Starting phenix.real_space_refine on Fri Apr 12 04:21:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2024/5k7l_8215_updated.pdb" } resolution = 3.78 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= -0.002 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 15972 2.51 5 N 4096 2.21 5 O 4500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 24": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 508": "NH1" <-> "NH2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A ARG 675": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "C ARG 24": "NH1" <-> "NH2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "C PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 508": "NH1" <-> "NH2" Residue "C ARG 564": "NH1" <-> "NH2" Residue "C ARG 666": "NH1" <-> "NH2" Residue "C ARG 675": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "E ARG 24": "NH1" <-> "NH2" Residue "E PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "E PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 508": "NH1" <-> "NH2" Residue "E ARG 564": "NH1" <-> "NH2" Residue "E ARG 666": "NH1" <-> "NH2" Residue "E ARG 675": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "G ARG 24": "NH1" <-> "NH2" Residue "G PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G PHE 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 493": "NH1" <-> "NH2" Residue "G TYR 499": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 508": "NH1" <-> "NH2" Residue "G ARG 564": "NH1" <-> "NH2" Residue "G ARG 666": "NH1" <-> "NH2" Residue "G ARG 675": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 24696 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5258 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 253 Chain: "B" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 881 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5258 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 253 Chain: "D" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 881 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5258 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 253 Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 881 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5258 Classifications: {'peptide': 701} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 24, 'TRANS': 676} Chain breaks: 2 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 503 Unresolved non-hydrogen dihedrals: 339 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 11, 'ASP:plan': 11, 'ASN:plan1': 5, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 16, 'ARG:plan': 15} Unresolved non-hydrogen planarities: 253 Chain: "H" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 881 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 70} Link IDs: {'PTRANS': 2, 'TRANS': 139} Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 185 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 3, 'ASN:plan1': 4, 'ASP:plan': 9, 'PHE:plan': 1, 'GLU:plan': 15, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 142 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 13.41, per 1000 atoms: 0.54 Number of scatterers: 24696 At special positions: 0 Unit cell: (167.7, 167.7, 144.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4500 8.00 N 4096 7.00 C 15972 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 388 " " NAG C 901 " - " ASN C 388 " " NAG E 901 " - " ASN E 388 " " NAG G 901 " - " ASN G 388 " Time building additional restraints: 10.21 Conformation dependent library (CDL) restraints added in 4.9 seconds 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 140 helices and 12 sheets defined 56.8% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 18 through 25 Processing helix chain 'A' and resid 47 through 53 Processing helix chain 'A' and resid 57 through 60 No H-bonds generated for 'chain 'A' and resid 57 through 60' Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 147 through 157 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 175 through 193 removed outlier: 5.041A pdb=" N LYS A 180 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 187 " --> pdb=" O ARG A 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 241 Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 248 through 270 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.672A pdb=" N PHE A 312 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 344 removed outlier: 3.525A pdb=" N LEU A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS A 327 " --> pdb=" O PHE A 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU A 334 " --> pdb=" O ARG A 330 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG A 339 " --> pdb=" O GLY A 335 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 378 removed outlier: 3.631A pdb=" N VAL A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 419 through 435 removed outlier: 3.920A pdb=" N TYR A 423 " --> pdb=" O LYS A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 499 removed outlier: 3.525A pdb=" N LEU A 462 " --> pdb=" O MET A 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN A 481 " --> pdb=" O GLN A 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR A 482 " --> pdb=" O MET A 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR A 485 " --> pdb=" O ASN A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 520 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 534 through 551 removed outlier: 5.170A pdb=" N LYS A 547 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL A 548 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 551 " --> pdb=" O LYS A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 569 removed outlier: 3.649A pdb=" N GLU A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 624 No H-bonds generated for 'chain 'A' and resid 621 through 624' Processing helix chain 'A' and resid 647 through 656 Processing helix chain 'A' and resid 658 through 667 removed outlier: 3.923A pdb=" N HIS A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER A 663 " --> pdb=" O ALA A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 3.791A pdb=" N MET A 694 " --> pdb=" O GLU A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 721 removed outlier: 4.155A pdb=" N HIS A 708 " --> pdb=" O PRO A 705 " (cutoff:3.500A) Proline residue: A 709 - end of helix removed outlier: 4.145A pdb=" N ARG A 712 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.520A pdb=" N PHE B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 13 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU B 14 " --> pdb=" O ALA B 10 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 16 " --> pdb=" O PHE B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.745A pdb=" N THR B 70 " --> pdb=" O PRO B 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Processing helix chain 'B' and resid 102 through 112 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.873A pdb=" N MET B 144 " --> pdb=" O GLU B 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 25 Processing helix chain 