Starting phenix.real_space_refine (version: dev) on Wed Feb 22 18:04:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6li9_0903/02_2023/6li9_0903_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A ASP 267": "OD1" <-> "OD2" Residue "A ARG 270": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 288": "NH1" <-> "NH2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ASP 512": "OD1" <-> "OD2" Residue "A TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "A PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 664": "OD1" <-> "OD2" Residue "B TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 487": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ASP 147": "OD1" <-> "OD2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C ASP 235": "OD1" <-> "OD2" Residue "C ASP 267": "OD1" <-> "OD2" Residue "C ARG 270": "NH1" <-> "NH2" Residue "C TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C GLU 295": "OE1" <-> "OE2" Residue "C GLU 298": "OE1" <-> "OE2" Residue "C GLU 321": "OE1" <-> "OE2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ASP 369": "OD1" <-> "OD2" Residue "C GLU 426": "OE1" <-> "OE2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C ASP 512": "OD1" <-> "OD2" Residue "C TYR 533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 539": "OD1" <-> "OD2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C GLU 585": "OE1" <-> "OE2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "C PHE 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 664": "OD1" <-> "OD2" Residue "D TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 282": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Residue "D GLU 478": "OE1" <-> "OE2" Residue "D GLU 487": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 17988 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "B" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "C" Number of atoms: 5084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 623, 5084 Classifications: {'peptide': 623} Link IDs: {'PTRANS': 25, 'TRANS': 597} Chain: "D" Number of atoms: 3538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3538 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 26, 'TRANS': 431} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 108 Unusual residues: {'3PH': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "C" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 116 Classifications: {'water': 116} Link IDs: {None: 115} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Time building chain proxies: 10.19, per 1000 atoms: 0.57 Number of scatterers: 17988 At special positions: 0 Unit cell: (81.825, 140.739, 138.557, 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) Ca 2 19.99 S 90 16.00 P 4 15.00 O 3500 8.00 N 2832 7.00 C 11560 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 114 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS A 242 " - pdb=" SG CYS A 273 " distance=2.04 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 666 " distance=2.03 Simple disulfide: pdb=" SG CYS C 114 " - pdb=" SG CYS D 144 " distance=2.03 Simple disulfide: pdb=" SG CYS C 242 " - pdb=" SG CYS C 273 " distance=2.04 Simple disulfide: pdb=" SG CYS C 571 " - pdb=" SG CYS C 666 " distance=2.03 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG E 1 " - " ASN A 261 " " NAG F 1 " - " ASN A 332 " " NAG G 1 " - " ASN A 495 " " NAG H 1 " - " ASN A 513 " " NAG I 1 " - " ASN A 575 " " NAG J 1 " - " ASN C 261 " " NAG K 1 " - " ASN C 332 " " NAG L 1 " - " ASN C 495 " " NAG M 1 " - " ASN C 513 " " NAG N 1 " - " ASN C 575 " Time building additional restraints: 7.16 Conformation dependent library (CDL) restraints added in 2.6 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 14 sheets defined 47.0% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.685A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 80 through 110 removed outlier: 3.669A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.682A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 120 No H-bonds generated for 'chain 'A' and resid 117 through 120' Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.643A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 202 Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.897A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP A 235 " --> pdb=" O LYS A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 290 through 306 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 357 through 371 removed outlier: 3.853A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.006A pdb=" N MET A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR A 397 " --> pdb=" O THR A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 434 Processing helix chain 'A' and resid 453 through 456 No H-bonds generated for 'chain 'A' and resid 453 through 456' Processing helix chain 'A' and resid 459 through 471 removed outlier: 4.863A pdb=" N ASN A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 515 through 518 Processing helix chain 'A' and resid 531 through 534 removed outlier: 4.474A pdb=" N HIS A 534 " --> pdb=" O SER A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 531 through 534' Processing helix chain 'A' and resid 538 through 541 No H-bonds generated for 'chain 'A' and resid 538 through 541' Processing helix chain 'A' and resid 548 through 561 Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 607 through 609 No H-bonds generated for 'chain 'A' and resid 607 through 609' Processing helix chain 'A' and resid 626 through 628 No H-bonds generated for 'chain 'A' and resid 626 through 628' Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.648A pdb=" N SER B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 56 Processing helix chain 'B' and resid 62 through 89 removed outlier: 