Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:26:29 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lid_0904/12_2022/6lid_0904_updated_updated.pdb" } resolution = 2.7 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 83": "NH1" <-> "NH2" Residue "A GLU 120": "OE1" <-> "OE2" Residue "A ARG 174": "NH1" <-> "NH2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ARG 270": "NH1" <-> "NH2" 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 GLU 384": "OE1" <-> "OE2" Residue "A TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 521": "OE1" <-> "OE2" Residue "A ARG 574": "NH1" <-> "NH2" Residue "A ARG 591": "NH1" <-> "NH2" Residue "A ARG 621": "NH1" <-> "NH2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "B ARG 400": "NH1" <-> "NH2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C ARG 174": "NH1" <-> "NH2" Residue "C GLU 268": "OE1" <-> "OE2" Residue "C ARG 270": "NH1" <-> "NH2" 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 GLU 384": "OE1" <-> "OE2" Residue "C TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 456": "NH1" <-> "NH2" Residue "C GLU 482": "OE1" <-> "OE2" Residue "C GLU 483": "OE1" <-> "OE2" Residue "C GLU 521": "OE1" <-> "OE2" Residue "C ARG 574": "NH1" <-> "NH2" Residue "C ARG 591": "NH1" <-> "NH2" Residue "C ARG 621": "NH1" <-> "NH2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 212": "OE1" <-> "OE2" Residue "D ARG 400": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 17964 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: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'3PH': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 10.31, per 1000 atoms: 0.57 Number of scatterers: 17964 At special positions: 0 Unit cell: (81.825, 138.557, 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 3496 8.00 N 2824 7.00 C 11548 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=2.86 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=2.95 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: 7.82 Conformation dependent library (CDL) restraints added in 2.9 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: 4048 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 12 sheets defined 47.0% alpha, 6.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.606A pdb=" N PHE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 4.903A 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: 3.581A pdb=" N ILE A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Proline residue: A 85 - end of helix removed outlier: 3.841A pdb=" N LEU A 89 " --> pdb=" O PRO A 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 93 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 106 " --> pdb=" O ALA A 102 " (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: 3.558A pdb=" N LYS A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ASP A 150 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR A 151 " --> pdb=" O ASP A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 203 removed outlier: 3.619A pdb=" N LYS A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.980A pdb=" N THR A 234 " --> pdb=" O GLY A 231 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.936A pdb=" N GLN A 370 " --> pdb=" O GLN A 366 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR A 371 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 397 removed outlier: 4.176A pdb=" N MET A 395 " --> pdb=" O ASP A 391 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TYR A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) removed outlier: 4.498A 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: 3.544A pdb=" N VAL A 462 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN A 463 " --> pdb=" O GLN A 460 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 464 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET A 465 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 467 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 468 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 3.631A 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 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 656 through 658 No H-bonds generated for 'chain 'A' and resid 656 through 658' 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: 3.837A pdb=" N ILE B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.506A pdb=" N PHE B 49 " --> pdb=" O SER B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 51 through 56 Processing helix chain 'B' and resid 62 through 90 removed outlier: 3.514A pdb=" N ILE B 67 " --> pdb=" O GLY B 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP B 69 " --> pdb=" O CYS B 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 103 removed outlier: 3.649A pdb=" N GLU B 102 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 3.535A 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 137 removed outlier: 3.806A pdb=" N TYR B 135 " --> pdb=" O SER B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 165 removed outlier: 3.519A pdb=" N ALA B 157 " --> pdb=" O CYS B 153 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR B 164 " --> pdb=" O LEU B 160 " (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 201 removed outlier: 3.607A pdb=" N LYS B 184 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE B 187 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE B 191 " --> pdb=" O ILE B 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 198 " --> pdb=" O SER B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 230 removed outlier: 3.621A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 223 " --> pdb=" O GLY B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 251 through 277 Proline residue: B 261 - end of helix removed outlier: 4.168A pdb=" N VAL B 277 " --> pdb=" O SER B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.709A 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 294 Processing helix chain 'B' and resid 302 through 321 removed outlier: 3.989A pdb=" N VAL B 305 " --> pdb=" O SER B 302 " (cutoff:3.500A) Proline residue: B 306 - end of helix removed outlier: 4.428A pdb=" N VAL B 309 " --> pdb=" O PRO B 306 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 311 " --> pdb=" O PHE B 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 313 " --> pdb=" O ALA B 310 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE B 314 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY B 315 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 318 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 319 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR B 320 " --> pdb=" O ALA B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.507A pdb=" N VAL B 330 " --> pdb=" O ARG B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 removed outlier: 3.869A 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 375 through 397 removed outlier: 3.847A pdb=" N ALA B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B 394 " --> pdb=" O ILE B 390 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 397 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 431 removed outlier: 3.511A pdb=" N SER B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 422 " --> pdb=" O THR B 418 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) Proline residue: B 428 - end of helix Processing helix chain 'B' and resid 436 through 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' Processing helix chain 'B' and resid 441 through 454 removed outlier: 3.726A pdb=" N GLY B 447 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 449 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 477 Proline residue: B 468 - end of helix removed outlier: 3.510A pdb=" N MET B 475 " --> pdb=" O MET B 471 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 75 removed outlier: 3.606A pdb=" N PHE C 74 " --> pdb=" O LYS C 70 " (cutoff:3.500A) removed outlier: 4.903A 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: 3.581A pdb=" N ILE C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Proline residue: C 85 - end of helix removed outlier: 3.841A pdb=" N LEU C 89 " --> pdb=" O PRO C 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR C 93 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 96 " --> pdb=" O LEU C 92 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 106 " --> pdb=" O ALA C 102 " (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: 3.557A pdb=" N LYS C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASP C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N TYR C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 203 removed outlier: 3.619A pdb=" N LYS C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 231 through 235 removed outlier: 3.980A pdb=" N THR C 234 " --> pdb=" O GLY C 231 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.936A pdb=" N GLN C 370 " --> pdb=" O GLN C 366 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR C 371 " --> pdb=" O THR C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 397 removed outlier: 4.177A pdb=" N MET C 395 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) removed outlier: 4.499A 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: 3.544A pdb=" N VAL C 462 " --> pdb=" O ASN C 459 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ASN C 463 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N VAL C 464 " --> pdb=" O TYR C 461 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 465 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET C 467 " --> pdb=" O VAL C 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 468 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 470 " --> pdb=" O MET C 467 " (cutoff:3.500A) removed outlier: 3.632A 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 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 656 through 658 No H-bonds generated for 'chain 'C' and resid 656 through 658' 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: 3.837A pdb=" N ILE D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 49 removed outlier: 3.506A pdb=" N PHE D 49 " --> pdb=" O SER D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 46 through 49' Processing helix chain 'D' and resid 51 through 56 Processing helix chain 'D' and resid 62 through 90 removed outlier: 3.513A pdb=" N ILE D 67 " --> pdb=" O GLY D 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TRP D 69 " --> pdb=" O CYS D 65 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR D 88 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE D 90 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 103 removed outlier: 3.649A pdb=" N GLU D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 3.534A 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 137 removed outlier: 3.806A pdb=" N TYR D 135 " --> pdb=" O SER D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.518A pdb=" N ALA D 157 " --> pdb=" O CYS D 153 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR D 164 " --> pdb=" O LEU D 160 " (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 201 removed outlier: 3.606A pdb=" N LYS D 184 " --> pdb=" O PHE D 180 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 187 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE D 191 " --> pdb=" O ILE D 187 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU D 198 " --> pdb=" O SER D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 230 removed outlier: 3.621A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU D 223 " --> pdb=" O GLY