Starting phenix.real_space_refine on Sat Mar 16 05:32:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cq7_30438/03_2024/7cq7_30438_updated.pdb" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 92 5.16 5 Cl 3 4.86 5 C 8926 2.51 5 N 2304 2.21 5 O 2481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 131": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 265": "NH1" <-> "NH2" Residue "C ARG 280": "NH1" <-> "NH2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 526": "NH1" <-> "NH2" Residue "C ARG 639": "NH1" <-> "NH2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 775": "NH1" <-> "NH2" Residue "D ARG 112": "NH1" <-> "NH2" Residue "D ARG 265": "NH1" <-> "NH2" Residue "D ARG 280": "NH1" <-> "NH2" Residue "D ARG 362": "NH1" <-> "NH2" Residue "D ARG 526": "NH1" <-> "NH2" Residue "D ARG 640": "NH1" <-> "NH2" Residue "D ARG 707": "NH1" <-> "NH2" Residue "D ARG 712": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13810 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1630 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1637 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5194 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 5236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5236 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 28, 'TRANS': 647} Chain breaks: 3 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 19 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CL': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CL': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.26, per 1000 atoms: 0.53 Number of scatterers: 13810 At special positions: 0 Unit cell: (136.14, 111.986, 132.846, 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) Cl 3 17.00 S 92 16.00 P 4 15.00 O 2481 8.00 N 2304 7.00 C 8926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 142 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 115 " distance=2.03 Simple disulfide: pdb=" SG CYS A 112 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 174 " - pdb=" SG CYS A 255 " distance=2.03 Simple disulfide: pdb=" SG CYS A 221 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 115 " distance=2.03 Simple disulfide: pdb=" SG CYS B 112 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 255 " distance=2.04 Simple disulfide: pdb=" SG CYS B 221 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 438 " - pdb=" SG CYS C 454 " distance=2.03 Simple disulfide: pdb=" SG CYS D 438 " - pdb=" SG CYS D 454 " 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=5, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN A 263 " " NAG F 1 " - " ASN B 263 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.69 Conformation dependent library (CDL) restraints added in 2.5 seconds 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3312 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 5 sheets defined 55.9% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.61 Creating SS restraints... Processing helix chain 'A' and resid 82 through 104 removed outlier: 3.783A pdb=" N GLU A 86 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N LEU A 87 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU A 97 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU A 98 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 114 No H-bonds generated for 'chain 'A' and resid 111 through 114' Processing helix chain 'A' and resid 116 through 128 removed outlier: 3.750A pdb=" N GLN A 120 " --> pdb=" O TYR A 116 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 154 through 169 Processing helix chain 'A' and resid 184 through 202 Processing helix chain 'A' and resid 218 through 221 No H-bonds generated for 'chain 'A' and resid 218 through 221' Processing helix chain 'A' and resid 225 through 244 removed outlier: 4.010A pdb=" N GLU A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 270 Processing helix chain 'A' and resid 282 through 293 Processing helix chain 'A' and resid 295 through 305 Processing helix chain 'B' and resid 82 through 104 removed outlier: 4.311A pdb=" N GLU B 86 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU B 87 " --> pdb=" O GLU B 83 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 91 " --> pdb=" O LEU B 87 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ALA B 96 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLU B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.710A pdb=" N ILE B 129 " --> pdb=" O LYS B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 154 through 169 Processing helix chain 'B' and resid 186 through 202 removed outlier: 3.586A pdb=" N ASN B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 No H-bonds generated for 'chain 'B' and resid 218 through 221' Processing helix chain 'B' and resid 225 through 245 removed outlier: 4.223A pdb=" N THR B 230 " --> pdb=" O GLU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.540A pdb=" N ALA B 261 " --> pdb=" O ASP B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 289 removed outlier: 3.625A pdb=" N VAL B 288 " --> pdb=" O PRO B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 305 Proline residue: B 296 - end of helix removed outlier: 3.610A pdb=" N SER B 303 " --> pdb=" O PHE B 299 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 114 Processing helix chain 'C' and resid 123 through 166 removed outlier: 3.630A pdb=" N VAL C 128 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG C 157 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N