3.946A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.611A pdb=" N ALA B 103 " --> pdb=" O TYR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 118 Processing helix chain 'B' and resid 120 through 140 removed outlier: 3.855A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Proline residue: B 139 - end of helix Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.738A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 177 through 200 removed outlier: 3.547A pdb=" N VAL B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 207 No H-bonds generated for 'chain 'B' and resid 205 through 207' Processing helix chain 'B' and resid 220 through 230 Processing helix chain 'B' and resid 236 through 238 No H-bonds generated for 'chain 'B' and resid 236 through 238' Processing helix chain 'B' and resid 251 through 274 removed outlier: 3.526A pdb=" N ILE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Proline residue: B 261 - end of helix Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.618A pdb=" N LEU B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 280 through 284' Processing helix chain 'B' and resid 289 through 296 removed outlier: 3.598A pdb=" N ARG B 296 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 318 removed outlier: 3.623A pdb=" N VAL B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Proline residue: B 306 - end of helix removed outlier: 4.495A pdb=" N VAL B 309 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA B 310 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 313 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 317 " --> pdb=" O ILE B 314 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.643A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.921A pdb=" N ILE B 367 " --> pdb=" O THR B 363 " (cutoff:3.500A) Proline residue: B 368 - end of helix Processing helix chain 'B' and resid 374 through 398 removed outlier: 3.800A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 387 " --> pdb=" O TRP B 383 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 389 " --> pdb=" O PHE B 385 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.512A pdb=" N VAL B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 435 through 454 removed outlier: 3.645A pdb=" N TYR B 439 " --> pdb=" O GLU B 436 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS B 440 " --> pdb=" O TYR B 437 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 442 " --> pdb=" O TYR B 439 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 443 " --> pdb=" O CYS B 440 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU B 445 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 446 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 449 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 451 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 453 " --> pdb=" O PHE B 450 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 454 " --> pdb=" O TYR B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 removed outlier: 4.005A pdb=" N LYS B 467 " --> pdb=" O GLN B 463 " (cutoff:3.500A) Proline residue: B 468 - end of helix Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.685A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN C 75 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 70 through 75' Processing helix chain 'C' and resid 80 through 110 removed outlier: 3.669A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.682A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 104 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 120 No H-bonds generated for 'chain 'C' and resid 117 through 120' Processing helix chain 'C' and resid 128 through 130 No H-bonds generated for 'chain 'C' and resid 128 through 130' Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.643A pdb=" N LYS C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 149 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ASP C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYR C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 202 Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.897A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 231 through 235' Processing helix chain 'C' and resid 290 through 306 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'C' and resid 357 through 371 removed outlier: 3.853A pdb=" N GLN C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.006A pdb=" N MET C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N TYR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N TYR C 397 " --> pdb=" O THR C 393 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 434 Processing helix chain 'C' and resid 453 through 456 No H-bonds generated for 'chain 'C' and resid 453 through 456' Processing helix chain 'C' and resid 459 through 471 removed outlier: 4.863A pdb=" N ASN C 463 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL C 464 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET C 465 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU C 468 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR C 471 " --> pdb=" O LEU C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 515 through 518 Processing helix chain 'C' and resid 531 through 534 removed outlier: 4.474A pdb=" N HIS C 534 " --> pdb=" O SER C 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 531 through 534' Processing helix chain 'C' and resid 538 through 541 No H-bonds generated for 'chain 'C' and resid 538 through 541' Processing helix chain 'C' and resid 548 through 561 Processing helix chain 'C' and resid 563 through 566 No H-bonds generated for 'chain 'C' and resid 563 through 566' Processing helix chain 'C' and resid 607 through 609 No H-bonds generated for 'chain 'C' and resid 607 through 609' Processing helix chain 'C' and resid 626 through 628 No H-bonds generated