D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 251 through 277 Proline residue: D 261 - end of helix removed outlier: 4.168A pdb=" N VAL D 277 " --> pdb=" O SER D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.709A 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 294 Processing helix chain 'D' and resid 302 through 321 removed outlier: 3.989A pdb=" N VAL D 305 " --> pdb=" O SER D 302 " (cutoff:3.500A) Proline residue: D 306 - end of helix removed outlier: 4.428A pdb=" N VAL D 309 " --> pdb=" O PRO D 306 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 311 " --> pdb=" O PHE D 308 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR D 313 " --> pdb=" O ALA D 310 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE D 314 " --> pdb=" O PHE D 311 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLY D 315 " --> pdb=" O SER D 312 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN D 318 " --> pdb=" O GLY D 315 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY D 319 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 320 " --> pdb=" O ALA D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.507A pdb=" N VAL D 330 " --> pdb=" O ARG D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 368 removed outlier: 3.869A 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 375 through 397 removed outlier: 3.848A pdb=" N ALA D 381 " --> pdb=" O TYR D 377 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE D 394 " --> pdb=" O ILE D 390 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 431 removed outlier: 3.510A pdb=" N SER D 421 " --> pdb=" O MET D 417 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D 422 " --> pdb=" O THR D 418 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL D 425 " --> pdb=" O SER D 421 " (cutoff:3.500A) Proline residue: D 428 - end of helix Processing helix chain 'D' and resid 436 through 439 No H-bonds generated for 'chain 'D' and resid 436 through 439' Processing helix chain 'D' and resid 441 through 454 removed outlier: 3.727A pdb=" N GLY D 447 " --> pdb=" O PHE D 443 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 448 " --> pdb=" O ILE D 444 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU D 449 " --> pdb=" O LEU D 445 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 450 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 477 Proline residue: D 468 - end of helix removed outlier: 3.511A pdb=" N MET D 475 " --> pdb=" O MET D 471 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET D 477 " --> pdb=" O LEU D 473 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 442 through 444 removed outlier: 6.544A pdb=" N THR A 475 " --> pdb=" O TRP A 443 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET A 123 " --> pdb=" O THR A 478 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR A 124 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL A 160 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE A 126 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 162 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 206 " --> pdb=" O VAL A 160 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE A 162 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE A 208 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY A 310 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N PHE A 211 " --> pdb=" O GLY A 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER A 312 " --> pdb=" O PHE A 211 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N PHE A 380 " --> pdb=" O PHE A 311 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU A 313 " --> pdb=" O PHE A 380 " (cutoff:3.500A) removed outlier: 6.754A 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: 3.536A 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: 6.588A pdb=" N GLU A 649 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 6.798A 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 removed outlier: 3.522A pdb=" N ILE A 680 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 442 through 444 removed outlier: 6.544A pdb=" N THR C 475 " --> pdb=" O TRP C 443 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N MET C 123 " --> pdb=" O THR C 478 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N TYR C 124 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N VAL C 160 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 126 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 162 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS C 206 " --> pdb=" O VAL C 160 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 162 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE C 208 " --> pdb=" O ILE C 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY C 310 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N PHE C 211 " --> pdb=" O GLY C 310 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N SER C 312 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 380 " --> pdb=" O PHE C 311 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 313 " --> pdb=" O PHE C 380 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLY C 382 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 264 through 267 removed outlier: 3.537A pdb=" N GLN C 272 " --> pdb=" O ASP C 267 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 569 through 572 removed outlier: 6.587A pdb=" N GLU C 649 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 620 " --> pdb=" O GLU C 649 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 603 through 605 Processing sheet with id= K, first strand: chain 'C' and resid 617 through 619 Processing sheet with id= L, first strand: chain 'C' and resid 673 through 675 removed outlier: 3.522A pdb=" N ILE C 680 " --> pdb=" O SER C 675 " (cutoff:3.500A) 552 