VAL C 158 " --> pdb=" O LEU C 154 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 159 " --> pdb=" O LYS C 155 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 195 removed outlier: 4.126A pdb=" N ILE C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL C 194 " --> pdb=" O GLY C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.863A pdb=" N CYS C 211 " --> pdb=" O PRO C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 238 removed outlier: 3.682A pdb=" N ILE C 235 " --> pdb=" O VAL C 231 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 262 removed outlier: 3.694A pdb=" N ILE C 251 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N HIS C 252 " --> pdb=" O PRO C 249 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE C 257 " --> pdb=" O GLY C 254 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE C 261 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER C 262 " --> pdb=" O ALA C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 279 No H-bonds generated for 'chain 'C' and resid 277 through 279' Processing helix chain 'C' and resid 283 through 301 removed outlier: 3.837A pdb=" N ASP C 287 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 311 removed outlier: 3.734A pdb=" N VAL C 308 " --> pdb=" O PRO C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 345 Processing helix chain 'C' and resid 372 through 406 Proline residue: C 376 - end of helix removed outlier: 3.726A pdb=" N ILE C 379 " --> pdb=" O PRO C 376 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 381 " --> pdb=" O PHE C 378 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 383 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 388 " --> pdb=" O GLY C 385 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 396 " --> pdb=" O ASN C 393 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE C 404 " --> pdb=" O MET C 401 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG C 405 " --> pdb=" O PHE C 402 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR C 406 " --> pdb=" O ARG C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 433 removed outlier: 3.805A pdb=" N ALA C 421 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N VAL C 423 " --> pdb=" O LEU C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 465 Processing helix chain 'C' and resid 470 through 479 Processing helix chain 'C' and resid 487 through 503 removed outlier: 4.084A pdb=" N PHE C 499 " --> pdb=" O LEU C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 514 through 530 removed outlier: 3.647A pdb=" N LEU C 527 " --> pdb=" O ALA C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 535 No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 544 through 559 removed outlier: 3.890A pdb=" N LEU C 549 " --> pdb=" O GLY C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 572 Processing helix chain 'C' and resid 577 through 595 removed outlier: 3.804A pdb=" N PHE C 581 " --> pdb=" O THR C 578 " (cutoff:3.500A) Proline residue: C 582 - end of helix removed outlier: 3.592A pdb=" N VAL C 593 " --> pdb=" O ALA C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 609 removed outlier: 4.345A pdb=" N GLN C 609 " --> pdb=" O HIS C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 651 Processing helix chain 'C' and resid 681 through 689 Processing helix chain 'C' and resid 708 through 710 No H-bonds generated for 'chain 'C' and resid 708 through 710' Processing helix chain 'C' and resid 721 through 723 No H-bonds generated for 'chain 'C' and resid 721 through 723' Processing helix chain 'C' and resid 754 through 762 removed outlier: 3.838A pdb=" N LYS C 759 " --> pdb=" O PRO C 755 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 111 Processing helix chain 'D' and resid 122 through 165 removed outlier: 3.843A pdb=" N ASP D 164 " --> pdb=" O LYS D 160 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LYS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 195 removed outlier: 3.673A pdb=" N LEU D 178 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N VAL D 194 " --> pdb=" O GLY D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 201 No H-bonds generated for 'chain 'D' and resid 199 through 201' Processing helix chain 'D' and resid 206 through 213 Processing helix chain 'D' and resid 224 through 238 Processing helix chain 'D' and resid 249 through 261 Processing helix chain 'D' and resid 282 through 301 Processing helix chain 'D' and resid 304 through 313 Processing helix chain 'D' and resid 321 through 345 Processing helix chain 'D' and resid 372 through 405 removed outlier: 3.582A pdb=" N ILE D 375 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Proline residue: D 376 - end of helix removed outlier: 3.693A pdb=" N GLY D 385 " --> pdb=" O GLY D 382 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 388 " --> pdb=" O GLY D 385 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY D 389 " --> pdb=" O GLY D 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 393 " --> pdb=" O ALA D 390 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 395 " --> pdb=" O PHE D 392 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP D 398 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 400 " --> pdb=" O TYR D 397 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N MET D 401 " --> pdb=" O TRP D 398 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 404 " --> pdb=" O MET D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 433 removed