Starting phenix.real_space_refine on Sat Feb 17 05:11:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8age_15421/02_2024/8age_15421_updated.pdb" } resolution = 2.8 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= 0.003 sd= 0.050 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 5 5.49 5 Mg 1 5.21 5 S 54 5.16 5 C 11558 2.51 5 N 2697 2.21 5 O 3219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 136": "OE1" <-> "OE2" Residue "A ARG 497": "NH1" <-> "NH2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 563": "OE1" <-> "OE2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 649": "NH1" <-> "NH2" Residue "A GLU 668": "OE1" <-> "OE2" Residue "A ARG 693": "NH1" <-> "NH2" Residue "A GLU 697": "OE1" <-> "OE2" Residue "A ARG 700": "NH1" <-> "NH2" Residue "A ARG 707": "NH1" <-> "NH2" Residue "D ARG 69": "NH1" <-> "NH2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "E GLU 111": "OE1" <-> "OE2" Residue "E ARG 113": "NH1" <-> "NH2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 204": "OE1" <-> "OE2" Residue "E GLU 209": "OE1" <-> "OE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 283": "NH1" <-> "NH2" Residue "E GLU 317": "OE1" <-> "OE2" Residue "E ARG 326": "NH1" <-> "NH2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E GLU 388": "OE1" <-> "OE2" Residue "E ARG 424": "NH1" <-> "NH2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F GLU 94": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F GLU 145": "OE1" <-> "OE2" Residue "F GLU 256": "OE1" <-> "OE2" Residue "F ARG 277": "NH1" <-> "NH2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G GLU 104": "OE1" <-> "OE2" Residue "G ARG 141": "NH1" <-> "NH2" Residue "G GLU 149": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G ARG 196": "NH1" <-> "NH2" Residue "G GLU 248": "OE1" <-> "OE2" Residue "G GLU 260": "OE1" <-> "OE2" Residue "G GLU 302": "OE1" <-> "OE2" Residue "G ARG 349": "NH1" <-> "NH2" Residue "H ARG 217": "NH1" <-> "NH2" Residue "H GLU 269": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17534 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 5191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 644, 5191 Classifications: {'peptide': 644} Link IDs: {'PTRANS': 24, 'TRANS': 619} Chain breaks: 3 Chain: "B" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 251 Classifications: {'peptide': 33} Link IDs: {'TRANS': 32} Chain: "C" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 666 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "D" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 883 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 105} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "E" Number of atoms: 3537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3537 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 24, 'TRANS': 413} Chain breaks: 1 Chain: "F" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1892 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 15, 'TRANS': 242} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 100 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 3201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3201 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain: "H" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1067 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "P" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 44 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 238 Unusual residues: {' MG': 1, 'CPL': 1, 'KZB': 3, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 138 Unusual residues: {'CPL': 1, 'KZB': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'CPL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 171 Unusual residues: {'CPL': 1, 'KZB': 2, 'MAN': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 107 Unusual residues: {'BMA': 1, 'KZB': 1, 'MAN': 1, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'323': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 10.83, per 1000 atoms: 0.62 Number of scatterers: 17534 At special positions: 0 Unit cell: (125.8, 119, 154.7, 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) S 54 16.00 P 5 15.00 Mg 1 11.99 O 3219 8.00 N 2697 7.00 C 11558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Links applied ALPHA1-2 " MAN F 301 " - " MAN G 503 " " MAN F 301 " - " MAN F 302 " ALPHA1-3 " BMA G 502 " - " MAN G 503 " ALPHA1-6 " MAN F 303 " - " BMA G 502 " ~> Even though BMA is a beta isomer, an alpha linkage is required... BETA1-4 " NAG A 801 " - " NAG G 501 " " NAG G 501 " - " BMA G 502 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 801 " - " ASN A 539 " " NAG G 504 " - " ASN G 332 " " NAG G 505 " - " ASN G 60 " " NAG I 1 " - " ASN E 336 " " NAG J 1 " - " ASN E 400 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3984 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 18 sheets defined 41.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 8 through 38 removed outlier: 4.552A pdb=" N PHE A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N VAL A 36 " --> pdb=" O ARG A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 89 through 103 Processing helix chain 'A' and resid 111 through 137 removed outlier: 5.170A pdb=" N ALA A 119 " --> pdb=" O CYS A 115 " (cutoff:3.500A) Proline residue: A 120 - end of helix removed outlier: 4.301A pdb=" N GLY A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N VAL A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 152 removed outlier: 3.994A pdb=" N ILE A 152 " --> pdb=" O GLY A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 159 removed outlier: 5.030A pdb=" N ARG A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.570A pdb=" N ILE A 170 " --> pdb=" O ASN A 167 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ILE A 172 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU A 175 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS A 187 " --> pdb=" O LYS A 184 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR A 188 " --> pdb=" O ALA A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 207 Processing helix chain 'A' and resid 209 through 227 removed outlier: 4.145A pdb=" N VAL A 212 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE A 218 " --> pdb=" O THR A 215 " (cutoff:3.500A) Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 