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: 5.24 Time building geometry restraints manager: 8.36 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: 4702 1.33 - 1.45: 3458 1.45 - 1.57: 9862 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 18172 Sorted by residual: bond pdb=" C31 3PH B 702 " pdb=" O31 3PH B 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C31 3PH D 702 " pdb=" O31 3PH D 702 " ideal model delta sigma weight residual 1.325 1.450 -0.125 2.00e-02 2.50e+03 3.89e+01 bond pdb=" C31 3PH B 701 " pdb=" O31 3PH B 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C21 3PH D 701 " pdb=" O21 3PH D 701 " ideal model delta sigma weight residual 1.328 1.450 -0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" C31 3PH D 701 " pdb=" O31 3PH D 701 " ideal model delta sigma weight residual 1.325 1.447 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 18167 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.05: 452 106.05 - 113.16: 9747 113.16 - 120.26: 7316 120.26 - 127.37: 6949 127.37 - 134.48: 232 Bond angle restraints: 24696 Sorted by residual: angle pdb=" C2 NAG H 1 " pdb=" N2 NAG H 1 " pdb=" C7 NAG H 1 " ideal model delta sigma weight residual 123.12 134.14 -11.02 1.28e+00 6.08e-01 7.38e+01 angle pdb=" C2 NAG M 1 " pdb=" N2 NAG M 1 " pdb=" C7 NAG M 1 " ideal model delta sigma weight residual 123.12 134.12 -11.00 1.28e+00 6.08e-01 7.35e+01 angle pdb=" C2 NAG I 1 " pdb=" N2 NAG I 1 " pdb=" C7 NAG I 1 " ideal model delta sigma weight residual 123.12 134.09 -10.97 1.28e+00 6.08e-01 7.32e+01 angle pdb=" C2 NAG N 1 " pdb=" N2 NAG N 1 " pdb=" C7 NAG N 1 " ideal model delta sigma weight residual 123.12 134.06 -10.94 1.28e+00 6.08e-01 7.27e+01 angle pdb=" C2 NAG F 2 " pdb=" N2 NAG F 2 " pdb=" C7 NAG F 2 " ideal model delta sigma weight residual 123.12 133.94 -10.82 1.28e+00 6.08e-01 7.11e+01 ... (remaining 24691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 9915 21.37 - 42.74: 616 42.74 - 64.11: 90 64.11 - 85.48: 25 85.48 - 106.85: 8 Dihedral angle restraints: 10654 sinusoidal: 4338 harmonic: 6316 Sorted by residual: 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 56.85 -106.85 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" C2 NAG G 1 " pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " pdb=" C5 NAG G 1 " ideal model delta sinusoidal sigma weight residual -50.00 56.84 -106.84 1 2.00e+01 2.50e-03 3.10e+01 dihedral pdb=" CA TYR A 259 " pdb=" C TYR A 259 " pdb=" N GLY A 260 " pdb=" CA GLY A 260 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 ... (remaining 10651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.146: 2767 0.146 - 0.293: 37 0.293 - 0.439: 10 0.439 - 0.585: 0 0.585 - 0.732: 4 Chirality restraints: 2818 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 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+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 -1.67 -0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN C 513 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.22e+00 ... (remaining 2815 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " -0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO B 261 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 260 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO D 261 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO D 261 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 261 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 427 " 0.045 5.00e-02 4.00e+02 6.70e-02 7.19e+00 pdb=" N PRO B 428 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 428 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 428 " 0.038 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 158 2.49 - 3.09: 11164 3.09 - 3.70: 27417 3.70 - 4.30: 43634 4.30 - 4.90: 67753 Nonbonded interactions: 150126 Sorted by model distance: nonbonded pdb=" ND1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 1.890 3.420 nonbonded pdb=" ND1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 1.894 3.420 nonbonded pdb=" CE1 HIS B 456 " pdb=" CE1 TYR B 457 " model vdw 2.208 3.560 nonbonded pdb=" O PRO B 482 " pdb=" N GLU B 484 " model vdw 2.238 2.520 nonbonded pdb=" CE1 HIS D 456 " pdb=" CE1 TYR D 457 " model vdw 2.238 3.560 ... (remaining 150121 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 11548 2.51 5 N 2824 2.21 5 O 3496 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.310 Check model and map are aligned: 0.250 Convert atoms to be neutral: 0.150 Process input model: 47.830 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:12.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 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 0.125 18172 Z= 0.466 Angle : 0.986 11.024 24696 Z= 0.564 Chirality : 0.063 0.732 2818 Planarity : 0.007 0.081 3056 Dihedral : 14.334 106.852 6588 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer Outliers : 1.96 % 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: -4.84 (0.13), residues: 2154 helix: -4.66 (0.05), residues: 998 sheet: -0.33 (0.34), residues: 182 loop : -1.96 (0.16), residues: 974 *********************** 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 380 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 343 time to evaluate : 2.