR cc_start: 0.8227 (t80) cc_final: 0.7914 (t80) REVERT: G 431 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5397 (pt) REVERT: H 454 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7088 (mp0) outliers start: 58 outliers final: 39 residues processed: 268 average time/residue: 1.3223 time to fit residues: 399.2729 Evaluate side-chains 269 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 2.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 490 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.0870 chunk 149 optimal weight: 4.9990 chunk 225 optimal weight: 0.2980 chunk 207 optimal weight: 2.9990 chunk 179 optimal weight: 0.3980 chunk 18 optimal weight: 0.6980 chunk 138 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 142 optimal weight: 1.9990 chunk 190 optimal weight: 0.8980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 118 GLN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN G 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18730 Z= 0.178 Angle : 0.548 12.948 25406 Z= 0.270 Chirality : 0.045 0.148 2844 Planarity : 0.004 0.053 3200 Dihedral : 9.074 159.509 2798 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.60 % Allowed : 24.17 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.17), residues: 2280 helix: -0.61 (0.19), residues: 772 sheet: -1.07 (0.24), residues: 422 loop : -1.38 (0.18), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 327 HIS 0.003 0.001 HIS G 185 PHE 0.010 0.001 PHE G 112 TYR 0.008 0.001 TYR F 377 ARG 0.003 0.000 ARG H 451 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 2.247 Fit side-chains REVERT: A 154 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6954 (mt) REVERT: B 373 MET cc_start: 0.7228 (mmt) cc_final: 0.7004 (mpm) REVERT: C 431 LEU cc_start: 0.5897 (OUTLIER) cc_final: 0.5394 (pt) REVERT: D 454 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: E 154 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6952 (mt) REVERT: F 373 MET cc_start: 0.7269 (mmt) cc_final: 0.7019 (mpm) REVERT: F 489 GLN cc_start: 0.7730 (pm20) cc_final: 0.7371 (pm20) REVERT: G 431 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5398 (pt) REVERT: H 454 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7052 (mp0) outliers start: 50 outliers final: 34 residues processed: 271 average time/residue: 1.3579 time to fit residues: 415.7270 Evaluate side-chains 265 residues out of total 1924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 225 time to evaluate : 2.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain D residue 454 GLU Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 60 THR Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 490 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 294 TYR Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain H residue 454 GLU Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 184 optimal weight: 1.9990 chunk 22 optimal weight: 0.0970 chunk 33 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 118 GLN F 355 ASN F 359 ASN G 118 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.160067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.119609 restraints weight = 20290.570| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.73 r_work: 0.3096 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18730 Z= 0.321 Angle : 0.616 7.416 25406 Z= 0.305 Chirality : 0.048 0.140 2844 Planarity : 0.004 0.057 3200 Dihedral : 9.367 156.245 2798 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.96 % Allowed : 24.27 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.17), residues: 2280 helix: -0.84 (0.18), residues: 798 sheet: -1.09 (0.24), residues: 414 loop : -1.38 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 327 HIS 0.004 0.001 HIS G 185 PHE 0.014 0.002 PHE B 382 TYR 0.021 0.002 TYR C 295 ARG 0.004 0.000 ARG D 451 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7377.61 seconds wall clock time: 133 minutes 37.92 seconds (8017.92 seconds total)