233 through 252 removed outlier: 3.650A pdb=" N MET A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 252 " --> pdb=" O VAL A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 Proline residue: A 260 - end of helix No H-bonds generated for 'chain 'A' and resid 257 through 262' Processing helix chain 'A' and resid 264 through 288 removed outlier: 5.370A pdb=" N ALA A 268 " --> pdb=" O ASP A 265 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA A 269 " --> pdb=" O HIS A 266 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 270 " --> pdb=" O MET A 267 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 275 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE A 276 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL A 279 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.675A pdb=" N PHE A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASP A 362 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 378 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 383 through 401 Processing helix chain 'A' and resid 403 through 428 removed outlier: 3.912A pdb=" N LEU A 407 " --> pdb=" O ARG A 404 " (cutoff:3.500A) Proline residue: A 411 - end of helix removed outlier: 4.383A pdb=" N LEU A 421 " --> pdb=" O ALA A 418 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR A 428 " --> pdb=" O PHE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 472 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 517 through 526 removed outlier: 5.111A pdb=" N TYR A 521 " --> pdb=" O ASP A 518 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 522 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 551 Processing helix chain 'A' and resid 554 through 563 Processing helix chain 'A' and resid 583 through 597 removed outlier: 4.492A pdb=" N LEU A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP A 589 " --> pdb=" O ASN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 607 Processing helix chain 'A' and resid 622 through 625 No H-bonds generated for 'chain 'A' and resid 622 through 625' Processing helix chain 'A' and resid 628 through 633 Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'B' and resid 4 through 31 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 22 through 48 Proline residue: C 26 - end of helix removed outlier: 3.584A pdb=" N ILE C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 82 removed outlier: 3.876A pdb=" N PHE C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU C 69 " --> pdb=" O VAL C 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 68 removed outlier: 3.782A pdb=" N GLY D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 99 removed outlier: 3.940A pdb=" N CYS D 84 " --> pdb=" O GLY D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 128 Processing helix chain 'E' and resid 72 through 77 Processing helix chain 'E' and resid 270 through 278 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 443 through 468 removed outlier: 4.325A pdb=" N LYS E 449 " --> pdb=" O SER E 445 " (cutoff:3.500A) Proline residue: E 450 - end of helix Processing helix chain 'F' and resid 117 through 125 removed outlier: 3.598A pdb=" N ALA F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 213 Processing helix chain 'F' and resid 227 through 250 Processing helix chain 'F' and resid 254 through 278 Proline residue: F 267 - end of helix Processing helix chain 'G' and resid 37 through 50 removed outlier: 4.892A pdb=" N VAL G 42 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR G 43 " --> pdb=" O TYR G 40 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 45 " --> pdb=" O VAL G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 93 Processing helix chain 'G' and resid 96 through 104 Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 155 through 157 No H-bonds generated for 'chain 'G' and resid 155 through 157' Processing helix chain 'G' and resid 212 through 214 No H-bonds generated for 'chain 'G' and resid 212 through 214' Processing helix chain 'G' and resid 240 through 242 No H-bonds generated for 'chain 'G' and resid 240 through 242' Processing helix chain 'G' and resid 247 through 258 removed outlier: 3.650A pdb=" N PHE G 258 " --> pdb=" O LEU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 386 through 388 No H-bonds generated for 'chain 'G' and resid 386 through 388' Processing helix chain 'G' and resid 390 through 414 removed outlier: 3.581A pdb=" N VAL G 394 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G 396 " --> pdb=" O TRP G 393 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER G 397 " --> pdb=" O VAL G 394 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA G 398 " --> pdb=" O TYR G 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 217 through 232 Processing helix chain 'H' and resid 237 through 240 No H-bonds generated for 'chain 'H' and resid 237 through 240' Processing helix chain 'H' and resid 268 through 289 Processing helix chain 'H' and resid 291 through 298 Processing helix chain 'H' and resid 306 through 334 removed outlier: 3.911A pdb=" N LYS H 334 " --> pdb=" O VAL H 330 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 568 through 572 removed outlier: 6.194A pdb=" N GLN A 681 " --> pdb=" O GLU A 668 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU A 668 " --> pdb=" O GLN A 681 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 645 through 648 removed outlier: 3.810A pdb=" N GLN A 653 " --> pdb=" O ASP A 648 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 197 through 199 removed outlier: 3.779A pdb=" N SER E 202 " --> pdb=" O ASN E 199 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR E 54 " --> pdb=" O VAL E 34 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR E 36 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLU E 52 " --> pdb=" O TYR E 36 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ARG E 38 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N THR E 50 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ILE E 40 " --> pdb=" O SER E 48 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER E 48 " --> pdb=" O ILE E 40 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE E 47 " --> pdb=" O TYR E 137 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 65 through 