'C' and resid 47 through 53 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 134 through 137 No H-bonds generated for 'chain 'C' and resid 134 through 137' Processing helix chain 'C' and resid 147 through 157 Processing helix chain 'C' and resid 160 through 163 No H-bonds generated for 'chain 'C' and resid 160 through 163' Processing helix chain 'C' and resid 175 through 193 removed outlier: 5.041A pdb=" N LYS C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS C 181 " --> pdb=" O ASN C 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL C 187 " --> pdb=" O ARG C 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 241 Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 248 through 270 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 296 through 302 Processing helix chain 'C' and resid 306 through 313 removed outlier: 3.672A pdb=" N PHE C 312 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 344 removed outlier: 3.525A pdb=" N LEU C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS C 327 " --> pdb=" O PHE C 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL C 328 " --> pdb=" O SER C 324 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU C 331 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU C 332 " --> pdb=" O VAL C 328 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG C 333 " --> pdb=" O VAL C 329 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU C 334 " --> pdb=" O ARG C 330 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA C 338 " --> pdb=" O LEU C 334 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG C 339 " --> pdb=" O GLY C 335 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 378 removed outlier: 3.631A pdb=" N VAL C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 419 through 435 removed outlier: 3.920A pdb=" N TYR C 423 " --> pdb=" O LYS C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 499 removed outlier: 3.525A pdb=" N LEU C 462 " --> pdb=" O MET C 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN C 481 " --> pdb=" O GLN C 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR C 482 " --> pdb=" O MET C 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR C 485 " --> pdb=" O ASN C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 520 Processing helix chain 'C' and resid 525 through 531 Processing helix chain 'C' and resid 534 through 551 removed outlier: 5.170A pdb=" N LYS C 547 " --> pdb=" O HIS C 543 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL C 548 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU C 551 " --> pdb=" O LYS C 547 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 removed outlier: 3.649A pdb=" N GLU C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 621 through 624 No H-bonds generated for 'chain 'C' and resid 621 through 624' Processing helix chain 'C' and resid 647 through 656 Processing helix chain 'C' and resid 658 through 667 removed outlier: 3.923A pdb=" N HIS C 662 " --> pdb=" O THR C 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER C 663 " --> pdb=" O ALA C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 694 removed outlier: 3.791A pdb=" N MET C 694 " --> pdb=" O GLU C 690 " (cutoff:3.500A) Processing helix chain 'C' and resid 705 through 721 removed outlier: 4.155A pdb=" N HIS C 708 " --> pdb=" O PRO C 705 " (cutoff:3.500A) Proline residue: C 709 - end of helix removed outlier: 4.145A pdb=" N ARG C 712 " --> pdb=" O PRO C 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.520A pdb=" N PHE D 12 " --> pdb=" O GLN D 8 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS D 13 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU D 14 " --> pdb=" O ALA D 10 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 16 " --> pdb=" O PHE D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 39 Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.745A pdb=" N THR D 70 " --> pdb=" O PRO D 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET D 71 " --> pdb=" O GLU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 138 through 146 removed outlier: 3.873A pdb=" N MET D 144 " --> pdb=" O GLU D 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET D 145 " --> pdb=" O PHE D 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 25 Processing helix chain 'E' and resid 47 through 53 Processing helix chain 'E' and resid 57 through 60 No H-bonds generated for 'chain 'E' and resid 57 through 60' Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 134 through 137 No H-bonds generated for 'chain 'E' and resid 134 through 137' Processing helix chain 'E' and resid 147 through 157 Processing helix chain 'E' and resid 160 through 163 No H-bonds generated for 'chain 'E' and resid 160 through 163' Processing helix chain 'E' and resid 175 through 193 removed outlier: 5.041A pdb=" N LYS E 180 " --> pdb=" O GLU E 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 187 " --> pdb=" O ARG E 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 215 through 241 Proline residue: E 236 - end of helix Processing helix chain 'E' and resid 248 through 270 Processing helix chain 'E' and resid 284 through 294 Processing helix chain 'E' and resid 296 through 302 Processing helix chain 'E' and resid 306 through 313 removed outlier: 3.672A pdb=" N PHE E 312 " --> pdb=" O VAL E 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 344 removed outlier: 3.525A pdb=" N LEU E 326 " --> pdb=" O LEU E 322 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS E 327 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL E 329 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG E 330 " --> pdb=" O LEU E 326 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU E 332 " --> pdb=" O VAL E 328 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG E 333 " --> pdb=" O VAL E 329 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU E 334 " --> pdb=" O ARG E 330 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY E 335 " --> pdb=" O LEU E 331 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL E 337 " --> pdb=" O ARG E 333 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA E 338 " --> pdb=" O LEU E 334 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG E 339 " --> pdb=" O GLY E 335 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS E 340 " --> pdb=" O ARG E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 378 removed outlier: 3.631A pdb=" N VAL E 353 " --> pdb=" O ALA E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 399 Processing helix chain 'E' and resid 419 through 435 removed outlier: 3.920A pdb=" N TYR E 423 " --> pdb=" O LYS E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 447 through 499 removed outlier: 3.525A pdb=" N LEU E 462 " --> pdb=" O MET E 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN E 481 " --> pdb=" O GLN E 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR E 482 " --> pdb=" O MET E 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR E 485 " --> pdb=" O ASN E 481 