for 'chain 'C' and resid 626 through 628' Processing helix chain 'C' and resid 663 through 665 No H-bonds generated for 'chain 'C' and resid 663 through 665' Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.648A pdb=" N SER D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 62 through 89 removed outlier: 3.946A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS D 82 " --> pdb=" O LEU D 78 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.611A pdb=" N ALA D 103 " --> pdb=" O TYR D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 118 Processing helix chain 'D' and resid 120 through 140 removed outlier: 3.855A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Proline residue: D 139 - end of helix Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.738A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 177 through 200 removed outlier: 3.547A pdb=" N VAL D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 220 through 230 Processing helix chain 'D' and resid 236 through 238 No H-bonds generated for 'chain 'D' and resid 236 through 238' Processing helix chain 'D' and resid 251 through 274 removed outlier: 3.526A pdb=" N ILE D 257 " --> pdb=" O PRO D 253 " (cutoff:3.500A) Proline residue: D 261 - end of helix Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.618A pdb=" N LEU D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 284' Processing helix chain 'D' and resid 289 through 296 removed outlier: 3.598A pdb=" N ARG D 296 " --> pdb=" O THR D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 318 removed outlier: 3.623A pdb=" N VAL D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Proline residue: D 306 - end of helix removed outlier: 4.495A pdb=" N VAL D 309 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA D 310 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE D 314 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY D 315 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 317 " --> pdb=" O ILE D 314 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASN D 318 " --> pdb=" O GLY D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 removed outlier: 3.643A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 368 removed outlier: 3.921A pdb=" N ILE D 367 " --> pdb=" O THR D 363 " (cutoff:3.500A) Proline residue: D 368 - end of helix Processing helix chain 'D' and resid 374 through 398 removed outlier: 3.800A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY D 387 " --> pdb=" O TRP D 383 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR D 389 " --> pdb=" O PHE D 385 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 398 " --> pdb=" O ILE D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 431 removed outlier: 3.512A pdb=" N VAL D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 435 through 454 removed outlier: 3.645A pdb=" N TYR D 439 " --> pdb=" O GLU D 436 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N CYS D 440 " --> pdb=" O TYR D 437 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 442 " --> pdb=" O TYR D 439 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 443 " --> pdb=" O CYS D 440 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LEU D 445 " --> pdb=" O LEU D 442 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER D 446 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU D 449 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 451 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU D 453 " --> pdb=" O PHE D 450 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE D 454 " --> pdb=" O TYR D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 477 removed outlier: 4.005A pdb=" N LYS D 467 " --> pdb=" O GLN D 463 " (cutoff:3.500A) Proline residue: D 468 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.571A pdb=" N THR A 475 " --> pdb=" O TRP A 443 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR A 124 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A 160 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 126 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 162 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE A 162 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE A 208 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 310 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 211 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER A 312 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE A 380 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU A 313 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY A 382 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 264 through 267 removed outlier: 3.654A pdb=" N GLN A 272 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 569 through 572 removed outlier: 6.460A pdb=" N GLU A 649 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE A 620 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 603 through 605 Processing sheet with id= E, first strand: chain 'A' and resid 617 through 619 Processing sheet with id= F, first strand: chain 'A' and resid 673 through 675 Processing sheet with id= G, first strand: chain 'B' and resid 343 through 345 Processing sheet with id= H, first strand: chain 'C' and resid 442 through 444 removed outlier: 6.571A pdb=" N THR C 475 " --> pdb=" O TRP C 443 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR C 124 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL C 160 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 126 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE C 162 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LYS C 206 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE C 162 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 208 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY C 310 