70 removed outlier: 3.922A pdb=" N ASN E 93 " --> pdb=" O GLN E 118 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 155 through 161 Processing sheet with id= F, first strand: chain 'E' and resid 400 through 406 removed outlier: 8.360A pdb=" N GLU E 378 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU E 236 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N SER E 380 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG E 238 " --> pdb=" O SER E 380 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N PHE E 382 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ILE E 240 " --> pdb=" O PHE E 382 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N GLU E 256 " --> pdb=" O VAL E 234 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU E 236 " --> pdb=" O TYR E 254 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR E 254 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ARG E 238 " --> pdb=" O GLU E 252 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLU E 252 " --> pdb=" O ARG E 238 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE E 240 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN E 250 " --> pdb=" O ILE E 240 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU E 242 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N THR E 248 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 291 through 294 Processing sheet with id= H, first strand: chain 'E' and resid 349 through 351 removed outlier: 6.259A pdb=" N ASP E 440 " --> pdb=" O ILE E 389 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE E 389 " --> pdb=" O ASP E 440 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 66 through 68 removed outlier: 6.698A pdb=" N SER F 104 " --> pdb=" O PHE F 26 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER F 28 " --> pdb=" O SER F 104 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR F 106 " --> pdb=" O SER F 28 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ALA F 30 " --> pdb=" O TYR F 106 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR F 108 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LYS F 32 " --> pdb=" O TYR F 108 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N ILE F 110 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 77 through 83 removed outlier: 3.765A pdb=" N LEU F 152 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU F 134 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLU F 150 " --> pdb=" O LEU F 134 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU F 136 " --> pdb=" O PHE F 148 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N PHE F 148 " --> pdb=" O LEU F 136 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 54 through 58 removed outlier: 6.466A pdb=" N THR G 26 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N LEU G 57 " --> pdb=" O THR G 26 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL G 28 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN G 78 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N LEU G 29 " --> pdb=" O ASN G 78 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ILE G 80 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASN G 108 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL G 81 " --> pdb=" O ASN G 108 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU G 110 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N GLY G 220 " --> pdb=" O PRO G 190 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLN G 222 " --> pdb=" O ILE G 188 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE G 188 " --> pdb=" O GLN G 222 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 131 through 133 Processing sheet with id= M, first strand: chain 'G' and resid 138 through 141 Processing sheet with id= N, first strand: chain 'G' and resid 152 through 154 Processing sheet with id= O, first strand: chain 'G' and resid 263 through 267 removed outlier: 3.854A pdb=" N VAL G 263 " --> pdb=" O TRP G 299 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR G 292 " --> pdb=" O THR G 341 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 270 through 273 Processing sheet with id= Q, first strand: chain 'G' and resid 297 through 299 Processing sheet with id= R, first strand: chain 'G' and resid 367 through 375 removed outlier: 4.278A pdb=" N ASP G 358 " --> pdb=" O GLN G 313 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN G 313 " --> pdb=" O ASP G 358 " (cutoff:3.500A) 759 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.27 Time building geometry restraints manager: 8.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2653 1.31 - 1.43: 5054 1.43 - 1.56: 10142 1.56 - 1.68: 81 1.68 - 1.81: 91 Bond restraints: 18021 Sorted by residual: bond pdb=" C03 KZB B 101 " pdb=" C04 KZB B 101 " ideal model delta sigma weight residual 2.203 1.524 0.679 2.00e-02 2.50e+03 1.15e+03 bond pdb=" C03 KZB F 305 " pdb=" C04 KZB F 305 " ideal model delta sigma weight residual 2.203 1.524 0.679 2.00e-02 2.50e+03 1.15e+03 bond pdb=" C03 KZB A 807 " pdb=" C04 KZB A 807 " ideal model delta sigma weight residual 2.203 1.525 0.678 2.00e-02 2.50e+03 1.15e+03 bond pdb=" C03 KZB F 306 " pdb=" C04 KZB F 306 " ideal model delta sigma weight residual 2.203 1.525 0.678 2.00e-02 2.50e+03 1.15e+03 bond pdb=" C03 KZB B 102 " pdb=" C04 KZB B 102 " ideal model delta sigma weight residual 2.203 1.526 0.677 2.00e-02 2.50e+03 1.14e+03 ... (remaining 18016 not shown) Histogram of bond angle deviations from ideal: 93.10 - 101.31: 64 101.31 - 109.51: 1999 109.51 - 117.72: 11572 117.72 - 125.92: 10627 125.92 - 134.12: 296 Bond angle restraints: 24558 Sorted by residual: angle pdb=" C ILE A 709 " pdb=" N LYS A 710 " pdb=" CA LYS A 710 " ideal model delta sigma weight residual 121.54 133.43 -11.89 1.91e+00 2.74e-01 3.87e+01 angle pdb=" O11 PTY A 803 " pdb=" P1 PTY A 803 " pdb=" O14 PTY A 803 " ideal model delta sigma weight residual 92.90 109.77 -16.87 3.00e+00 1.11e-01 3.16e+01 angle pdb=" N ARG F 34 " pdb=" CA ARG F 34 " pdb=" C ARG F 34 " ideal model delta sigma weight residual 113.97 106.99 6.98 1.28e+00 6.10e-01 2.98e+01 angle pdb=" O3P CPL F 304 " pdb=" P CPL F 304 " pdb=" O4P CPL F 304 " ideal model delta sigma weight residual 93.29 109.53 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" O3P CPL E 501 " pdb=" P