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 4 residues processed: 368 average time/residue: 0.9892 time to fit residues: 414.2891 Evaluate side-chains 201 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 197 time to evaluate : 1.567 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 3 average time/residue: 0.8928 time to fit residues: 5.1300 ------------------------------------------------------------------------------- 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: 6.9990 chunk 162 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 194 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 156 ASN A 201 HIS A 220 HIS A 324 HIS A 330 GLN A 422 ASN A 442 ASN A 493 ASN A 510 GLN ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 ASN A 606 ASN A 609 ASN A 625 ASN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN C 125 GLN C 156 ASN C 201 HIS C 220 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 HIS C 330 GLN C 422 ASN C 442 ASN C 493 ASN C 510 GLN ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 598 ASN C 606 ASN C 609 ASN C 625 ASN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 ASN D 474 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.048 18172 Z= 0.433 Angle : 0.795 9.881 24696 Z= 0.428 Chirality : 0.059 0.772 2818 Planarity : 0.007 0.051 3056 Dihedral : 9.021 109.719 2612 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.09 % Favored : 95.82 % Rotamer Outliers : 3.28 % 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: -2.75 (0.15), residues: 2154 helix: -2.29 (0.13), residues: 976 sheet: -0.01 (0.35), residues: 182 loop : -1.54 (0.17), residues: 996 *********************** 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 279 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 217 time to evaluate : 2.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 23 residues processed: 257 average time/residue: 1.1307 time to fit residues: 330.4932 Evaluate side-chains 204 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 18 residues processed: 7 average time/residue: 0.2237 time to fit residues: 5.5922 ------------------------------------------------------------------------------- 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: 8.9990 chunk 60 optimal weight: 5.9990 chunk 161 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 194 optimal weight: 0.0270 chunk 210 optimal weight: 0.0980 chunk 173 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN A 609 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 609 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 18172 Z= 0.170 Angle : 0.608 9.544 24696 Z= 0.326 Chirality : 0.048 0.587 2818 Planarity : 0.004 0.038 3056 Dihedral : 8.543 111.022 2612 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.80 % 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: -1.53 (0.17), residues: 2154 helix: -0.85 (0.15), residues: 982 sheet: -0.03 (0.36), residues: 180 loop : -1.27 (0.18), residues: 992 *********************** 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 276 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 223 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 21 residues processed: 253 average time/residue: 1.1987 time to fit residues: 344.7749 Evaluate side-chains 213 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 192 time to evaluate : 2.114 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 14 residues processed: 8 average time/residue: 0.3731 time to fit residues: 7.1000 ------------------------------------------------------------------------------- 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: 3.9990 chunk 101 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 0.9980 chunk 195 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 102 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 657 HIS C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 18172 Z= 0.281 Angle : 0.657 8.169 24696 Z= 0.351 Chirality : 0.052 0.636 2818 Planarity : 0.005 0.044 3056 Dihedral : 8.640 111.117 2612 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 3.22 % 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: -1.00 (0.17), residues: 2154 helix: -0.24 (0.16), residues: 980 sheet: -0.01 (0.36), residues: 182 loop : -1.15 (0.18), residues: 992 *********************** 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 272 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 211 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 27 residues processed: 252 average time/residue: 1.1087 time to fit residues: 319.6059 Evaluate side-chains 229 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.328 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 8 average time/residue: 0.4176 time to fit residues: 7.4241 ------------------------------------------------------------------------------- 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: 0.9980 chunk 117 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 176 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.0980 chunk 185 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 ASN A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 609 ASN C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 18172 Z= 0.173 Angle : 0.584 10.918 24696 Z= 0.312 Chirality : 0.048 0.556 2818 Planarity : 0.004 0.045 3056 Dihedral : 8.372 111.376 2612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 2.85 % 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: -0.57 (0.18), residues: 2154 helix: 0.24 (0.17), residues: 970 sheet: 0.06 (0.37), residues: 180 loop : -1.01 (0.19), residues: 1004 *********************** 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 264 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 210 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 32 residues processed: 245 average time/residue: 1.1437 time to fit residues: 320.4277 Evaluate side-chains 217 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 185 time to evaluate : 2.209 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 10 average time/residue: 0.6881 time to fit residues: 11.3513 ------------------------------------------------------------------------------- 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: 0.0980 chunk 186 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 171 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 68 optimal weight: 6.9990 chunk 108 optimal weight: 0.0010 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 206 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 18172 Z= 0.151 Angle : 0.567 11.992 24696 Z= 0.302 Chirality : 0.047 0.526 2818 Planarity : 0.004 0.049 3056 Dihedral : 8.185 111.798 2612 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 2.48 % 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: -0.23 (0.18), residues: 2154 helix: 0.52 (0.17), residues: 972 sheet: 0.16 (0.37), residues: 180 loop : -0.83 (0.19), residues: 1002 *********************** 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 250 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 203 time to evaluate : 2.