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 520 Processing helix chain 'E' and resid 525 through 531 Processing helix chain 'E' and resid 534 through 551 removed outlier: 5.170A pdb=" N LYS E 547 " --> pdb=" O HIS E 543 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL E 548 " --> pdb=" O LEU E 544 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU E 551 " --> pdb=" O LYS E 547 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 569 removed outlier: 3.649A pdb=" N GLU E 569 " --> pdb=" O ALA E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 621 through 624 No H-bonds generated for 'chain 'E' and resid 621 through 624' Processing helix chain 'E' and resid 647 through 656 Processing helix chain 'E' and resid 658 through 667 removed outlier: 3.923A pdb=" N HIS E 662 " --> pdb=" O THR E 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER E 663 " --> pdb=" O ALA E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 694 removed outlier: 3.791A pdb=" N MET E 694 " --> pdb=" O GLU E 690 " (cutoff:3.500A) Processing helix chain 'E' and resid 705 through 721 removed outlier: 4.155A pdb=" N HIS E 708 " --> pdb=" O PRO E 705 " (cutoff:3.500A) Proline residue: E 709 - end of helix removed outlier: 4.145A pdb=" N ARG E 712 " --> pdb=" O PRO E 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.520A pdb=" N PHE F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS F 13 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE F 16 " --> pdb=" O PHE F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 45 through 55 Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.745A pdb=" N THR F 70 " --> pdb=" O PRO F 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET F 71 " --> pdb=" O GLU F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Processing helix chain 'F' and resid 102 through 112 Processing helix chain 'F' and resid 118 through 128 Processing helix chain 'F' and resid 138 through 146 removed outlier: 3.873A pdb=" N MET F 144 " --> pdb=" O GLU F 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET F 145 " --> pdb=" O PHE F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 25 Processing helix chain 'G' and resid 47 through 53 Processing helix chain 'G' and resid 57 through 60 No H-bonds generated for 'chain 'G' and resid 57 through 60' Processing helix chain 'G' and resid 77 through 89 Processing helix chain 'G' and resid 134 through 137 No H-bonds generated for 'chain 'G' and resid 134 through 137' Processing helix chain 'G' and resid 147 through 157 Processing helix chain 'G' and resid 160 through 163 No H-bonds generated for 'chain 'G' and resid 160 through 163' Processing helix chain 'G' and resid 175 through 193 removed outlier: 5.041A pdb=" N LYS G 180 " --> pdb=" O GLU G 176 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N HIS G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL G 187 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER G 192 " --> pdb=" O LEU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 215 through 241 Proline residue: G 236 - end of helix Processing helix chain 'G' and resid 248 through 270 Processing helix chain 'G' and resid 284 through 294 Processing helix chain 'G' and resid 296 through 302 Processing helix chain 'G' and resid 306 through 313 removed outlier: 3.672A pdb=" N PHE G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLU G 313 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 344 removed outlier: 3.525A pdb=" N LEU G 326 " --> pdb=" O LEU G 322 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS G 327 " --> pdb=" O PHE G 323 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL G 328 " --> pdb=" O SER G 324 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL G 329 " --> pdb=" O SER G 325 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ARG G 330 " --> pdb=" O LEU G 326 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU G 331 " --> pdb=" O LYS G 327 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU G 332 " --> pdb=" O VAL G 328 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG G 333 " --> pdb=" O VAL G 329 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU G 334 " --> pdb=" O ARG G 330 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY G 335 " --> pdb=" O LEU G 331 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ARG G 336 " --> pdb=" O LEU G 332 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL G 337 " --> pdb=" O ARG G 333 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ALA G 338 " --> pdb=" O LEU G 334 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N ARG G 339 " --> pdb=" O GLY G 335 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS G 340 " --> pdb=" O ARG G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 378 removed outlier: 3.631A pdb=" N VAL G 353 " --> pdb=" O ALA G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 399 Processing helix chain 'G' and resid 419 through 435 removed outlier: 3.920A pdb=" N TYR G 423 " --> pdb=" O LYS G 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 447 through 499 removed outlier: 3.525A pdb=" N LEU G 462 " --> pdb=" O MET G 458 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N ASN G 481 " --> pdb=" O GLN G 477 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR G 482 " --> pdb=" O MET G 478 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR G 485 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 520 Processing helix chain 'G' and resid 525 through 531 Processing helix chain 'G' and resid 534 through 551 removed outlier: 5.170A pdb=" N LYS G 547 " --> pdb=" O HIS G 543 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N VAL G 548 " --> pdb=" O LEU G 544 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU G 551 " --> pdb=" O LYS G 547 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 569 removed outlier: 3.649A pdb=" N GLU G 569 " --> pdb=" O ALA G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 621 through 624 No H-bonds generated for 'chain 'G' and resid 621 through 624' Processing helix chain 'G' and resid 647 through 656 Processing helix chain 'G' and resid 658 through 667 removed outlier: 3.923A pdb=" N HIS G 662 " --> pdb=" O THR G 658 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER G 663 " --> pdb=" O ALA G 659 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 694 removed outlier: 3.791A pdb=" N MET G 694 " --> pdb=" O GLU G 690 " (cutoff:3.500A) Processing helix chain 'G' and resid 705 through 721 removed outlier: 4.155A pdb=" N HIS G 708 " --> pdb=" O PRO G 705 " (cutoff:3.500A) Proline residue: G 709 - end of helix removed outlier: 4.145A pdb=" N ARG G 712 " --> pdb=" O PRO G 709 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 3.520A pdb=" N PHE H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS H 13 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE H 16 " --> pdb=" O PHE H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 39 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 65 through 76 removed outlier: 