CPL E 501 " pdb=" O4P CPL E 501 " ideal model delta sigma weight residual 93.29 109.00 -15.71 3.00e+00 1.11e-01 2.74e+01 ... (remaining 24553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 10324 35.73 - 71.46: 331 71.46 - 107.19: 66 107.19 - 142.91: 29 142.91 - 178.64: 4 Dihedral angle restraints: 10754 sinusoidal: 4587 harmonic: 6167 Sorted by residual: dihedral pdb=" CA TRP A 75 " pdb=" C TRP A 75 " pdb=" N TYR A 76 " pdb=" CA TYR A 76 " ideal model delta harmonic sigma weight residual 180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" O2 CPL F 304 " pdb=" C1 CPL F 304 " pdb=" C2 CPL F 304 " pdb=" O3P CPL F 304 " ideal model delta sinusoidal sigma weight residual -50.82 127.82 -178.64 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3 CPL F 304 " pdb=" C1 CPL F 304 " pdb=" C2 CPL F 304 " pdb=" O3P CPL F 304 " ideal model delta sinusoidal sigma weight residual 72.09 -112.36 -175.55 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 10751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.953: 2844 0.953 - 1.906: 0 1.906 - 2.859: 0 2.859 - 3.813: 0 3.813 - 4.766: 8 Chirality restraints: 2852 Sorted by residual: chirality pdb=" C23 KZB A 805 " pdb=" C74 KZB A 805 " pdb=" O22 KZB A 805 " pdb=" O24 KZB A 805 " both_signs ideal model delta sigma weight residual False 2.35 -2.41 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" C23 KZB G 506 " pdb=" C74 KZB G 506 " pdb=" O22 KZB G 506 " pdb=" O24 KZB G 506 " both_signs ideal model delta sigma weight residual False 2.35 -2.41 4.77 2.00e-01 2.50e+01 5.68e+02 chirality pdb=" C23 KZB F 306 " pdb=" C74 KZB F 306 " pdb=" O22 KZB F 306 " pdb=" O24 KZB F 306 " both_signs ideal model delta sigma weight residual False 2.35 -2.41 4.76 2.00e-01 2.50e+01 5.67e+02 ... (remaining 2849 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 323 P 101 " -0.033 2.00e-02 2.50e+03 3.28e-01 5.10e+03 pdb=" C10 323 P 101 " 0.151 2.00e-02 2.50e+03 pdb=" C11 323 P 101 " 0.170 2.00e-02 2.50e+03 pdb=" C12 323 P 101 " 0.022 2.00e-02 2.50e+03 pdb=" C13 323 P 101 " -0.141 2.00e-02 2.50e+03 pdb=" C16 323 P 101 " -0.848 2.00e-02 2.50e+03 pdb=" C17 323 P 101 " 1.006 2.00e-02 2.50e+03 pdb=" C18 323 P 101 " 0.069 2.00e-02 2.50e+03 pdb=" C2 323 P 101 " -0.012 2.00e-02 2.50e+03 pdb=" C3 323 P 101 " -0.158 2.00e-02 2.50e+03 pdb=" C4 323 P 101 " -0.157 2.00e-02 2.50e+03 pdb=" C5 323 P 101 " -0.012 2.00e-02 2.50e+03 pdb=" C6 323 P 101 " -0.142 2.00e-02 2.50e+03 pdb=" C7 323 P 101 " 0.020 2.00e-02 2.50e+03 pdb=" C8 323 P 101 " 0.167 2.00e-02 2.50e+03 pdb=" C9 323 P 101 " 0.152 2.00e-02 2.50e+03 pdb=" N1 323 P 101 " 0.042 2.00e-02 2.50e+03 pdb=" N2 323 P 101 " 0.033 2.00e-02 2.50e+03 pdb=" O1 323 P 101 " -0.328 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 31 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C GLY F 31 " 0.060 2.00e-02 2.50e+03 pdb=" O GLY F 31 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS F 32 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 405 " 0.017 2.00e-02 2.50e+03 3.43e-02 1.18e+01 pdb=" C ALA G 405 " -0.059 2.00e-02 2.50e+03 pdb=" O ALA G 405 " 0.022 2.00e-02 2.50e+03 pdb=" N TRP G 406 " 0.020 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 411 2.69 - 3.24: 16626 3.24 - 3.79: 26385 3.79 - 4.35: 37093 4.35 - 4.90: 60872 Nonbonded interactions: 141387 Sorted by model distance: nonbonded pdb=" O LYS A 548 " pdb=" OG SER A 552 " model vdw 2.136 2.440 nonbonded pdb=" O SER A 392 " pdb=" OG SER A 396 " model vdw 2.191 2.440 nonbonded pdb=" OD2 ASP A 166 " pdb="MG MG A 804 " model vdw 2.192 2.170 nonbonded pdb=" NH1 ARG A 32 " pdb=" OG SER A 160 " model vdw 2.198 2.520 nonbonded pdb=" OD2 ASP A 582 " pdb=" NH2 ARG A 651 " model vdw 2.251 2.520 ... (remaining 141382 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 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 14.950 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 51.600 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.080 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:10.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.031 0.679 18021 Z= 1.994 Angle : 1.003 16.873 24558 Z= 0.447 Chirality : 0.264 4.766 2852 Planarity : 0.008 0.328 2957 Dihedral : 19.761 178.643 6770 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.34 % Favored : 95.52 % Rotamer: Outliers : 3.88 % Allowed : 18.85 % Favored : 77.27 % 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: -2.02 (0.17), residues: 2074 helix: -0.41 (0.16), residues: 869 sheet: -0.84 (0.26), residues: 378 loop : -2.57 (0.18), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 31 HIS 0.005 0.001 HIS A 465 PHE 0.017 0.001 PHE A 370 TYR 0.019 0.001 TYR A 239 ARG 0.010 0.001 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 218 time to evaluate : 2.234 Fit side-chains REVERT: B 32 MET cc_start: 0.7188 (mmt) cc_final: 0.6793 (mpt) REVERT: E 32 GLU cc_start: 0.7419 (pp20) cc_final: 0.7217 (pp20) REVERT: E 172 LYS cc_start: 0.7286 (OUTLIER) cc_final: 0.7011 (tptm) REVERT: E 192 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6661 (tp30) REVERT: E 195 LEU cc_start: 0.7566 (mt) cc_final: 0.7082 (mp) REVERT: E 209 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: E 219 THR cc_start: 0.8505 (OUTLIER) cc_final: 0.8253 (t) REVERT: E 278 GLN cc_start: 0.7393 (mt0) cc_final: 0.6893 (tm-30) REVERT: F 90 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7604 (mt-10) REVERT: F 91 MET cc_start: 0.8028 (mtp) cc_final: 0.7557 (mtp) REVERT: F 122 GLU cc_start: 0.7595 (tp30) cc_final: 0.7066 (tm-30) REVERT: F 142 LYS cc_start: 0.8401 (mttt) cc_final: 0.7953 (mmtm) REVERT: G 51 ASN cc_start: 0.8606 (m110) cc_final: 0.8308 (t0) REVERT: H 304 LYS cc_start: 0.6769 (mmtp) cc_final: 0.6468 (pttt) outliers start: 70 outliers final: 31 residues processed: 272 average time/residue: 1.1890 time to fit residues: 365.3017 Evaluate side-chains 197 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 162 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 CYS Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 600 GLU Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 219 THR Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 355 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 417 VAL Chi-restraints excluded: chain F residue 104 