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE C 211 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N SER C 312 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE C 380 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N LEU C 313 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY C 382 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.654A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 569 through 572 removed outlier: 6.460A pdb=" N GLU C 649 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 620 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 603 through 605 Processing sheet with id= L, first strand: chain 'C' and resid 617 through 619 Processing sheet with id= M, first strand: chain 'C' and resid 673 through 675 Processing sheet with id= N, first strand: chain 'D' and resid 343 through 345 570 hydrogen bonds defined for protein. 1584 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: 5.63 Time building geometry restraints manager: 7.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4654 1.33 - 1.45: 3708 1.45 - 1.57: 9680 1.57 - 1.70: 6 1.70 - 1.82: 146 Bond restraints: 18194 Sorted by residual: bond pdb=" C31 3PH B 603 " pdb=" O31 3PH B 603 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 603 " pdb=" O31 3PH D 603 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH B 602 " pdb=" O31 3PH B 602 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C31 3PH D 602 " pdb=" O31 3PH D 602 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C21 3PH B 602 " pdb=" O21 3PH B 602 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18189 not shown) Histogram of bond angle deviations from ideal: 99.61 - 106.68: 574 106.68 - 113.76: 10106 113.76 - 120.83: 8408 120.83 - 127.90: 5430 127.90 - 134.97: 204 Bond angle restraints: 24722 Sorted by residual: angle pdb=" C2 NAG M 1 " pdb=" N2 NAG M 1 " pdb=" C7 NAG M 1 " ideal model delta sigma weight residual 123.12 134.21 -11.09 1.28e+00 6.08e-01 7.48e+01 angle pdb=" C2 NAG H 1 " pdb=" N2 NAG H 1 " pdb=" C7 NAG H 1 " ideal model delta sigma weight residual 123.12 134.21 -11.09 1.28e+00 6.08e-01 7.48e+01 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 123.12 134.05 -10.93 1.28e+00 6.08e-01 7.26e+01 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 123.12 134.05 -10.93 1.28e+00 6.08e-01 7.26e+01 angle pdb=" C2 NAG G 2 " pdb=" N2 NAG G 2 " pdb=" C7 NAG G 2 " ideal model delta sigma weight residual 123.12 133.90 -10.78 1.28e+00 6.08e-01 7.06e+01 ... (remaining 24717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 10030 21.69 - 43.37: 546 43.37 - 65.06: 60 65.06 - 86.75: 28 86.75 - 108.43: 6 Dihedral angle restraints: 10670 sinusoidal: 4350 harmonic: 6320 Sorted by residual: dihedral pdb=" CB CYS C 114 " pdb=" SG CYS C 114 " pdb=" SG CYS D 144 " pdb=" CB CYS D 144 " ideal model delta sinusoidal sigma weight residual 93.00 146.82 -53.82 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" CB CYS A 114 " pdb=" SG CYS A 114 " pdb=" SG CYS B 144 " pdb=" CB CYS B 144 " ideal model delta sinusoidal sigma weight residual 93.00 146.82 -53.82 1 1.00e+01 1.00e-02 3.93e+01 dihedral pdb=" C2 NAG L 1 " pdb=" C1 NAG L 1 " pdb=" O5 NAG L 1 " pdb=" C5 NAG L 1 " ideal model delta sinusoidal sigma weight residual -50.00 58.43 -108.43 1 2.00e+01 2.50e-03 3.16e+01 ... (remaining 10667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.180: 2792 0.180 - 0.360: 16 0.360 - 0.540: 8 0.540 - 0.719: 2 0.719 - 0.899: 2 Chirality restraints: 2820 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 261 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 261 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.50 -0.90 2.00e-01 2.50e+01 2.02e+01 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 513 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 2817 not shown) Planarity restraints: 3070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO B 428 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 427 " -0.046 5.00e-02 4.00e+02 6.86e-02 7.54e+00 pdb=" N PRO D 428 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 428 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 428 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 370 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.76e+00 pdb=" C ASP B 370 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP B 370 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE B 371 " -0.015 2.00e-02 2.50e+03 ... (remaining 3067 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 4672 2.79 - 3.32: 15619 3.32 - 3.85: 30834 3.85 - 4.37: 38778 4.37 - 4.90: 61248 Nonbonded interactions: 151151 Sorted by model distance: nonbonded pdb=" OG SER D 379 " pdb=" O HOH D 701 " model vdw 2.265 2.440 nonbonded pdb=" OG SER B 379 " pdb=" O HOH B 701 " model vdw 2.265 2.440 nonbonded pdb=" OD1 ASP D 233 " pdb=" O HOH D 702 " model vdw 2.292 2.440 nonbonded pdb=" OD1 ASP B 233 " pdb=" O HOH B 702 " model vdw 2.292 2.440 nonbonded pdb=" O LEU D 238 " pdb=" OG1 THR D 242 " model vdw 2.302 2.440 ... (remaining 151146 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 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 P 4 5.49 5 S 90 5.16 5 C 11560 2.51 5 N 2832 2.21 5 O 3500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.540 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: 0.010 Extract box with map and model: 8.550 Check model and map are aligned: 0.250 Process input model: 45.390 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.007 0.122 18194 Z= 0.457 Angle : 0.995 11.094 24722 Z= 0.563 Chirality : 0.066 0.899 2820 Planarity : 0.007 0.069 3060 Dihedral : 13.936 108.432 6600 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.31 (0.14), residues: 2154 helix: -4.29 (0.07), residues: 1018 sheet: 0.35 (0.37), residues: 160 loop : -1.57 (0.18), residues: 976 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 366 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 370 average time/residue: 1.2508 time to fit residues: 521.0062 Evaluate side-chains 254 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.8724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 8.