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 26 residues processed: 238 average time/residue: 1.1869 time to fit residues: 322.1083 Evaluate side-chains 214 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 2.105 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 22 residues processed: 5 average time/residue: 0.5414 time to fit residues: 6.3191 ------------------------------------------------------------------------------- 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: 8.9990 chunk 23 optimal weight: 0.5980 chunk 117 optimal weight: 4.9990 chunk 151 optimal weight: 0.3980 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 206 optimal weight: 0.1980 chunk 129 optimal weight: 0.9980 chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 18172 Z= 0.158 Angle : 0.568 9.694 24696 Z= 0.301 Chirality : 0.047 0.516 2818 Planarity : 0.004 0.051 3056 Dihedral : 8.104 112.042 2612 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer Outliers : 2.64 % 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: -0.08 (0.18), residues: 2154 helix: 0.65 (0.17), residues: 976 sheet: 0.21 (0.38), residues: 180 loop : -0.76 (0.19), residues: 998 *********************** 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 251 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 201 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 26 residues processed: 238 average time/residue: 1.1661 time to fit residues: 317.1510 Evaluate side-chains 215 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 2.234 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.2812 time to fit residues: 5.0486 ------------------------------------------------------------------------------- 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: 0.3980 chunk 123 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 0.0070 chunk 162 optimal weight: 9.9990 chunk 187 optimal weight: 8.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 ASN B 237 GLN ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 679 ASN D 237 GLN ** D 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.044 18172 Z= 0.155 Angle : 0.567 11.114 24696 Z= 0.300 Chirality : 0.047 0.498 2818 Planarity : 0.004 0.057 3056 Dihedral : 8.035 112.214 2612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer Outliers : 2.33 % 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: 0.03 (0.18), residues: 2154 helix: 0.77 (0.17), residues: 972 sheet: 0.27 (0.37), residues: 182 loop : -0.73 (0.19), residues: 1000 *********************** 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 234 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 2.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 226 average time/residue: 1.1326 time to fit residues: 292.3852 Evaluate side-chains 205 residues out of total 1892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 2.051 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 0.2888 time to fit residues: 3.6494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 57.0513 > 50: distance: 26 - 27: 3.141 distance: 27 - 32: 5.645 distance: 32 - 33: 4.822 distance: 33 - 34: 5.697 distance: 34 - 35: 6.153 distance: 34 - 40: 6.569 distance: 36 - 37: 3.974 distance: 37 - 38: 4.109 distance: 40 - 41: 16.390 distance: 41 - 42: 11.634 distance: 41 - 44: 13.458 distance: 42 - 43: 16.053 distance: 42 - 48: 6.441 distance: 44 - 45: 4.149 distance: 45 - 47: 4.430 distance: 48 - 49: 5.510 distance: 49 - 50: 4.837 distance: 49 - 52: 8.599 distance: 50 - 51: 7.854 distance: 50 - 62: 6.235 distance: 52 - 53: 7.927 distance: 53 - 54: 3.523 distance: 53 - 55: 7.642 distance: 54 - 56: 8.512 distance: 55 - 57: 7.425 distance: 55 - 58: 6.196 distance: 56 - 57: 9.208 distance: 57 - 59: 7.685 distance: 58 - 60: 4.983 distance: 59 - 61: 4.609 distance: 63 - 64: 3.558 distance: 63 - 66: 4.595 distance: 64 - 70: 3.013 distance: 66 - 67: 8.895 distance: 67 - 68: 6.637 distance: 67 - 69: 8.231 distance: 70 - 71: 5.279 distance: 71 - 72: 7.862 distance: 71 - 74: 3.726 distance: 72 - 73: 3.746 distance: 72 - 76: 4.869 distance: 74 - 75: 4.273 distance: 76 - 77: 3.017 distance: 77 - 78: 10.150 distance: 77 - 80: 4.175 distance: 78 - 79: 10.479 distance: 78 - 83: 6.657 distance: 80 - 81: 3.986 distance: 80 - 82: 11.244 distance: 83 - 84: 11.480 distance: 84 - 85: 11.530 distance: 84 - 87: 4.775 distance: 85 - 86: 18.351 distance: 85 - 95: 20.366 distance: 87 - 88: 4.775 distance: 88 - 89: 4.323 distance: 88 - 90: 3.635 distance: 89 - 91: 9.305 distance: 90 - 92: 4.292 distance: 91 - 93: 5.152 distance: 92 - 93: 7.784 distance: 93 - 94: 4.593 distance: 95 - 96: 25.755 distance: 96 - 97: 28.290 distance: 97 - 98: 19.250 distance: 97 - 99: 38.009 distance: 99 - 100: 18.247 distance: 100 - 101: 13.325 distance: 100 - 103: 29.638 distance: 101 - 102: 17.755 distance: 101 - 107: 9.307 distance: 103 - 104: 6.484 distance: 104 - 105: 14.919 distance: 104 - 106: 4.348 distance: 106 - 226: 9.736