SER Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain G residue 65 THR Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 7.9990 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 186 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 60 ASN A 221 HIS A 277 GLN A 351 HIS A 352 GLN A 364 HIS ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN A 652 GLN A 653 GLN B 26 HIS C 80 ASN D 127 HIS E 126 GLN E 201 ASN E 232 GLN E 350 HIS E 413 ASN E 416 HIS E 429 GLN ** F 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 179 HIS G 93 GLN G 105 ASN G 108 ASN G 138 HIS G 214 GLN G 222 GLN G 226 ASN G 242 ASN G 271 HIS G 273 HIS G 318 GLN H 244 GLN H 263 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18021 Z= 0.348 Angle : 0.720 9.910 24558 Z= 0.339 Chirality : 0.050 0.524 2852 Planarity : 0.005 0.044 2957 Dihedral : 19.092 176.434 3034 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.95 % Favored : 95.90 % Rotamer: Outliers : 4.88 % Allowed : 19.96 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.18), residues: 2074 helix: 0.61 (0.17), residues: 866 sheet: -0.52 (0.28), residues: 380 loop : -2.21 (0.18), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 387 HIS 0.005 0.001 HIS A 465 PHE 0.024 0.002 PHE A 370 TYR 0.017 0.002 TYR A 239 ARG 0.007 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 166 time to evaluate : 2.028 Fit side-chains REVERT: A 555 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 639 GLN cc_start: 0.8821 (OUTLIER) cc_final: 0.7996 (mp-120) REVERT: A 651 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7951 (mtt-85) REVERT: E 172 LYS cc_start: 0.7375 (OUTLIER) cc_final: 0.7152 (tptm) REVERT: E 192 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6639 (tp30) REVERT: E 195 LEU cc_start: 0.7670 (mt) cc_final: 0.7103 (mp) REVERT: E 209 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7145 (tp30) REVERT: E 278 GLN cc_start: 0.7401 (mt0) cc_final: 0.6869 (tm-30) REVERT: F 91 MET cc_start: 0.8048 (mtp) cc_final: 0.7617 (mtp) REVERT: F 122 GLU cc_start: 0.7692 (tp30) cc_final: 0.7037 (tm-30) REVERT: F 142 LYS cc_start: 0.8404 (mttt) cc_final: 0.8128 (mptp) REVERT: G 50 ARG cc_start: 0.8048 (mtm-85) cc_final: 0.7717 (mtm-85) REVERT: G 51 ASN cc_start: 0.8644 (m110) cc_final: 0.8293 (t0) REVERT: G 255 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8603 (ttmm) REVERT: H 214 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8384 (pp) REVERT: H 304 LYS cc_start: 0.6770 (mmtp) cc_final: 0.6481 (pttt) outliers start: 88 outliers final: 44 residues processed: 235 average time/residue: 1.1806 time to fit residues: 313.9105 Evaluate side-chains 214 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 162 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 651 ARG Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain C residue 2 THR Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 297 GLU Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 444 SER Chi-restraints excluded: chain E residue 467 LEU Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 110 ILE Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 33 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 298 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 154 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 166 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 63 optimal weight: 20.0000 chunk 149 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 146 ASN G 105 ASN H 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18021 Z= 0.195 Angle : 0.622 10.782 24558 Z= 0.291 Chirality : 0.044 0.377 2852 Planarity : 0.004 0.042 2957 Dihedral : 17.120 171.868 3010 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.62 % Favored : 96.24 % Rotamer: Outliers : 4.05 % Allowed : 21.01 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2074 helix: 1.21 (0.18), residues: 862 sheet: -0.33 (0.28), residues: 382 loop : -1.95 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.005 0.001 HIS A 465 PHE 0.015 0.001 PHE A 370 TYR 0.015 0.001 TYR A 243 ARG 0.005 0.000 ARG A 651 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 173 time to evaluate : 1.963 Fit side-chains REVERT: A 344 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8790 (tp) REVERT: A 555 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7473 (mp0) REVERT: E 168 TYR cc_start: 0.7943 (m-10) cc_final: 0.7670 (m-10) REVERT: E 172 LYS cc_start: 0.7285 (OUTLIER) cc_final: 0.6983 (tptm) REVERT: E 175 PHE cc_start: 0.8592 (t80) cc_final: 0.8382 (t80) REVERT: E 192 GLU cc_start: 0.6982 (tm-30) cc_final: 0.6694 (tp30) REVERT: E 195 LEU cc_start: 0.7712 (mt) cc_final: 0.7192 (mp) REVERT: E 209 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6922 (tp30) REVERT: E 278 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6726 (tm-30) REVERT: F 91 MET cc_start: 0.8239 (mtp) cc_final: 0.7830 (mtp) REVERT: F 122 GLU cc_start: 0.7722 (tp30) cc_final: 0.6848 (tp30) REVERT: F 142 LYS cc_start: 0.8380 (mttt) cc_final: 0.8113 (mptp) REVERT: H 214 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.8371 (pp) REVERT: H 304 LYS cc_start: 0.6759 (mmtp) cc_final: 0.6432 (pttt) outliers start: 73 outliers final: 36 residues processed: 227 average time/residue: 1.1051 time to fit residues: 285.7936 Evaluate side-chains 207 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 2.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 4.9990 chunk 140 optimal weight: 30.0000 chunk 96 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 198 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 177 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 434 GLN G 105 ASN H 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 18021 Z= 0.429 Angle : 0.711 11.484 24558 Z= 0.340 Chirality : 0.049 0.372 2852 Planarity : 0.005 0.048 2957 Dihedral : 16.672 178.257 3001 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 5.54 % Allowed : 20.34 % Favored : 74.