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 201 HIS A 220 HIS A 244 HIS A 324 HIS A 370 GLN A 422 ASN A 442 ASN A 524 ASN A 598 ASN A 609 ASN A 654 ASN A 670 ASN B 166 ASN B 271 ASN B 285 GLN B 336 HIS B 372 ASN C 125 GLN C 201 HIS C 220 HIS C 244 HIS C 324 HIS C 370 GLN C 422 ASN C 442 ASN C 524 ASN C 598 ASN C 609 ASN C 654 ASN C 670 ASN D 166 ASN D 271 ASN D 285 GLN D 336 HIS D 372 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.075 18194 Z= 0.425 Angle : 0.848 11.648 24722 Z= 0.462 Chirality : 0.063 0.963 2820 Planarity : 0.008 0.073 3060 Dihedral : 9.030 112.692 2616 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.18 % Favored : 95.73 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.53 (0.16), residues: 2154 helix: -2.27 (0.12), residues: 988 sheet: 0.54 (0.36), residues: 162 loop : -1.27 (0.18), residues: 1004 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 286 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 20 residues processed: 318 average time/residue: 1.2766 time to fit residues: 458.1123 Evaluate side-chains 274 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 254 time to evaluate : 1.974 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 14 residues processed: 6 average time/residue: 0.5519 time to fit residues: 7.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 132 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 194 optimal weight: 0.0270 chunk 210 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 193 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 156 optimal weight: 0.9980 overall best weight: 1.0840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 ASN A 370 GLN A 501 ASN A 524 ASN B 206 ASN C 135 ASN C 370 GLN C 501 ASN C 524 ASN D 206 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 18194 Z= 0.210 Angle : 0.669 8.891 24722 Z= 0.372 Chirality : 0.054 0.795 2820 Planarity : 0.005 0.058 3060 Dihedral : 7.477 56.178 2616 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.20 (0.17), residues: 2154 helix: -0.77 (0.15), residues: 970 sheet: 0.66 (0.37), residues: 142 loop : -0.92 (0.18), residues: 1042 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 266 time to evaluate : 2.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 14 residues processed: 306 average time/residue: 1.2921 time to fit residues: 444.4349 Evaluate side-chains 266 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 252 time to evaluate : 2.029 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 12 residues processed: 2 average time/residue: 0.1670 time to fit residues: 3.4162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 192 optimal weight: 1.9990 chunk 146 optimal weight: 0.6980 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 185 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 370 GLN A 501 ASN A 524 ASN B 166 ASN C 289 ASN C 370 GLN C 501 ASN C 524 ASN D 166 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 18194 Z= 0.267 Angle : 0.715 13.525 24722 Z= 0.384 Chirality : 0.056 0.826 2820 Planarity : 0.005 0.056 3060 Dihedral : 7.440 57.380 2616 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.85 (0.17), residues: 2154 helix: -0.19 (0.16), residues: 950 sheet: -0.32 (0.35), residues: 192 loop : -0.88 (0.19), residues: 1012 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 264 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 24 residues processed: 306 average time/residue: 1.3047 time to fit residues: 447.9549 Evaluate side-chains 272 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 248 time to evaluate : 2.006 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 6 average time/residue: 0.9290 time to fit residues: 9.3054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 172 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 154 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 176 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 58 ASN B 166 ASN C 501 ASN D 58 ASN D 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 18194 Z= 0.347 Angle : 0.781 11.941 24722 Z= 0.421 Chirality : 0.060 0.898 2820 Planarity : 0.006 0.050 3060 Dihedral : 7.686 49.574 2616 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.55 % Favored : 95.36 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.73 (0.17), residues: 2154 helix: -0.16 (0.16), residues: 958 sheet: 0.55 (0.37), residues: 162 loop : -0.89 (0.19), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 263 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 321 average time/residue: 1.2205 time to fit residues: 442.7052 Evaluate side-chains 281 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 1.960 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 32 residues processed: 8 average time/residue: 0.2071 time to fit residues: 5.5101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 69 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN B 166 ASN B 474 GLN C 501 ASN D 166 ASN D 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 18194 Z= 0.204 Angle : 0.653 11.187 24722 Z= 0.354 Chirality : 0.054 0.772 2820 Planarity : 0.005 0.051 3060 Dihedral : 7.288 48.903 2616 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 3.