3.745A pdb=" N THR H 70 " --> pdb=" O PRO H 66 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET H 71 " --> pdb=" O GLU H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 92 Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 118 through 128 Processing helix chain 'H' and resid 138 through 146 removed outlier: 3.873A pdb=" N MET H 144 " --> pdb=" O GLU H 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET H 145 " --> pdb=" O PHE H 141 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN A 93 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 125 " --> pdb=" O ILE A 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 33 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS A 128 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 31 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN A 29 " --> pdb=" O PHE A 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN A 34 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A 42 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 573 through 575 removed outlier: 3.606A pdb=" N SER A 596 " --> pdb=" O ASP A 641 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS A 643 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 594 " --> pdb=" O HIS A 643 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE A 645 " --> pdb=" O CYS A 592 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS A 592 " --> pdb=" O ILE A 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP A 615 " --> pdb=" O VAL A 594 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 633 through 636 removed outlier: 3.612A pdb=" N ALA A 609 " --> pdb=" O VAL A 601 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN C 93 " --> pdb=" O ILE C 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU C 125 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 33 " --> pdb=" O PHE C 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 128 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C 31 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN C 29 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN C 34 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE C 42 " --> pdb=" O ASN C 34 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 573 through 575 removed outlier: 3.606A pdb=" N SER C 596 " --> pdb=" O ASP C 641 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS C 643 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL C 594 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE C 645 " --> pdb=" O CYS C 592 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS C 592 " --> pdb=" O ILE C 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP C 615 " --> pdb=" O VAL C 594 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 633 through 636 removed outlier: 3.612A pdb=" N ALA C 609 " --> pdb=" O VAL C 601 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN E 93 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 125 " --> pdb=" O ILE E 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY E 33 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS E 128 " --> pdb=" O VAL E 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL E 31 " --> pdb=" O CYS E 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN E 29 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN E 34 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE E 42 " --> pdb=" O ASN E 34 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 573 through 575 removed outlier: 3.606A pdb=" N SER E 596 " --> pdb=" O ASP E 641 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS E 643 " --> pdb=" O VAL E 594 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL E 594 " --> pdb=" O HIS E 643 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE E 645 " --> pdb=" O CYS E 592 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS E 592 " --> pdb=" O ILE E 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP E 615 " --> pdb=" O VAL E 594 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 633 through 636 removed outlier: 3.612A pdb=" N ALA E 609 " --> pdb=" O VAL E 601 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN G 93 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 125 " --> pdb=" O ILE G 116 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY G 33 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS G 128 " --> pdb=" O VAL G 31 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL G 31 " --> pdb=" O CYS G 128 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASN G 29 " --> pdb=" O PHE G 130 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ASN G 34 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE G 42 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 573 through 575 removed outlier: 3.606A pdb=" N SER G 596 " --> pdb=" O ASP G 641 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N HIS G 643 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL G 594 " --> pdb=" O HIS G 643 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N ILE G 645 " --> pdb=" O CYS G 592 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N CYS G 592 " --> pdb=" O ILE G 645 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP G 615 " --> pdb=" O VAL G 594 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 633 through 636 removed outlier: 3.612A pdb=" N ALA G 609 " --> pdb=" O VAL G 601 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3672 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: 8.46 Time building geometry restraints manager: 11.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5120 1.33 - 1.45: 5924 1.45 - 1.57: 14020 1.57 - 1.69: 8 1.69 - 1.81: 196 Bond restraints: 25268 Sorted by residual: bond pdb=" CA PRO C 705 " pdb=" C PRO C 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO E 705 " pdb=" C PRO E 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO A 705 " pdb=" C PRO A 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA PRO G 705 " pdb=" C PRO G 705 " ideal model delta sigma weight residual 1.517 1.546 -0.029 9.30e-03 1.16e+04 9.54e+00 bond pdb=" CA GLU A 313 " pdb=" C GLU A 313 " ideal model delta sigma weight residual 1.522 1.560 -0.038 1.39e-02 5.18e+03 7.48e+00 ... (remaining 25263 not shown) Histogram of bond angle deviations from ideal: 100.51 - 107.25: 748 107.25 - 113.98: 13708 113.98 - 120.71: 10152 120.71 - 127.45: 9736 127.45 - 134.18: 240 Bond angle restraints: 34584 Sorted by residual: angle pdb=" O VAL G 235 " pdb=" C VAL G 235 " pdb=" N PRO G 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL A 235 " pdb=" C VAL A 235 " pdb=" N PRO A 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL E 235 " pdb=" C VAL E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" O VAL C 235 " pdb=" C VAL C 235 " pdb=" N PRO C 236 " ideal model delta sigma weight residual 120.07 124.14 -4.07 7.10e-01 1.98e+00 3.28e+01 angle pdb=" CA VAL E 235 " pdb=" C VAL E 235 " pdb=" N PRO E 236 " ideal model delta sigma weight residual 121.00 116.49 4.51 8.30e-01 1.45e+00 2.95e+01 ... (remaining 