outlier: 3.644A pdb=" N ALA D 417 " --> pdb=" O GLN D 413 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D 418 " --> pdb=" O VAL D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 465 No H-bonds generated for 'chain 'D' and resid 462 through 465' Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'D' and resid 487 through 503 removed outlier: 4.601A pdb=" N PHE D 499 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 514 through 535 removed outlier: 3.509A pdb=" N ALA D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG D 526 " --> pdb=" O ALA D 522 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY D 529 " --> pdb=" O GLY D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 544 through 559 removed outlier: 4.367A pdb=" N LEU D 549 " --> pdb=" O GLY D 545 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 550 " --> pdb=" O LYS D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 573 Processing helix chain 'D' and resid 578 through 595 removed outlier: 3.850A pdb=" N PHE D 581 " --> pdb=" O THR D 578 " (cutoff:3.500A) Proline residue: D 582 - end of helix removed outlier: 3.509A pdb=" N MET D 588 " --> pdb=" O LEU D 585 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 593 " --> pdb=" O ALA D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 609 removed outlier: 4.100A pdb=" N GLN D 609 " --> pdb=" O HIS D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 651 Processing helix chain 'D' and resid 681 through 684 No H-bonds generated for 'chain 'D' and resid 681 through 684' Processing helix chain 'D' and resid 686 through 689 No H-bonds generated for 'chain 'D' and resid 686 through 689' Processing helix chain 'D' and resid 754 through 761 removed outlier: 3.902A pdb=" N LYS D 759 " --> pdb=" O PRO D 755 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 438 through 440 Processing sheet with id= B, first strand: chain 'C' and resid 660 through 664 Processing sheet with id= C, first strand: chain 'D' and resid 641 through 643 removed outlier: 3.632A pdb=" N GLU D 642 " --> pdb=" O MET D 735 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 661 through 663 removed outlier: 3.714A pdb=" N GLY D 677 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 747 through 749 removed outlier: 6.169A pdb=" N VAL D 770 " --> pdb=" O VAL D 748 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 624 hydrogen bonds defined for protein. 1671 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: 3.65 Time building geometry restraints manager: 6.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4350 1.34 - 1.47: 3464 1.47 - 1.59: 6154 1.59 - 1.71: 6 1.71 - 1.83: 140 Bond restraints: 14114 Sorted by residual: bond pdb=" C4 ADP D 901 " pdb=" C5 ADP D 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP C 901 " pdb=" C5 ADP C 901 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C5 ADP D 901 " pdb=" C6 ADP D 901 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP C 901 " pdb=" C6 ADP C 901 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" CB VAL C 586 " pdb=" CG1 VAL C 586 " ideal model delta sigma weight residual 1.521 1.451 0.070 3.30e-02 9.18e+02 4.49e+00 ... (remaining 14109 not shown) Histogram of bond angle deviations from ideal: 98.68 - 105.81: 318 105.81 - 112.94: 7623 112.94 - 120.07: 5412 120.07 - 127.20: 5654 127.20 - 134.33: 178 Bond angle restraints: 19185 Sorted by residual: angle pdb=" C THR A 282 " pdb=" N VAL A 283 " pdb=" CA VAL A 283 " ideal model delta sigma weight residual 120.24 125.32 -5.08 6.30e-01 2.52e+00 6.50e+01 angle pdb=" N GLN D 722 " pdb=" CA GLN D 722 " pdb=" C GLN D 722 " ideal model delta sigma weight residual 114.75 105.85 8.90 1.26e+00 6.30e-01 4.99e+01 angle pdb=" C ARG B 271 " pdb=" N THR B 272 " pdb=" CA THR B 272 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 angle pdb=" C ARG A 271 " pdb=" N THR A 272 " pdb=" CA THR A 272 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE D 724 " pdb=" CA ILE D 724 " pdb=" C ILE D 724 " ideal model delta sigma weight residual 110.62 115.92 -5.30 1.14e+00 7.69e-01 2.16e+01 ... (remaining 19180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.84: 8213 22.84 - 45.68: 182 45.68 - 68.52: 10 68.52 - 91.36: 8 91.36 - 114.20: 1 Dihedral angle restraints: 8414 sinusoidal: 3299 harmonic: 5115 Sorted by residual: dihedral pdb=" CA ASP C 282 " pdb=" C ASP C 282 " pdb=" N THR C 283 " pdb=" CA THR C 283 " ideal model delta harmonic sigma weight residual 180.00 150.26 29.74 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" C5' ADP D 901 " pdb=" O5' ADP D 901 " pdb=" PA ADP D 901 " pdb=" O2A ADP D 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.20 114.20 1 2.00e+01 2.50e-03 3.38e+01 dihedral pdb=" CA ARG A 107 " pdb=" C ARG A 107 " pdb=" N PRO A 108 " pdb=" CA PRO A 108 " ideal model delta harmonic sigma weight residual 180.00 152.58 27.42 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1658 0.060 - 0.120: 513 0.120 - 0.180: 68 0.180 - 0.240: 11 0.240 - 0.301: 2 Chirality restraints: 2252 Sorted by residual: chirality pdb=" CB ILE D 721 " pdb=" CA ILE D 721 " pdb=" CG1 ILE D 721 " pdb=" CG2 ILE D 721 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE C 724 " pdb=" CA ILE C 724 " pdb=" CG1 ILE C 724 " pdb=" CG2 ILE C 724 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CB ILE D 275 " pdb=" CA ILE D 275 " pdb=" CG1 ILE D 275 " pdb=" CG2 ILE D 275 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 2249 