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.55 (0.18), residues: 2074 helix: 1.04 (0.17), residues: 863 sheet: -0.30 (0.28), residues: 382 loop : -1.93 (0.19), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 387 HIS 0.005 0.001 HIS A 465 PHE 0.025 0.002 PHE A 370 TYR 0.019 0.002 TYR E 409 ARG 0.005 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 167 time to evaluate : 2.169 Fit side-chains revert: symmetry clash REVERT: A 344 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8817 (tp) REVERT: A 555 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: A 639 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8014 (mp-120) REVERT: C 45 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.6144 (t80) REVERT: E 168 TYR cc_start: 0.8009 (m-10) cc_final: 0.7701 (m-10) REVERT: E 172 LYS cc_start: 0.7297 (OUTLIER) cc_final: 0.6928 (tptm) REVERT: E 192 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6698 (tp30) REVERT: E 195 LEU cc_start: 0.7785 (mt) cc_final: 0.7305 (mp) REVERT: E 209 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6888 (tp30) REVERT: E 278 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6796 (tm-30) REVERT: F 91 MET cc_start: 0.8262 (mtp) cc_final: 0.7892 (mtp) REVERT: F 122 GLU cc_start: 0.7799 (tp30) cc_final: 0.6903 (tp30) REVERT: F 142 LYS cc_start: 0.8451 (mttt) cc_final: 0.8029 (mmtm) REVERT: G 67 ASP cc_start: 0.8318 (m-30) cc_final: 0.7980 (m-30) REVERT: H 214 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8444 (pp) REVERT: H 304 LYS cc_start: 0.6755 (mmtp) cc_final: 0.6425 (pttt) outliers start: 100 outliers final: 55 residues processed: 241 average time/residue: 1.0754 time to fit residues: 296.6759 Evaluate side-chains 223 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 159 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 639 GLN Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 296 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 18021 Z= 0.365 Angle : 0.677 10.648 24558 Z= 0.323 Chirality : 0.047 0.341 2852 Planarity : 0.004 0.047 2957 Dihedral : 16.071 177.219 2999 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.76 % Favored : 96.09 % Rotamer: Outliers : 4.93 % Allowed : 21.62 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.44 (0.18), residues: 2074 helix: 1.11 (0.17), residues: 863 sheet: -0.15 (0.29), residues: 372 loop : -1.89 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 368 HIS 0.005 0.001 HIS A 465 PHE 0.023 0.002 PHE A 370 TYR 0.016 0.002 TYR E 409 ARG 0.004 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 165 time to evaluate : 1.989 Fit side-chains REVERT: A 555 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: C 45 PHE cc_start: 0.6394 (OUTLIER) cc_final: 0.6091 (t80) REVERT: E 38 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7321 (ttt180) REVERT: E 168 TYR cc_start: 0.7974 (m-10) cc_final: 0.7768 (m-10) REVERT: E 172 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6969 (tptm) REVERT: E 192 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6715 (tp30) REVERT: E 195 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7298 (mp) REVERT: E 209 GLU cc_start: 0.7407 (tt0) cc_final: 0.6822 (tp30) REVERT: E 278 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: F 91 MET cc_start: 0.8259 (mtp) cc_final: 0.7822 (mtp) REVERT: F 122 GLU cc_start: 0.7779 (tp30) cc_final: 0.6900 (tp30) REVERT: F 134 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7709 (mt) REVERT: F 142 LYS cc_start: 0.8539 (mttt) cc_final: 0.8113 (mptt) REVERT: G 67 ASP cc_start: 0.8271 (m-30) cc_final: 0.7934 (m-30) REVERT: G 255 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8948 (ttmt) REVERT: H 214 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8426 (pp) REVERT: H 304 LYS cc_start: 0.6812 (mmtp) cc_final: 0.6473 (pttt) outliers start: 89 outliers final: 58 residues processed: 232 average time/residue: 1.0968 time to fit residues: 290.5746 Evaluate side-chains 227 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 159 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 45 GLU Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 623 THR Chi-restraints excluded: chain A residue 656 THR Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain C residue 73 LEU Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 346 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain G residue 27 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 234 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 213 ILE Chi-restraints excluded: chain H residue 214 ILE Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 296 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 198 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18021 Z= 0.163 Angle : 0.581 9.465 24558 Z= 0.276 Chirality : 0.043 0.307 2852 Planarity : 0.004 0.044 2957 Dihedral : 15.229 176.551 2996 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.86 % Favored : 96.00 % Rotamer: Outliers : 3.60 % Allowed : 23.00 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.18), residues: 2074 helix: 1.46 (0.18), residues: 863 sheet: -0.08 (0.28), residues: 374 loop : -1.78 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 31 HIS 0.005 0.001 HIS A 465 PHE 0.013 0.001 PHE A 370 TYR 0.015 0.001 TYR A 243 ARG 0.002 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 173 time to evaluate : 1.951 Fit side-chains REVERT: A 555 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: A 711 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.8255 (mtp85) REVERT: E 38 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7205 (ttt180) REVERT: E 55 ILE cc_start: 0.8139 (pp) cc_final: 0.7934 (pp) REVERT: E 168 TYR cc_start: 0.7885 (m-10) cc_final: 0.7681 (m-10) REVERT: E 172 LYS cc_start: 0.7506 (OUTLIER) cc_final: 0.7079 (tptm) REVERT: E 192 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6686 (tp30) REVERT: E 195 LEU cc_start: 0.7703 (mt) cc_final: 0.7374 (mp) REVERT: E 209 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.6978 (tp30) REVERT: E 278 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6616 (tm-30) REVERT: F 90 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7647 (mt-10) REVERT: F 91 MET cc_start: 0.8305 (mtp) cc_final: 0.7911 (mtp) REVERT: F 108 TYR cc_start: 0.5069 (OUTLIER) cc_final: 0.4713 (p90) REVERT: F 122 GLU cc_start: 0.7808 (tp30) cc_final: 0.6947 (tp30) REVERT: F 142 LYS cc_start: 0.8430 (mttt) cc_final: 0.8097 (mptt) REVERT: G 52 TYR cc_start: 0.7838 (m-80) cc_final: 0.7621 (m-80) REVERT: G 67 ASP cc_start: 0.8278 (m-30) cc_final: 0.7910 (m-30) REVERT: G 112 MET cc_start: 