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.30 (0.17), residues: 2154 helix: 0.34 (0.16), residues: 944 sheet: 0.47 (0.36), residues: 162 loop : -0.74 (0.19), residues: 1048 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 262 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 36 residues processed: 319 average time/residue: 1.3163 time to fit residues: 472.3861 Evaluate side-chains 275 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 239 time to evaluate : 2.011 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 33 residues processed: 3 average time/residue: 0.2231 time to fit residues: 3.8608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 199 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 174 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 206 optimal weight: 0.0370 chunk 129 optimal weight: 0.5980 chunk 125 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 460 GLN A 501 ASN A 510 GLN A 679 ASN B 166 ASN C 156 ASN C 460 GLN C 501 ASN C 510 GLN D 166 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 18194 Z= 0.153 Angle : 0.606 12.315 24722 Z= 0.326 Chirality : 0.050 0.681 2820 Planarity : 0.004 0.059 3060 Dihedral : 6.828 50.326 2616 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.05 (0.18), residues: 2154 helix: 0.57 (0.17), residues: 960 sheet: 0.46 (0.36), residues: 162 loop : -0.62 (0.19), residues: 1032 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 255 time to evaluate : 2.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 26 residues processed: 304 average time/residue: 1.2499 time to fit residues: 428.0771 Evaluate side-chains 258 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 1.861 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 0.1570 time to fit residues: 3.1809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 501 ASN B 166 ASN C 289 ASN C 501 ASN C 679 ASN D 166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18194 Z= 0.175 Angle : 0.629 16.330 24722 Z= 0.337 Chirality : 0.052 0.717 2820 Planarity : 0.004 0.060 3060 Dihedral : 6.843 52.932 2616 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 2.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.05 (0.18), residues: 2154 helix: 0.67 (0.17), residues: 964 sheet: 0.48 (0.37), residues: 162 loop : -0.59 (0.19), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 31 residues processed: 274 average time/residue: 1.3970 time to fit residues: 431.6057 Evaluate side-chains 258 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 227 time to evaluate : 1.997 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 27 residues processed: 4 average time/residue: 0.2868 time to fit residues: 4.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 197 optimal weight: 5.9990 chunk 180 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 115 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 181 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 679 ASN B 166 ASN C 501 ASN C 679 ASN D 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18194 Z= 0.163 Angle : 0.609 14.403 24722 Z= 0.327 Chirality : 0.051 0.694 2820 Planarity : 0.004 0.062 3060 Dihedral : 6.720 56.509 2616 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 2.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.18), residues: 2154 helix: 0.82 (0.17), residues: 958 sheet: 0.48 (0.37), residues: 162 loop : -0.56 (0.19), residues: 1034 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 240 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 29 residues processed: 274 average time/residue: 1.3688 time to fit residues: 420.4278 Evaluate side-chains 266 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 4 average time/residue: 0.2141 time to fit residues: 4.3111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 203 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 141 optimal weight: 1.9990 chunk 213 optimal weight: 7.9990 chunk 196 optimal weight: 0.0060 chunk 169 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 501 ASN A 679 ASN B 166 ASN C 289 ASN C 501 ASN D 166 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 18194 Z= 0.249 Angle : 0.697 14.408 24722 Z= 0.373 Chirality : 0.056 0.779 2820 Planarity : 0.005 0.061 3060 Dihedral : 7.037 55.920 2616 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.18), residues: 2154 helix: 0.68 (0.17), residues: 946 sheet: 0.48 (0.37), residues: 162 loop : -0.64 (0.19), residues: 1046 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 235 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 26 residues processed: 266 average time/residue: 1.3940 time to fit residues: 414.3340 Evaluate side-chains 252 residues out of total 1894 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 226 time to evaluate : 2.222 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 26 residues processed: 2 average time/residue: 0.2042 time to fit residues: 3.5228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 180 optimal weight: 0.3980 chunk 52 optimal weight: 0.2980 chunk 156 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 174 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN A 679 ASN B 166 ASN C 501 ASN C 679 ASN D 166 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.209372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167131 restraints weight = 15533.406| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 0.87 r_work: 0.3413 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work: 0.3129 rms_B_bonded: 3.87 restraints_weight: 0.1250 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 18194 Z= 0.163 Angle : 0.615 14.348 24722 Z= 0.328 Chirality : 0.051 0.681 2820 Planarity : 0.004 0.063 3060 Dihedral : 6.733 54.053 2616 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.17 (0.18), residues: 2154 helix: 0.78 (0.17), residues: 948 sheet: 0.49 (0.37), residues: 162 loop : -0.51 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 7336.92 seconds wall clock time: 132 minutes 41.25 seconds (7961.25 seconds total)