34579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.29: 13076 13.29 - 26.58: 1200 26.58 - 39.87: 480 39.87 - 53.16: 108 53.16 - 66.45: 24 Dihedral angle restraints: 14888 sinusoidal: 5012 harmonic: 9876 Sorted by residual: dihedral pdb=" CA ILE C 233 " pdb=" C ILE C 233 " pdb=" N LEU C 234 " pdb=" CA LEU C 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE G 233 " pdb=" C ILE G 233 " pdb=" N LEU G 234 " pdb=" CA LEU G 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE E 233 " pdb=" C ILE E 233 " pdb=" N LEU E 234 " pdb=" CA LEU E 234 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 14885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 3376 0.092 - 0.184: 648 0.184 - 0.276: 44 0.276 - 0.369: 20 0.369 - 0.461: 12 Chirality restraints: 4100 Sorted by residual: chirality pdb=" C4 NAG C 901 " pdb=" C3 NAG C 901 " pdb=" C5 NAG C 901 " pdb=" O4 NAG C 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C4 NAG E 901 " pdb=" C3 NAG E 901 " pdb=" C5 NAG E 901 " pdb=" O4 NAG E 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" C4 NAG G 901 " pdb=" C3 NAG G 901 " pdb=" C5 NAG G 901 " pdb=" O4 NAG G 901 " both_signs ideal model delta sigma weight residual False -2.53 -2.07 -0.46 2.00e-01 2.50e+01 5.31e+00 ... (remaining 4097 not shown) Planarity restraints: 4408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 65 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 66 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 66 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 65 " -0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO B 66 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 66 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 66 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE F 65 " 0.035 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO F 66 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO F 66 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO F 66 " 0.030 5.00e-02 4.00e+02 ... (remaining 4405 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 6824 2.83 - 3.35: 25548 3.35 - 3.87: 40416 3.87 - 4.38: 43016 4.38 - 4.90: 71690 Nonbonded interactions: 187494 Sorted by model distance: nonbonded pdb=" O LEU A 190 " pdb=" N ILE A 194 " model vdw 2.315 2.520 nonbonded pdb=" O LEU E 190 " pdb=" N ILE E 194 " model vdw 2.315 2.520 nonbonded pdb=" O LEU C 190 " pdb=" N ILE C 194 " model vdw 2.315 2.520 nonbonded pdb=" O LEU G 190 " pdb=" N ILE G 194 " model vdw 2.315 2.520 nonbonded pdb=" O PHE C 429 " pdb=" OG1 THR C 432 " model vdw 2.336 2.440 ... (remaining 187489 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 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: 4.530 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 68.530 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.038 25268 Z= 0.515 Angle : 1.363 7.802 34584 Z= 1.031 Chirality : 0.074 0.461 4100 Planarity : 0.005 0.054 4404 Dihedral : 13.100 66.453 8488 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.31 % Favored : 92.57 % Rotamer: Outliers : 0.35 % Allowed : 7.03 % Favored : 92.62 % Cbeta Deviations : 0.62 % 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 (0.13), residues: 3340 helix: 1.54 (0.10), residues: 1908 sheet: -3.18 (0.35), residues: 148 loop : -2.46 (0.15), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 370 HIS 0.005 0.001 HIS G 208 PHE 0.026 0.002 PHE A 323 TYR 0.028 0.002 TYR E 237 ARG 0.003 0.001 ARG E 647 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 164 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9557 (mtm) REVERT: A 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9256 (mmm) REVERT: A 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: A 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: B 99 TYR cc_start: 0.9708 (m-80) cc_final: 0.9269 (m-80) REVERT: B 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8788 (mtp) REVERT: C 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9557 (mtm) REVERT: C 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9261 (mmm) REVERT: C 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: C 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: D 99 TYR cc_start: 0.9707 (m-80) cc_final: 0.9269 (m-80) REVERT: D 145 MET cc_start: 0.9164 (mmm) cc_final: 0.8789 (mtp) REVERT: E 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9555 (mtm) REVERT: E 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9261 (mmm) REVERT: E 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: E 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: F 99 TYR cc_start: 0.9707 (m-80) cc_final: 0.9269 (m-80) REVERT: F 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8789 (mtp) REVERT: G 99 MET cc_start: 0.9819 (mtm) cc_final: 0.9556 (mtm) REVERT: G 431 MET cc_start: 0.9904 (tpt) cc_final: 0.9262 (mmm) REVERT: G 478 MET cc_start: 0.9665 (ptp) cc_final: 0.9314 (ppp) REVERT: G 488 MET cc_start: 0.9763 (ttp) cc_final: 0.9439 (tmm) REVERT: H 99 TYR cc_start: 0.9708 (m-80) cc_final: 0.9269 (m-80) REVERT: H 145 MET cc_start: 0.9163 (mmm) cc_final: 0.8788 (mtp) outliers start: 8 outliers final: 0 residues processed: 172 average time/residue: 0.3606 time to fit residues: 100.9541 Evaluate side-chains 128 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 2.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 9.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 263 optimal weight: 7.9990 chunk 101 optimal weight: 40.0000 chunk 160 optimal weight: 0.9980 chunk 196 optimal weight: 8.9990 chunk 305 optimal weight: 5.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN A 667 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN C 667 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN E 667 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 603 GLN G 667 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25268 Z= 0.164 Angle : 0.537 7.113 34584 Z= 0.280 Chirality : 0.038 0.136 4100 Planarity : 0.004 0.046 4404 Dihedral : 4.408 25.272 3880 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 9.58 % Favored : 88.62 % 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: 1.85 (0.16), residues: 3340 helix: 3.31 (0.13), residues: 1932 sheet: -2.37 (0.30), residues: 208 loop : -1.80 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP E 370 HIS 0.001 0.001 HIS G 486 PHE 0.015 0.001 PHE G 379 TYR 0.015 0.001 TYR C 464 ARG 0.002 0.000 ARG E 57 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 124 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9696 (mtm) cc_final: 0.9367 (mtm) REVERT: A 269 PHE cc_start: 0.9658 (OUTLIER) cc_final: 0.9311 (m-80) REVERT: A 435 THR cc_start: 0.9777 (OUTLIER) cc_final: 0.9510 (p) REVERT: A 488 MET cc_start: 0.9765 (ttp) cc_final: 0.9505 (tmm) REVERT: A 519 MET cc_start: 0.9797 (ttp) cc_final: 0.9382 (mmp) REVERT: A 568 MET cc_start: 0.9477 (mmm) cc_final: 0.9145 (mmm) REVERT: B 145 MET cc_start: 0.9139 (mmm) cc_final: 0.8648 (mtp) REVERT: C 99 MET cc_start: 0.9696 (mtm) cc_final: 0.9367 (mtm) REVERT: C 269 PHE cc_start: 0.9659 (OUTLIER) cc_final: 0.9312 (m-80) REVERT: C 431 MET cc_start: 0.9884 (tpt) cc_final: 0.9387 (mmm) REVERT: C 435 THR cc_start: 0.9762 (OUTLIER) cc_final: 0.9503 (t) REVERT: C 488 MET cc_start: 0.9766 (ttp) cc_final: 0.9505 (tmm) REVERT: C 519 MET cc_start: 0.9798 (ttp) cc_final: 0.9383 (mmp) REVERT: C 568 MET cc_start: 0.9477 (mmm) cc_final: 0.9145 (mmm) REVERT: D 145 MET cc_start: 0.9138 (mmm) cc_final: 0.8647 (mtp) REVERT: E 99 MET cc_start: 0.9697 (mtm) cc_final: 0.9369 (mtm) REVERT: E 269 PHE cc_start: 0.9658 (OUTLIER) cc_final: 0.9311 (m-80) REVERT: E 431 MET cc_start: 0.9884 (tpt) cc_final: 0.9387 (mmm) REVERT: E 435 THR cc_start: 0.9761 (OUTLIER) cc_final: 0.9503 (t) REVERT: E 488 MET cc_start: 0.9765 (ttp) cc_final: 0.9504 (tmm) REVERT: E 519 MET cc_start: 0.9798 (ttp) cc_final: 0.9382 (mmp) REVERT: E 568 MET cc_start: 0.9477 (mmm) cc_final: 0.9144 (mmm) REVERT: F 145 MET cc_start: 0.9141 (mmm) cc_final: 0.8649 (mtp) REVERT: G 99 MET cc_start: 0.9695 (mtm) cc_final: 0.9368 (mtm) REVERT: G 269 PHE cc_start: 0.9658 (OUTLIER) cc_final: 0.9312 (m-80) REVERT: G 431 MET cc_start: 0.9884 (tpt) cc_final: 0.9387 (mmm) REVERT: G 435 THR cc_start: 0.9761 (OUTLIER) cc_final: 0.9502 (t) REVERT: G 488 MET cc_start: 0.9766 (ttp) cc_final: 0.9505 (tmm) REVERT: G 519 MET cc_start: 0.9797 (ttp) cc_final: 0.9382 (mmp) REVERT: G 568 MET cc_start: 0.9476 (mmm) cc_final: 0.9145 (mmm) REVERT: H 145 MET cc_start: 0.9140 (mmm) cc_final: 0.8648 (mtp) outliers start: 41 outliers final: 0 residues processed: 156 average time/residue: 0.3269 time to fit residues: 88.0561 Evaluate side-chains 125 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 435 THR Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 435 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 0.0170 chunk 253 optimal weight: 10.0000 chunk 207 optimal weight: 0.0170 chunk 84 optimal weight: 20.0000 chunk 305 optimal weight: 0.5980 chunk 330 optimal weight: 40.0000 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 0.9990 chunk 104 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 overall best weight: 1.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 603 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 603 GLN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 603 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 25268 Z= 0.141 Angle : 0.492 8.454 34584 Z= 0.250 Chirality : 0.038 0.195 4100 Planarity : 0.003 0.051 4404 Dihedral : 3.853 17.348 3880 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.88 % Allowed : 11.20 % Favored : 87.92 % 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: 1.88 (0.16), residues: 3340 helix: 3.17 (0.12), residues: 1928 sheet: -2.39 (0.29), residues: 200 loop : -1.46 (0.17), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 370 HIS 0.001 0.000 HIS G 574 PHE 0.015 0.001 PHE A 359 TYR 0.013 0.001 TYR C 464 ARG 0.002 0.000 ARG G 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 128 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9744 (mtm) cc_final: 0.9476 (mtm) REVERT: A 269 PHE cc_start: 0.9588 (OUTLIER) cc_final: 0.9323 (m-80) REVERT: A 366 MET cc_start: 0.9717 (mmm) cc_final: 0.9514 (mpp) REVERT: A 434 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9394 (mm) REVERT: A 488 MET cc_start: 0.9786 (ttp) cc_final: 0.9525 (tmm) REVERT: A 519 MET cc_start: 0.9800 (ttp) cc_final: 0.9386 (mmp) REVERT: A 605 ASP cc_start: 0.9788 (m-30) cc_final: 0.9472 (t0) REVERT: B 145 MET cc_start: 0.9154 (mmm) cc_final: 0.8649 (mtp) REVERT: C 99 MET cc_start: 0.9744 (mtm) cc_final: 0.9477 (mtm) REVERT: C 269 PHE cc_start: 0.9587 (OUTLIER) cc_final: 0.9324 (m-80) REVERT: C 366 MET cc_start: 0.9719 (mmm) cc_final: 0.9517 (mpp) REVERT: C 431 MET cc_start: 0.9778 (tpt) cc_final: 0.9502 (tpp) REVERT: C 434 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9376 (mm) REVERT: C 488 MET cc_start: 0.9785 (ttp) cc_final: 0.9525 (tmm) REVERT: C 519 MET cc_start: 0.9799 (ttp) cc_final: 0.9386 (mmp) REVERT: C 605 ASP cc_start: 0.9788 (m-30) cc_final: 0.9471 (t0) REVERT: D 145 MET cc_start: 0.9154 (mmm) cc_final: 0.8648 (mtp) REVERT: E 99 MET cc_start: 0.9744 (mtm) cc_final: 0.9476 (mtm) REVERT: E 269 PHE cc_start: 0.9587 (OUTLIER) cc_final: 0.9323 (m-80) REVERT: E 366 MET cc_start: 0.9718 (mmm) cc_final: 0.9516 (mpp) REVERT: E 431 MET cc_start: 0.9777 (tpt) cc_final: 0.9499 (tpp) REVERT: E 434 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9377 (mm) REVERT: E 488 MET cc_start: 0.9785 (ttp) cc_final: 0.9525 (tmm) REVERT: E 519 MET cc_start: 0.9800 (ttp) cc_final: 0.9386 (mmp) REVERT: E 605 ASP cc_start: 0.9788 (m-30) cc_final: 0.9471 (t0) REVERT: F 145 MET cc_start: 0.9155 (mmm) cc_final: 0.8649 (mtp) REVERT: G 99 MET cc_start: 0.9744 (mtm) cc_final: 0.9476 (mtm) REVERT: G 269 PHE cc_start: 0.9587 (OUTLIER) cc_final: 0.9323 (m-80) REVERT: G 431 MET cc_start: 0.9778 (tpt) cc_final: 0.9499 (tpp) REVERT: G 434 LEU cc_start: 0.9634 (OUTLIER) cc_final: 0.9381 (mm) REVERT: G 488 MET cc_start: 0.9785 (ttp) cc_final: 0.9525 (tmm) REVERT: G 519 MET cc_start: 0.9800 (ttp) cc_final: 0.9386 (mmp) REVERT: G 605 ASP cc_start: 0.9788 (m-30) cc_final: 0.9471 (t0) REVERT: H 145 MET cc_start: 0.9154 (mmm) cc_final: 0.8648 (mtp) outliers start: 20 outliers final: 4 residues processed: 144 average time/residue: 0.3084 time to fit residues: 76.8901 Evaluate side-chains 136 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 PHE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 269 PHE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 269 PHE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 20.0000 chunk 229 optimal weight: 30.0000 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 9.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 160 optimal weight: 20.0000 chunk 290 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25268 Z= 0.329 Angle : 0.611 9.899 34584 Z= 0.320 Chirality : 0.039 0.192 4100 Planarity : 0.004 0.053 4404 Dihedral : 4.234 17.884 3880 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.27 % Allowed : 10.76 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.15), residues: 3340 helix: 2.48 (0.12), residues: 1980 sheet: -2.49 (0.29), residues: 200 loop : -1.38 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 108 HIS 0.005 0.001 HIS C 574 PHE 0.016 0.002 PHE G 241 TYR 0.015 0.002 TYR E 44 ARG 0.005 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 124 time to evaluate : 3.