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 179 " 0.028 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP C 179 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP C 179 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP C 179 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 179 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 179 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 179 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 179 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 179 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 179 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 783 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.78e+00 pdb=" C THR C 783 " 0.048 2.00e-02 2.50e+03 pdb=" O THR C 783 " -0.018 2.00e-02 2.50e+03 pdb=" N ARG C 784 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 349 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C MET D 349 " -0.044 2.00e-02 2.50e+03 pdb=" O MET D 349 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP D 350 " 0.015 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 75 2.51 - 3.11: 10253 3.11 - 3.71: 21285 3.71 - 4.30: 29477 4.30 - 4.90: 49539 Nonbonded interactions: 110629 Sorted by model distance: nonbonded pdb=" OD2 ASP D 786 " pdb=" O2' ADP D 901 " model vdw 1.915 2.440 nonbonded pdb=" O MET C 368 " pdb=" OH TYR C 579 " model vdw 2.236 2.440 nonbonded pdb=" CG HIS C 658 " pdb=" N7 ADP C 901 " model vdw 2.251 2.672 nonbonded pdb=" O MET D 368 " pdb=" OH TYR D 579 " model vdw 2.261 2.440 nonbonded pdb=" NH2 ARG D 767 " pdb=" O2B ADP D 901 " model vdw 2.261 2.520 ... (remaining 110624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 73 through 306) selection = (chain 'B' and (resid 73 through 130 or resid 142 through 245 or resid 253 throu \ gh 306)) } ncs_group { reference = (chain 'C' and (resid 94 through 115 or (resid 116 and (name N or name CA or nam \ e C or name O or name CB )) or resid 121 through 652 or (resid 653 through 656 a \ nd (name N or name CA or name C or name O or name CB )) or resid 657 through 664 \ or resid 673 through 693 or resid 706 through 789 or (resid 790 and (name N or \ name CA or name C or name O or name CB )) or resid 901 through 902)) selection = (chain 'D' and (resid 94 through 116 or resid 121 through 366 or (resid 367 and \ (name N or name CA or name C or name O or name CB )) or resid 368 through 619 or \ (resid 620 and (name N or name CA or name C or name O or name CB )) or resid 62 \ 1 through 642 or (resid 643 and (name N or name CA or name C or name O or name C \ B )) or resid 644 through 690 or (resid 691 and (name N or name CA or name C or \ name O or name CB )) or resid 692 or (resid 693 and (name N or name CA or name C \ or name O or name CB )) or resid 706 through 707 or (resid 708 and (name N or n \ ame CA or name C or name O or name CB )) or resid 709 through 716 or (resid 717 \ and (name N or name CA or name C or name O or name CB )) or resid 718 or (resid \ 719 and (name N or name CA or name C or name O or name CB )) or resid 720 throug \ h 724 or (resid 725 through 732 and (name N or name CA or name C or name O or na \ me CB )) or resid 733 through 790 or resid 901 through 902)) } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.240 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: 5.320 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.640 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4342 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 : 0.008 0.109 14114 Z= 0.528 Angle : 1.069 10.899 19185 Z= 0.570 Chirality : 0.056 0.301 2252 Planarity : 0.008 0.063 2397 Dihedral : 10.352 114.200 5066 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.28 % Favored : 90.72 % Rotamer: Outliers : 0.07 % Allowed : 2.95 % Favored : 96.98 % 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: -4.47 (0.15), residues: 1734 helix: -2.46 (0.12), residues: 1046 sheet: None (None), residues: 0 loop : -3.68 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.004 TRP C 179 HIS 0.020 0.002 HIS D 725 PHE 0.031 0.003 PHE D 279 TYR 0.022 0.002 TYR D 370 ARG 0.011 0.001 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 468 time to evaluate : 1.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 239 VAL cc_start: 0.5320 (t) cc_final: 0.4732 (m) REVERT: C 588 MET cc_start: 0.4373 (mtp) cc_final: 0.4139 (ppp) REVERT: D 227 LEU cc_start: 0.6605 (tp) cc_final: 0.6105 (tt) REVERT: D 275 ILE cc_start: 0.5375 (tp) cc_final: 0.5134 (mp) REVERT: D 513 VAL cc_start: 0.7961 (p) cc_final: 0.7596 (p) outliers start: 1 outliers final: 0 residues processed: 469 average time/residue: 0.2681 time to fit residues: 178.3717 Evaluate side-chains 250 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 146 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 70 optimal weight: 3.9990 chunk 136 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 101 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN A 202 HIS ** B 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 173 ASN C 183 ASN C 220 HIS C 468 ASN C 774 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 373 HIS D 725 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.3897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14114 Z= 0.242 Angle : 0.798 11.332 19185 Z= 0.394 Chirality : 0.045 0.350 2252 Planarity : 0.006 0.048 2397 Dihedral : 6.680 104.192 1996 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.22 % Allowed : 12.01 % Favored : 84.77 % 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: -2.78 (0.18), residues: 1734 helix: -0.83 (0.15), residues: 1050 sheet: -4.61 (1.52), residues: 10 loop : -3.47 (0.20), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP D 179 HIS 0.010 0.001 HIS C 658 PHE 0.029 0.002 PHE A 193 TYR 0.016 0.002 TYR D 99 ARG 0.007 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 290 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.6770 (tpp) cc_final: 0.5237 (tpp) REVERT: B 192 LEU cc_start: 0.8324 (tp) cc_final: 0.7755 (mp) REVERT: B 241 MET cc_start: 0.6175 (tmm) cc_final: 0.5939 (ptm) REVERT: B 255 CYS cc_start: 0.2894 (OUTLIER) cc_final: 0.2335 (t) REVERT: C 218 ILE cc_start: 0.7456 (tp) cc_final: 0.7227 (tt) REVERT: C 399 LEU cc_start: 0.6142 (tp) cc_final: 0.5606 (tt) REVERT: C 462 MET cc_start: 0.3526 (tpp) cc_final: 0.3138 (tpp) REVERT: C 588 MET cc_start: 0.5469 (mtp) cc_final: 0.5267 (ppp) REVERT: C 589 THR cc_start: 0.6288 (m) cc_final: 0.6060 (m) REVERT: C 599 GLU cc_start: 0.3810 (OUTLIER) cc_final: 0.2662 (pm20) REVERT: D 143 PHE cc_start: 0.7221 (t80) cc_final: 0.5875 (m-10) REVERT: D 368 MET cc_start: 0.6989 (mtt) cc_final: 0.6666 (mpp) REVERT: D 588 MET cc_start: 0.4196 (ptm) cc_final: 0.3953 (ptm) REVERT: D 598 ILE cc_start: 0.7553 (mm) cc_final: 0.7297 (mm) outliers start: 48 outliers final: 23 residues processed: 320 average time/residue: 0.2171 time to fit residues: 108.2253 Evaluate side-chains 258 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 256 ILE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 297 VAL Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 517 SER Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 766 LEU Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 0.0470 chunk 43 optimal weight: 0.9980 chunk 158 optimal weight: 0.1980 chunk 171 optimal weight: 0.5980 chunk 140 optimal weight: 0.8980 chunk 156 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN B 113 GLN B 173 ASN ** C 576 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 683 GLN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5201 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14114 Z= 0.196 Angle : 0.724 9.956 19185 Z= 0.353 Chirality : 0.044 0.429 2252 Planarity : 0.004 0.039 2397 Dihedral : 6.099 87.867 1996 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.43 % Allowed : 13.29 % Favored : 82.28 % 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: -1.98 (0.19), residues: 1734 helix: -0.14 (0.15), residues: 1056 sheet: -4.49 (1.58), residues: 10 loop : -3.27 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 541 HIS 0.012 0.001 HIS C 658 PHE 0.024 0.002 PHE B 119 TYR 0.020 0.002 TYR D 715 ARG 0.009 0.001 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 255 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 126 MET cc_start: 0.5476 (ttp) cc_final: 0.5066 (tmm) REVERT: A 152 MET cc_start: 0.6540 (tpp) cc_final: 0.6310 (tpp) REVERT: A 295 LEU cc_start: 0.5256 (mt) cc_final: 0.5038 (mp) REVERT: B 173 ASN cc_start: 0.3783 (OUTLIER) cc_final: 0.3187 (m-40) REVERT: B 192 LEU cc_start: 0.8020 (tp) cc_final: 0.7560 (mp) REVERT: C 399 LEU cc_start: 0.6290 (tp) cc_final: 0.6022 (tt) REVERT: C 781 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6442 (pt) REVERT: D 143 PHE cc_start: 0.7314 (t80) cc_final: 0.5615 (m-10) REVERT: D 562 MET cc_start: 0.5158 (OUTLIER) cc_final: 0.4542 (mtm) REVERT: D 615 HIS cc_start: 0.5487 (t-90) cc_final: 0.4996 (t-90) REVERT: D 741 MET cc_start: 0.7125 (ppp) cc_final: 0.6838 (tmm) REVERT: D 766 LEU cc_start: 0.3184 (mt) cc_final: 0.1825 (mp) outliers start: 66 outliers final: 27 residues processed: 293 average time/residue: 0.2153 time to fit residues: 97.7630 Evaluate side-chains 261 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 231 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain B residue 173 ASN Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 781 LEU Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 399 LEU Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 424 THR Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 684 LEU Chi-restraints excluded: chain D residue 787 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 2.9990 chunk 119 optimal weight: 0.3980 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 158 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 ASN C 683 GLN D 162 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 GLN D 451 GLN ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.6866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 14114 Z= 0.296 Angle : 0.770 10.284 19185 Z= 0.388 Chirality : 0.046 0.266 2252 Planarity : 0.005 0.078 2397 Dihedral : 5.737 52.589 1996 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.61 % Favored : 92.33 % Rotamer: Outliers : 4.36 % Allowed : 14.63 % Favored : 81.01 % 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: -1.50 (0.20), residues: 1734 helix: 0.24 (0.16), residues: 1038 sheet: -3.20 (3.26), residues: 5 loop : -3.00 (0.21), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 325 HIS 0.010 0.001 HIS D 605 PHE 0.032 0.002 PHE D 613 TYR 0.019 0.002 TYR D 99 ARG 0.006 0.001 ARG D 628 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 317 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 192 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7399 (mp) REVERT: C 95 GLU cc_start: 0.4716 (mp0) cc_final: 0.4362 (tt0) REVERT: C 599 GLU cc_start: 0.5471 (OUTLIER) cc_final: 0.4977 (pm20) REVERT: C 786 ASP cc_start: 0.4571 (OUTLIER) cc_final: 0.3936 (t0) REVERT: D 301 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6472 (t80) REVERT: D 407 ILE cc_start: 0.5864 (mp) cc_final: 0.5555 (mt) REVERT: D 488 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6538 (tp) REVERT: D 562 MET cc_start: 0.5377 (OUTLIER) cc_final: 0.4890 (mtm) REVERT: D 606 ILE cc_start: 0.6703 (OUTLIER) cc_final: 0.6395 (mt) REVERT: D 766 LEU cc_start: 0.4280 (mt) cc_final: 0.2851 (mp) outliers start: 65 outliers final: 35 residues processed: 357 average time/residue: 0.2333 time to fit residues: 127.9151 Evaluate side-chains 297 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 193 PHE Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 519 LEU Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 586 VAL Chi-restraints excluded: chain C residue 599 GLU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 786 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 156 TYR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 453 PHE Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 513 VAL Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 577 VAL Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 143 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 202 HIS B 242 ASN D 162 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 623 HIS ** D 768 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.7725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.175 14114 Z= 0.238 Angle : 0.696 10.126 19185 Z= 0.340 Chirality : 0.043 0.333 2252 Planarity : 0.004 0.038 2397 Dihedral : 5.555 48.372 1996 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 2.75 % Allowed : 19.60 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.22 (0.20), residues: 1734 helix: 0.40 (0.16), residues: 1053 sheet: -2.95 (3.42), residues: 5 loop : -2.83 (0.22), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 325 HIS 0.013 0.001 HIS B 202 PHE 0.034 0.002 PHE A 193 TYR 0.030 0.002 TYR C 397 ARG 0.007 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 286 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7114 (tpp) cc_final: 0.5657 (tpp) REVERT: B 123 VAL cc_start: 0.7092 (m) cc_final: 0.6863 (p) REVERT: C 95 GLU cc_start: 0.4751 (mp0) cc_final: 0.4403 (tt0) REVERT: C 599 GLU cc_start: 0.5266 (pm20) cc_final: 0.4588 (pm20) REVERT: D 407 ILE cc_start: 0.5997 (mp) cc_final: 0.5685 (mp) REVERT: D 462 MET cc_start: 0.7967 (mmm) cc_final: 0.7530 (tpp) REVERT: D 766 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.3198 (mp) outliers start: 41 outliers final: 24 residues processed: 308 average time/residue: 0.2209 time to fit residues: 104.4886 Evaluate side-chains 281 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 256 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 549 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 162 ASN Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 301 PHE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 598 ILE Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 766 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.0070 chunk 88 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.3204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 203 ASN D 162 ASN D 623 HIS D 725 HIS D 768 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.9473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 14114 Z= 0.275 Angle : 0.778 14.493 19185 Z= 0.392 Chirality : 0.046 0.274 2252 Planarity : 0.005 0.071 2397 Dihedral : 5.579 39.771 1996 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.96 % Favored : 91.98 % Rotamer: Outliers : 3.89 % Allowed : 19.87 % Favored : 76.24 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.18 (0.20), residues: 1734 helix: 0.46 (0.16), residues: 1037 sheet: -3.25 (3.20), residues: 5 loop : -2.80 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D 325 HIS 0.008 0.001 HIS C 658 PHE 0.034 0.002 PHE A 193 TYR 0.023 0.002 TYR D 448 ARG 0.008 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 333 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7765 (pt0) cc_final: 0.7484 (pt0) REVERT: A 152 MET cc_start: 0.7575 (tpp) cc_final: 0.6333 (tpp) REVERT: A 168 GLU cc_start: 0.7188 (tm-30) cc_final: 0.6911 (tm-30) REVERT: A 231 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8234 (mm) REVERT: B 123 VAL cc_start: 0.7354 (m) cc_final: 0.7122 (p) REVERT: C 127 TRP cc_start: 0.7658 (m100) cc_final: 0.6805 (m-10) REVERT: C 352 LEU cc_start: 0.6096 (mt) cc_final: 0.5573 (mp) REVERT: C 505 TYR cc_start: 0.7339 (t80) cc_final: 0.6452 (t80) REVERT: C 587 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8697 (mm) REVERT: C 599 GLU cc_start: 0.6259 (pm20) cc_final: 0.5785 (pm20) REVERT: D 224 LEU cc_start: 0.8593 (tp) cc_final: 0.8339 (mm) REVERT: D 401 MET cc_start: 0.6087 (mtp) cc_final: 0.5860 (mtp) REVERT: D 572 GLU cc_start: 0.6841 (tp30) cc_final: 0.6572 (tp30) outliers start: 58 outliers final: 34 residues processed: 361 average time/residue: 0.2111 time to fit residues: 117.6209 Evaluate side-chains 310 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 274 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 146 ILE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 323 LEU Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 556 LEU Chi-restraints excluded: chain C residue 587 LEU Chi-restraints excluded: chain C residue 604 