0.8669 (mtm) cc_final: 0.8121 (mtt) REVERT: G 255 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.9007 (ttmt) REVERT: H 304 LYS cc_start: 0.6771 (mmtp) cc_final: 0.6474 (pttt) outliers start: 65 outliers final: 36 residues processed: 226 average time/residue: 1.1371 time to fit residues: 292.5535 Evaluate side-chains 215 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 555 GLU Chi-restraints excluded: chain A residue 711 ARG Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 38 ARG Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 108 TYR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 275 LEU Chi-restraints excluded: chain H residue 296 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 144 optimal weight: 0.0570 chunk 112 optimal weight: 0.8980 chunk 166 optimal weight: 0.0370 chunk 110 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 91 optimal weight: 0.0470 overall best weight: 0.3274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN H 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18021 Z= 0.139 Angle : 0.562 9.930 24558 Z= 0.263 Chirality : 0.042 0.306 2852 Planarity : 0.004 0.043 2957 Dihedral : 14.480 170.421 2996 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % Rotamer: Outliers : 3.27 % Allowed : 23.45 % Favored : 73.28 % 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: 0.07 (0.18), residues: 2074 helix: 1.63 (0.18), residues: 875 sheet: -0.05 (0.28), residues: 382 loop : -1.72 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.005 0.000 HIS A 465 PHE 0.009 0.001 PHE A 370 TYR 0.010 0.001 TYR A 239 ARG 0.003 0.000 ARG A 625 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 178 time to evaluate : 1.944 Fit side-chains REVERT: A 654 MET cc_start: 0.7475 (mmm) cc_final: 0.7240 (mmt) REVERT: E 172 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6816 (tmtt) REVERT: E 192 GLU cc_start: 0.6980 (OUTLIER) cc_final: 0.6708 (tp30) REVERT: E 195 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7250 (mp) REVERT: E 209 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: E 278 GLN cc_start: 0.7012 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: F 91 MET cc_start: 0.8354 (mtp) cc_final: 0.7973 (mtp) REVERT: F 122 GLU cc_start: 0.7816 (tp30) cc_final: 0.7075 (tp30) REVERT: F 142 LYS cc_start: 0.8429 (mttt) cc_final: 0.8036 (mmtm) REVERT: F 184 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.5512 (mp0) REVERT: G 46 ASP cc_start: 0.7637 (t0) cc_final: 0.7410 (t0) REVERT: G 52 TYR cc_start: 0.7810 (m-80) cc_final: 0.7550 (m-80) REVERT: G 67 ASP cc_start: 0.8273 (m-30) cc_final: 0.7917 (m-30) REVERT: G 112 MET cc_start: 0.8634 (mtm) cc_final: 0.8106 (mtt) REVERT: G 255 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.9011 (ttmt) REVERT: H 304 LYS cc_start: 0.6753 (mmtp) cc_final: 0.6421 (pttt) outliers start: 59 outliers final: 27 residues processed: 227 average time/residue: 1.1718 time to fit residues: 301.2528 Evaluate side-chains 201 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 53 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 255 LYS Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 332 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN A 626 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN G 105 ASN H 263 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.1983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18021 Z= 0.226 Angle : 0.598 9.693 24558 Z= 0.285 Chirality : 0.043 0.314 2852 Planarity : 0.004 0.045 2957 Dihedral : 14.391 164.451 2992 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 3.44 % Allowed : 23.56 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.18), residues: 2074 helix: 1.61 (0.18), residues: 869 sheet: 0.05 (0.28), residues: 378 loop : -1.63 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 368 HIS 0.005 0.001 HIS A 465 PHE 0.020 0.001 PHE A 370 TYR 0.021 0.001 TYR E 25 ARG 0.003 0.000 ARG E 238 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 174 time to evaluate : 2.175 Fit side-chains REVERT: E 172 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6789 (tmtt) REVERT: E 192 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6688 (tp30) REVERT: E 195 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7306 (mp) REVERT: E 209 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.7201 (tp30) REVERT: E 278 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6561 (tm-30) REVERT: F 91 MET cc_start: 0.8330 (mtp) cc_final: 0.7949 (mtp) REVERT: F 122 GLU cc_start: 0.7834 (tp30) cc_final: 0.7004 (tp30) REVERT: F 142 LYS cc_start: 0.8361 (mttt) cc_final: 0.8033 (mptt) REVERT: F 184 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5477 (mp0) REVERT: G 46 ASP cc_start: 0.7649 (t0) cc_final: 0.7417 (t0) REVERT: G 67 ASP cc_start: 0.8289 (m-30) cc_final: 0.7927 (m-30) REVERT: G 112 MET cc_start: 0.8656 (mtm) cc_final: 0.8132 (mtt) REVERT: H 304 LYS cc_start: 0.6735 (mmtp) cc_final: 0.6422 (pttt) outliers start: 62 outliers final: 35 residues processed: 221 average time/residue: 1.1018 time to fit residues: 277.2609 Evaluate side-chains 211 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 408 THR Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 685 ASP Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain C residue 23 ASP Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 170 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 278 GLN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 0.9990 chunk 172 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 144 optimal weight: 3.9990 chunk 56 optimal weight: 0.3980 chunk 166 optimal weight: 0.3980 chunk 174 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN H 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18021 Z= 0.165 Angle : 0.572 9.198 24558 Z= 0.272 Chirality : 0.042 0.304 2852 Planarity : 0.004 0.043 2957 Dihedral : 14.104 162.786 2992 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.47 % Favored : 96.38 % Rotamer: Outliers : 3.33 % Allowed : 24.00 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.18), residues: 2074 helix: 1.69 (0.18), residues: 869 sheet: 0.10 (0.28), residues: 377 loop : -1.59 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.004 0.001 HIS A 465 PHE 0.013 0.001 PHE A 370 TYR 0.023 