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9753 (mpp) cc_final: 0.9494 (mmp) REVERT: A 99 MET cc_start: 0.9642 (mtm) cc_final: 0.9357 (mtm) REVERT: A 519 MET cc_start: 0.9853 (ttp) cc_final: 0.9494 (mmp) REVERT: B 145 MET cc_start: 0.9205 (mmm) cc_final: 0.8775 (mtp) REVERT: C 92 MET cc_start: 0.9753 (mpp) cc_final: 0.9494 (mmp) REVERT: C 99 MET cc_start: 0.9642 (mtm) cc_final: 0.9357 (mtm) REVERT: C 431 MET cc_start: 0.9860 (tpt) cc_final: 0.9230 (mmm) REVERT: C 519 MET cc_start: 0.9853 (ttp) cc_final: 0.9494 (mmp) REVERT: D 145 MET cc_start: 0.9205 (mmm) cc_final: 0.8775 (mtp) REVERT: E 92 MET cc_start: 0.9752 (mpp) cc_final: 0.9493 (mmp) REVERT: E 99 MET cc_start: 0.9641 (mtm) cc_final: 0.9356 (mtm) REVERT: E 431 MET cc_start: 0.9860 (tpt) cc_final: 0.9231 (mmm) REVERT: E 519 MET cc_start: 0.9852 (ttp) cc_final: 0.9493 (mmp) REVERT: F 145 MET cc_start: 0.9205 (mmm) cc_final: 0.8775 (mtp) REVERT: G 92 MET cc_start: 0.9752 (mpp) cc_final: 0.9492 (mmp) REVERT: G 99 MET cc_start: 0.9641 (mtm) cc_final: 0.9356 (mtm) REVERT: G 431 MET cc_start: 0.9869 (tpt) cc_final: 0.9295 (mmm) REVERT: G 519 MET cc_start: 0.9853 (ttp) cc_final: 0.9493 (mmp) REVERT: H 145 MET cc_start: 0.9206 (mmm) cc_final: 0.8775 (mtp) outliers start: 29 outliers final: 12 residues processed: 148 average time/residue: 0.2998 time to fit residues: 79.0299 Evaluate side-chains 132 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 2.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 604 ASP Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 604 ASP Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 604 ASP Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 604 ASP Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.0980 chunk 184 optimal weight: 0.0980 chunk 4 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 291 optimal weight: 10.0000 chunk 81 optimal weight: 30.0000 overall best weight: 4.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25268 Z= 0.203 Angle : 0.545 10.228 34584 Z= 0.269 Chirality : 0.037 0.166 4100 Planarity : 0.003 0.054 4404 Dihedral : 3.920 17.854 3880 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.01 % Allowed : 12.21 % Favored : 86.78 % 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: 1.55 (0.16), residues: 3340 helix: 2.59 (0.12), residues: 1972 sheet: -2.10 (0.27), residues: 228 loop : -1.19 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 370 HIS 0.002 0.001 HIS G 364 PHE 0.012 0.001 PHE E 241 TYR 0.011 0.001 TYR C 464 ARG 0.003 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 2.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9716 (mpp) cc_final: 0.9456 (mmp) REVERT: A 99 MET cc_start: 0.9713 (mtm) cc_final: 0.9421 (mtm) REVERT: A 431 MET cc_start: 0.9876 (mmm) cc_final: 0.9606 (tpp) REVERT: A 478 MET cc_start: 0.9657 (tmm) cc_final: 0.9218 (ppp) REVERT: A 479 TYR cc_start: 0.9617 (OUTLIER) cc_final: 0.9079 (m-80) REVERT: A 488 MET cc_start: 0.9573 (tmm) cc_final: 0.9261 (ppp) REVERT: A 519 MET cc_start: 0.9839 (ttp) cc_final: 0.9463 (mmp) REVERT: B 145 MET cc_start: 0.9214 (mmm) cc_final: 0.8780 (mtp) REVERT: C 92 MET cc_start: 0.9716 (mpp) cc_final: 0.9457 (mmp) REVERT: C 99 MET cc_start: 0.9712 (mtm) cc_final: 0.9421 (mtm) REVERT: C 431 MET cc_start: 0.9858 (tpt) cc_final: 0.9416 (mmm) REVERT: C 435 THR cc_start: 0.9619 (OUTLIER) cc_final: 0.9249 (t) REVERT: C 478 MET cc_start: 0.9657 (tmm) cc_final: 0.9218 (ppp) REVERT: C 479 TYR cc_start: 0.9618 (OUTLIER) cc_final: 0.9079 (m-80) REVERT: C 488 MET cc_start: 0.9573 (tmm) cc_final: 0.9261 (ppp) REVERT: C 519 MET cc_start: 0.9839 (ttp) cc_final: 0.9462 (mmp) REVERT: D 145 MET cc_start: 0.9214 (mmm) cc_final: 0.8780 (mtp) REVERT: E 92 MET cc_start: 0.9716 (mpp) cc_final: 0.9457 (mmp) REVERT: E 99 MET cc_start: 0.9712 (mtm) cc_final: 0.9419 (mtm) REVERT: E 431 MET cc_start: 0.9856 (tpt) cc_final: 0.9413 (mmm) REVERT: E 435 THR cc_start: 0.9620 (OUTLIER) cc_final: 0.9257 (t) REVERT: E 478 MET cc_start: 0.9656 (tmm) cc_final: 0.9217 (ppp) REVERT: E 479 TYR cc_start: 0.9617 (OUTLIER) cc_final: 0.9080 (m-80) REVERT: E 488 MET cc_start: 0.9572 (tmm) cc_final: 0.9261 (ppp) REVERT: E 519 MET cc_start: 0.9839 (ttp) cc_final: 0.9463 (mmp) REVERT: F 145 MET cc_start: 0.9214 (mmm) cc_final: 0.8780 (mtp) REVERT: G 92 MET cc_start: 0.9715 (mpp) cc_final: 0.9456 (mmp) REVERT: G 99 MET cc_start: 0.9712 (mtm) cc_final: 0.9420 (mtm) REVERT: G 431 MET cc_start: 0.9864 (tpt) cc_final: 0.9271 (mmm) REVERT: G 434 LEU cc_start: 0.9601 (OUTLIER) cc_final: 0.9357 (mm) REVERT: G 457 MET cc_start: 0.9420 (ptm) cc_final: 0.9078 (ptm) REVERT: G 479 TYR cc_start: 0.9626 (OUTLIER) cc_final: 0.9166 (m-80) REVERT: G 519 MET cc_start: 0.9840 (ttp) cc_final: 0.9463 (mmp) REVERT: H 145 MET cc_start: 0.9214 (mmm) cc_final: 0.8780 (mtp) outliers start: 23 outliers final: 5 residues processed: 143 average time/residue: 0.3007 time to fit residues: 76.1223 Evaluate side-chains 132 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 3.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 479 TYR Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 190 optimal weight: 6.9990 chunk 80 optimal weight: 30.0000 chunk 325 optimal weight: 20.0000 chunk 269 optimal weight: 30.0000 chunk 150 optimal weight: 10.0000 chunk 27 optimal weight: 30.0000 chunk 107 optimal weight: 0.6980 chunk 170 optimal weight: 10.0000 overall best weight: 6.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 708 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 708 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 25268 Z= 0.296 Angle : 0.590 9.079 34584 Z= 0.303 Chirality : 0.038 0.178 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.220 19.388 3880 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.54 % Allowed : 12.52 % Favored : 85.94 % 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: 1.28 (0.15), residues: 3340 helix: 2.29 (0.12), residues: 1968 sheet: -2.31 (0.29), residues: 216 loop : -1.10 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 108 HIS 0.004 0.001 HIS A 574 PHE 0.015 0.002 PHE G 241 TYR 0.013 0.002 TYR C 44 ARG 0.005 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 116 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9691 (mtm) cc_final: 0.9436 (mtm) REVERT: A 431 MET cc_start: 0.9895 (mmm) cc_final: 0.9604 (tpp) REVERT: A 478 MET cc_start: 0.9673 (tmm) cc_final: 0.9470 (ppp) REVERT: A 479 TYR cc_start: 0.9604 (OUTLIER) cc_final: 0.9220 (m-10) REVERT: A 519 MET cc_start: 0.9850 (ttp) cc_final: 0.9508 (mmp) REVERT: B 145 MET cc_start: 0.9206 (mmm) cc_final: 0.8872 (mtp) REVERT: C 99 MET cc_start: 0.9691 (mtm) cc_final: 0.9437 (mtm) REVERT: C 431 MET cc_start: 0.9864 (tpt) cc_final: 0.9224 (mmm) REVERT: C 478 MET cc_start: 0.9673 (tmm) cc_final: 0.9469 (ppp) REVERT: C 479 TYR cc_start: 0.9604 (OUTLIER) cc_final: 0.9220 (m-10) REVERT: C 519 MET cc_start: 0.9850 (ttp) cc_final: 0.9507 (mmp) REVERT: D 145 MET cc_start: 0.9206 (mmm) cc_final: 0.8872 (mtp) REVERT: E 99 MET cc_start: 0.9690 (mtm) cc_final: 0.9435 (mtm) REVERT: E 431 MET cc_start: 0.9862 (tpt) cc_final: 0.9224 (mmm) REVERT: E 478 MET cc_start: 0.9673 (tmm) cc_final: 0.9470 (ppp) REVERT: E 479 TYR cc_start: 0.9604 (OUTLIER) cc_final: 0.9221 (m-10) REVERT: E 519 MET cc_start: 0.9850 (ttp) cc_final: 0.9507 (mmp) REVERT: F 145 MET cc_start: 0.9206 (mmm) cc_final: 0.8873 (mtp) REVERT: G 99 MET cc_start: 0.9690 (mtm) cc_final: 0.9436 (mtm) REVERT: G 431 MET cc_start: 0.9877 (tpt) cc_final: 0.9328 (mmm) REVERT: G 434 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9361 (mm) REVERT: G 458 MET cc_start: 0.9879 (tpp) cc_final: 0.9634 (tpp) REVERT: G 478 MET cc_start: 0.9562 (ppp) cc_final: 0.9251 (ppp) REVERT: G 479 TYR cc_start: 0.9556 (OUTLIER) cc_final: 0.9189 (m-10) REVERT: G 519 MET cc_start: 0.9849 (ttp) cc_final: 0.9506 (mmp) REVERT: H 145 MET cc_start: 0.9206 (mmm) cc_final: 0.8873 (mtp) outliers start: 35 outliers final: 17 residues processed: 147 average time/residue: 0.3005 time to fit residues: 78.1214 Evaluate side-chains 138 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 2.