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 679 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 104 ASN Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 519 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 122 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 GLN B 128 ASN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 14114 Z= 0.200 Angle : 0.714 10.993 19185 Z= 0.344 Chirality : 0.044 0.204 2252 Planarity : 0.004 0.040 2397 Dihedral : 5.456 41.507 1996 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.82 % Allowed : 22.82 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.97 (0.20), residues: 1734 helix: 0.62 (0.16), residues: 1043 sheet: -3.14 (3.33), residues: 5 loop : -2.71 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 541 HIS 0.007 0.001 HIS C 658 PHE 0.042 0.001 PHE A 193 TYR 0.028 0.002 TYR C 397 ARG 0.008 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 304 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7710 (pt0) cc_final: 0.7504 (pt0) REVERT: A 152 MET cc_start: 0.7756 (tpp) cc_final: 0.6332 (tpp) REVERT: A 153 GLN cc_start: 0.7226 (tp-100) cc_final: 0.6954 (pt0) REVERT: B 123 VAL cc_start: 0.7499 (m) cc_final: 0.7276 (p) REVERT: C 127 TRP cc_start: 0.7729 (m100) cc_final: 0.6791 (m-10) REVERT: C 505 TYR cc_start: 0.7415 (t80) cc_final: 0.6674 (t80) REVERT: C 599 GLU cc_start: 0.6297 (pm20) cc_final: 0.5858 (pm20) REVERT: C 711 PHE cc_start: 0.7149 (m-10) cc_final: 0.6853 (m-80) REVERT: D 224 LEU cc_start: 0.8635 (tp) cc_final: 0.8369 (mm) REVERT: D 314 GLU cc_start: 0.7288 (mp0) cc_final: 0.6771 (mp0) REVERT: D 401 MET cc_start: 0.6190 (mtp) cc_final: 0.5815 (mtp) outliers start: 42 outliers final: 29 residues processed: 327 average time/residue: 0.2118 time to fit residues: 107.3033 Evaluate side-chains 307 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 278 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain B residue 119 PHE Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 297 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 433 TYR Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 566 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 216 VAL Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 396 ASN Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 452 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 560 VAL Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Chi-restraints excluded: chain D residue 648 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.0060 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 160 optimal weight: 0.0980 chunk 146 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN B 173 ASN D 442 GLN ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 1.0517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14114 Z= 0.185 Angle : 0.708 10.601 19185 Z= 0.345 Chirality : 0.044 0.240 2252 Planarity : 0.004 0.048 2397 Dihedral : 5.184 34.026 1996 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.42 % Allowed : 23.96 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.90 (0.20), residues: 1734 helix: 0.68 (0.16), residues: 1044 sheet: None (None), residues: 0 loop : -2.72 (0.22), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 269 HIS 0.007 0.001 HIS C 658 PHE 0.023 0.001 PHE A 193 TYR 0.020 0.001 TYR D 433 ARG 0.007 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 301 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 GLN cc_start: 0.7327 (tp-100) cc_final: 0.6970 (pt0) REVERT: A 305 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6313 (tp) REVERT: C 127 TRP cc_start: 0.7897 (m100) cc_final: 0.6745 (m-10) REVERT: C 352 LEU cc_start: 0.6902 (mt) cc_final: 0.6260 (mp) REVERT: C 499 PHE cc_start: 0.7725 (m-80) cc_final: 0.7401 (m-80) REVERT: C 505 TYR cc_start: 0.7365 (t80) cc_final: 0.6651 (t80) REVERT: C 599 GLU cc_start: 0.6411 (pm20) cc_final: 0.5994 (pm20) REVERT: D 401 MET cc_start: 0.6944 (mtp) cc_final: 0.6649 (mtp) REVERT: D 416 GLU cc_start: 0.8031 (tp30) cc_final: 0.7826 (tp30) REVERT: D 652 SER cc_start: 0.8272 (m) cc_final: 0.7929 (t) outliers start: 36 outliers final: 23 residues processed: 322 average time/residue: 0.2146 time to fit residues: 105.2287 Evaluate side-chains 299 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 275 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Chi-restraints excluded: chain D residue 646 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 0.8980 chunk 160 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.0370 chunk 122 optimal weight: 0.0870 chunk 47 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 155 optimal weight: 0.5980 chunk 102 optimal weight: 5.9990 chunk 165 optimal weight: 0.0670 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 1.0820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14114 Z= 0.185 Angle : 0.726 11.493 19185 Z= 0.346 Chirality : 0.043 0.213 2252 Planarity : 0.004 0.045 2397 Dihedral : 5.187 40.208 1996 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.01 % Allowed : 24.90 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.87 (0.20), residues: 1734 helix: 0.69 (0.16), residues: 1048 sheet: None (None), residues: 0 loop : -2.69 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 269 HIS 0.007 0.001 HIS C 658 PHE 0.037 0.001 PHE A 119 TYR 0.019 0.001 TYR D 433 ARG 0.008 0.000 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 293 time to evaluate : 1.