0.001 TYR D 41 ARG 0.002 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 177 time to evaluate : 2.213 Fit side-chains REVERT: E 172 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.6760 (tmtt) REVERT: E 192 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: E 195 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7330 (mp) REVERT: E 209 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7302 (tp30) REVERT: E 278 GLN cc_start: 0.6994 (mt0) cc_final: 0.6613 (tm-30) REVERT: E 470 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7084 (pp) REVERT: F 91 MET cc_start: 0.8365 (mtp) cc_final: 0.8026 (mtp) REVERT: F 122 GLU cc_start: 0.7845 (tp30) cc_final: 0.7161 (tp30) REVERT: F 142 LYS cc_start: 0.8373 (mttt) cc_final: 0.8059 (mptt) REVERT: F 184 GLU cc_start: 0.6420 (OUTLIER) cc_final: 0.5471 (mp0) REVERT: G 46 ASP cc_start: 0.7624 (t0) cc_final: 0.7418 (t0) REVERT: G 67 ASP cc_start: 0.8277 (m-30) cc_final: 0.7926 (m-30) REVERT: G 112 MET cc_start: 0.8656 (mtm) cc_final: 0.8142 (mtt) REVERT: H 304 LYS cc_start: 0.6744 (mmtp) cc_final: 0.6430 (pttt) outliers start: 60 outliers final: 39 residues processed: 221 average time/residue: 1.2573 time to fit residues: 320.0499 Evaluate side-chains 210 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 165 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 180 MET Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain B residue 4 ASP Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 192 GLU Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 140 THR Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 224 THR Chi-restraints excluded: chain F residue 260 SER Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain G residue 412 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 314 SER Chi-restraints excluded: chain H residue 332 THR Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 92 optimal weight: 0.0060 chunk 135 optimal weight: 0.0670 chunk 204 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 GLN G 105 ASN H 263 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18021 Z= 0.145 Angle : 0.558 9.372 24558 Z= 0.265 Chirality : 0.042 0.302 2852 Planarity : 0.004 0.042 2957 Dihedral : 13.800 163.018 2991 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.38 % Favored : 96.48 % Rotamer: Outliers : 2.49 % Allowed : 24.94 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.19), residues: 2074 helix: 1.75 (0.18), residues: 875 sheet: 0.12 (0.28), residues: 377 loop : -1.58 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP E 31 HIS 0.005 0.000 HIS A 465 PHE 0.011 0.001 PHE E 175 TYR 0.028 0.001 TYR D 41 ARG 0.002 0.000 ARG G 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4148 Ramachandran restraints generated. 2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 175 time to evaluate : 1.990 Fit side-chains REVERT: A 247 THR cc_start: 0.8769 (t) cc_final: 0.8542 (m) REVERT: E 172 LYS cc_start: 0.7312 (OUTLIER) cc_final: 0.6611 (tmtp) REVERT: E 209 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: E 278 GLN cc_start: 0.6805 (mt0) cc_final: 0.6548 (tm-30) REVERT: E 470 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7059 (pp) REVERT: F 91 MET cc_start: 0.8349 (mtp) cc_final: 0.8037 (mtp) REVERT: F 122 GLU cc_start: 0.7856 (tp30) cc_final: 0.7163 (tp30) REVERT: F 142 LYS cc_start: 0.8361 (mttt) cc_final: 0.7985 (mmtm) REVERT: F 184 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5492 (mp0) REVERT: G 46 ASP cc_start: 0.7633 (t0) cc_final: 0.7387 (t0) REVERT: G 67 ASP cc_start: 0.8264 (m-30) cc_final: 0.7903 (m-30) REVERT: G 112 MET cc_start: 0.8660 (mtm) cc_final: 0.8144 (mtt) REVERT: H 255 MET cc_start: 0.7167 (mtp) cc_final: 0.6850 (ttm) REVERT: H 304 LYS cc_start: 0.6812 (mmtp) cc_final: 0.6542 (pttt) outliers start: 45 outliers final: 30 residues processed: 214 average time/residue: 1.0436 time to fit residues: 256.3011 Evaluate side-chains 203 residues out of total 1850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 169 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 378 PHE Chi-restraints excluded: chain A residue 383 ASP Chi-restraints excluded: chain A residue 395 CYS Chi-restraints excluded: chain A residue 542 HIS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 684 LYS Chi-restraints excluded: chain A residue 714 LEU Chi-restraints excluded: chain D residue 99 CYS Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 172 LYS Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 310 LEU Chi-restraints excluded: chain E residue 312 SER Chi-restraints excluded: chain E residue 352 SER Chi-restraints excluded: chain E residue 373 VAL Chi-restraints excluded: chain E residue 470 LEU Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 272 SER Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 169 SER Chi-restraints excluded: chain G residue 177 SER Chi-restraints excluded: chain G residue 245 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 312 ILE Chi-restraints excluded: chain G residue 367 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 390 SER Chi-restraints excluded: chain H residue 298 LEU Chi-restraints excluded: chain H residue 333 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 162 optimal weight: 0.4980 chunk 68 optimal weight: 0.3980 chunk 167 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 263 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.090888 restraints weight = 24675.093| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.09 r_work: 0.2920 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 18021 Z= 0.161 Angle : 0.571 10.006 24558 Z= 0.270 Chirality : 0.042 0.304 2852 Planarity : 0.004 0.043 2957 Dihedral : 13.655 164.233 2991 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.42 % Favored : 96.48 % Rotamer: Outliers : 2.61 % Allowed : 24.72 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.19), residues: 2074 helix: 1.75 (0.18), residues: 875 sheet: 0.19 (0.28), residues: 377 loop : -1.51 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.005 0.001 HIS A 465 PHE 0.014 0.001 PHE A 370 TYR 0.026 0.001 TYR D 41 ARG 0.006 0.000 ARG G 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5945.12 seconds wall clock time: 107 minutes 27.05 seconds (6447.05 seconds total)