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7468 (mt-10) REVERT: A 97 GLU cc_start: 0.7666 (pt0) cc_final: 0.7413 (pt0) REVERT: A 152 MET cc_start: 0.7694 (tpp) cc_final: 0.6757 (ttp) REVERT: A 153 GLN cc_start: 0.7254 (tp-100) cc_final: 0.6883 (pt0) REVERT: A 305 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6354 (tp) REVERT: C 127 TRP cc_start: 0.7765 (m100) cc_final: 0.6774 (m-10) REVERT: C 352 LEU cc_start: 0.6817 (mt) cc_final: 0.6151 (mp) REVERT: C 413 GLN cc_start: 0.7823 (mt0) cc_final: 0.7314 (mp10) REVERT: C 504 THR cc_start: 0.8809 (OUTLIER) cc_final: 0.8490 (m) REVERT: C 505 TYR cc_start: 0.7361 (t80) cc_final: 0.6724 (t80) REVERT: C 599 GLU cc_start: 0.6418 (pm20) cc_final: 0.6022 (pm20) REVERT: D 401 MET cc_start: 0.6888 (mtp) cc_final: 0.6555 (mtp) REVERT: D 497 TYR cc_start: 0.8028 (t80) cc_final: 0.7655 (t80) REVERT: D 652 SER cc_start: 0.8300 (m) cc_final: 0.7968 (t) outliers start: 30 outliers final: 23 residues processed: 312 average time/residue: 0.2153 time to fit residues: 103.3229 Evaluate side-chains 300 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 275 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 114 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 159 optimal weight: 0.0980 chunk 138 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 0.0870 chunk 109 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 overall best weight: 0.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 1.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 14114 Z= 0.206 Angle : 0.757 10.314 19185 Z= 0.366 Chirality : 0.045 0.304 2252 Planarity : 0.004 0.042 2397 Dihedral : 5.166 35.715 1996 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.04 % Favored : 92.91 % Rotamer: Outliers : 2.08 % Allowed : 25.57 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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 (0.20), residues: 1734 helix: 0.67 (0.16), residues: 1047 sheet: -3.12 (3.40), residues: 5 loop : -2.60 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 269 HIS 0.008 0.001 HIS B 253 PHE 0.029 0.002 PHE A 119 TYR 0.019 0.001 TYR D 433 ARG 0.010 0.000 ARG C 756 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3468 Ramachandran restraints generated. 1734 Oldfield, 0 Emsley, 1734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 319 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7575 (mt-10) REVERT: A 97 GLU cc_start: 0.7863 (pt0) cc_final: 0.7650 (pt0) REVERT: A 153 GLN cc_start: 0.7383 (tp-100) cc_final: 0.7096 (pt0) REVERT: A 305 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.6421 (tp) REVERT: B 262 MET cc_start: 0.6846 (tpp) cc_final: 0.6490 (tpp) REVERT: C 127 TRP cc_start: 0.7975 (m100) cc_final: 0.7095 (m-10) REVERT: C 325 TRP cc_start: 0.8241 (t-100) cc_final: 0.8034 (t60) REVERT: C 332 MET cc_start: 0.7765 (tpp) cc_final: 0.7466 (mmm) REVERT: C 413 GLN cc_start: 0.7982 (mt0) cc_final: 0.7564 (mp10) REVERT: C 499 PHE cc_start: 0.8171 (m-80) cc_final: 0.7934 (m-80) REVERT: C 504 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8583 (m) REVERT: C 505 TYR cc_start: 0.7715 (t80) cc_final: 0.7337 (t80) REVERT: C 599 GLU cc_start: 0.6719 (pm20) cc_final: 0.6435 (pm20) REVERT: C 711 PHE cc_start: 0.6854 (m-10) cc_final: 0.6358 (m-80) REVERT: C 767 ARG cc_start: 0.5212 (ptm160) cc_final: 0.3857 (ptm160) REVERT: D 401 MET cc_start: 0.7064 (mtp) cc_final: 0.6795 (mtp) REVERT: D 652 SER cc_start: 0.8425 (m) cc_final: 0.7999 (t) outliers start: 31 outliers final: 23 residues processed: 340 average time/residue: 0.2283 time to fit residues: 117.5339 Evaluate side-chains 310 residues out of total 1526 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 285 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 166 TRP Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 359 ASN Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 771 VAL Chi-restraints excluded: chain C residue 773 ASP Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain D residue 333 ILE Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 431 LEU Chi-restraints excluded: chain D residue 532 LEU Chi-restraints excluded: chain D residue 611 VAL Chi-restraints excluded: chain D residue 630 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 0.2980 chunk 20 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 17 optimal weight: 0.0980 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 555 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.128037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.112211 restraints weight = 32667.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.115031 restraints weight = 15620.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.116885 restraints weight = 9230.878| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 1.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 14114 Z= 0.281 Angle : 0.812 11.538 19185 Z= 0.400 Chirality : 0.047 0.248 2252 Planarity : 0.005 0.039 2397 Dihedral : 5.390 34.473 1996 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.42 % Allowed : 26.91 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.02 (0.20), residues: 1734 helix: 0.54 (0.16), residues: 1043 sheet: -4.16 (1.68), residues: 10 loop : -2.64 (0.22), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP A 269 HIS 0.008 0.001 HIS C 658 PHE 0.022 0.002 PHE D 528 TYR 0.020 0.002 TYR D 433 ARG 0.008 0.001 ARG D 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3061.44 seconds wall clock time: 55 minutes 55.96 seconds (3355.96 seconds total)