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 434 LEU Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 479 TYR Chi-restraints excluded: chain G residue 671 THR Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 20.0000 chunk 36 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 183 optimal weight: 20.0000 chunk 273 optimal weight: 10.0000 chunk 181 optimal weight: 20.0000 chunk 323 optimal weight: 50.0000 chunk 202 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 149 optimal weight: 10.0000 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 25268 Z= 0.308 Angle : 0.584 10.346 34584 Z= 0.302 Chirality : 0.038 0.207 4100 Planarity : 0.004 0.054 4404 Dihedral : 4.370 23.766 3880 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.97 % Allowed : 13.97 % Favored : 85.06 % 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: 1.21 (0.15), residues: 3340 helix: 2.17 (0.12), residues: 1964 sheet: -2.34 (0.27), residues: 232 loop : -0.95 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 370 HIS 0.004 0.001 HIS C 574 PHE 0.013 0.002 PHE G 241 TYR 0.013 0.002 TYR C 44 ARG 0.005 0.000 ARG G 508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9420 (mtm) REVERT: A 431 MET cc_start: 0.9903 (mmm) cc_final: 0.9616 (tpp) REVERT: A 478 MET cc_start: 0.9654 (tmm) cc_final: 0.9298 (ppp) REVERT: A 479 TYR cc_start: 0.9579 (OUTLIER) cc_final: 0.9202 (m-10) REVERT: A 519 MET cc_start: 0.9847 (ttp) cc_final: 0.9511 (mmp) REVERT: B 145 MET cc_start: 0.9172 (mmm) cc_final: 0.8855 (mtp) REVERT: C 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9420 (mtm) REVERT: C 431 MET cc_start: 0.9862 (tpt) cc_final: 0.9284 (mmm) REVERT: C 478 MET cc_start: 0.9653 (tmm) cc_final: 0.9298 (ppp) REVERT: C 479 TYR cc_start: 0.9580 (OUTLIER) cc_final: 0.9202 (m-10) REVERT: C 519 MET cc_start: 0.9847 (ttp) cc_final: 0.9510 (mmp) REVERT: D 145 MET cc_start: 0.9172 (mmm) cc_final: 0.8855 (mtp) REVERT: E 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9421 (mtm) REVERT: E 431 MET cc_start: 0.9860 (tpt) cc_final: 0.9448 (mmm) REVERT: E 435 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9198 (t) REVERT: E 478 MET cc_start: 0.9653 (tmm) cc_final: 0.9299 (ppp) REVERT: E 479 TYR cc_start: 0.9580 (OUTLIER) cc_final: 0.9202 (m-10) REVERT: E 519 MET cc_start: 0.9846 (ttp) cc_final: 0.9510 (mmp) REVERT: F 145 MET cc_start: 0.9173 (mmm) cc_final: 0.8855 (mtp) REVERT: G 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9419 (mtm) REVERT: G 431 MET cc_start: 0.9868 (tpt) cc_final: 0.9375 (mmm) REVERT: G 478 MET cc_start: 0.9567 (ppp) cc_final: 0.9203 (ppp) REVERT: G 479 TYR cc_start: 0.9571 (OUTLIER) cc_final: 0.9136 (m-10) REVERT: G 519 MET cc_start: 0.9846 (ttp) cc_final: 0.9510 (mmp) REVERT: H 145 MET cc_start: 0.9173 (mmm) cc_final: 0.8856 (mtp) outliers start: 22 outliers final: 15 residues processed: 134 average time/residue: 0.3046 time to fit residues: 73.1585 Evaluate side-chains 135 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 3.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 671 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain C residue 671 THR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain E residue 671 THR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 479 TYR Chi-restraints excluded: chain G residue 671 THR Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 205 optimal weight: 0.5980 chunk 220 optimal weight: 7.9990 chunk 160 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 254 optimal weight: 3.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25268 Z= 0.245 Angle : 0.557 11.812 34584 Z= 0.281 Chirality : 0.038 0.203 4100 Planarity : 0.003 0.054 4404 Dihedral : 4.300 24.348 3880 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.71 % Allowed : 12.96 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.15), residues: 3340 helix: 2.20 (0.12), residues: 1952 sheet: -2.02 (0.29), residues: 200 loop : -0.85 (0.19), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 370 HIS 0.003 0.001 HIS A 574 PHE 0.013 0.001 PHE G 241 TYR 0.011 0.001 TYR C 44 ARG 0.004 0.000 ARG E 387 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 120 time to evaluate : 3.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9690 (mtm) cc_final: 0.9407 (mtm) REVERT: A 287 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9326 (pt) REVERT: A 431 MET cc_start: 0.9902 (mmm) cc_final: 0.9565 (mmm) REVERT: A 479 TYR cc_start: 0.9597 (OUTLIER) cc_final: 0.9279 (m-10) REVERT: A 519 MET cc_start: 0.9842 (ttp) cc_final: 0.9500 (mmp) REVERT: A 568 MET cc_start: 0.9538 (mmm) cc_final: 0.9053 (mmm) REVERT: B 145 MET cc_start: 0.9154 (mmm) cc_final: 0.8851 (mtp) REVERT: C 99 MET cc_start: 0.9691 (mtm) cc_final: 0.9408 (mtm) REVERT: C 287 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9325 (pt) REVERT: C 431 MET cc_start: 0.9858 (tpt) cc_final: 0.9355 (mmm) REVERT: C 479 TYR cc_start: 0.9598 (OUTLIER) cc_final: 0.9281 (m-10) REVERT: C 519 MET cc_start: 0.9842 (ttp) cc_final: 0.9501 (mmp) REVERT: C 568 MET cc_start: 0.9537 (mmm) cc_final: 0.9052 (mmm) REVERT: D 145 MET cc_start: 0.9152 (mmm) cc_final: 0.8850 (mtp) REVERT: E 99 MET cc_start: 0.9690 (mtm) cc_final: 0.9407 (mtm) REVERT: E 287 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9326 (pt) REVERT: E 431 MET cc_start: 0.9858 (tpt) cc_final: 0.9354 (mmm) REVERT: E 479 TYR cc_start: 0.9598 (OUTLIER) cc_final: 0.9282 (m-10) REVERT: E 519 MET cc_start: 0.9842 (ttp) cc_final: 0.9501 (mmp) REVERT: E 568 MET cc_start: 0.9538 (mmm) cc_final: 0.9054 (mmm) REVERT: F 145 MET cc_start: 0.9153 (mmm) cc_final: 0.8851 (mtp) REVERT: G 99 MET cc_start: 0.9689 (mtm) cc_final: 0.9407 (mtm) REVERT: G 287 ILE cc_start: 0.9615 (OUTLIER) cc_final: 0.9326 (pt) REVERT: G 431 MET cc_start: 0.9862 (tpt) cc_final: 0.9365 (mmm) REVERT: G 458 MET cc_start: 0.9870 (tpp) cc_final: 0.9527 (mmm) REVERT: G 478 MET cc_start: 0.9602 (ppp) cc_final: 0.9292 (ppp) REVERT: G 479 TYR cc_start: 0.9562 (OUTLIER) cc_final: 0.9137 (m-10) REVERT: G 519 MET cc_start: 0.9842 (ttp) cc_final: 0.9501 (mmp) REVERT: G 568 MET cc_start: 0.9538 (mmm) cc_final: 0.9052 (mmm) REVERT: H 145 MET cc_start: 0.9154 (mmm) cc_final: 0.8852 (mtp) outliers start: 39 outliers final: 14 residues processed: 155 average time/residue: 0.3072 time to fit residues: 83.5477 Evaluate side-chains 142 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 3.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 448 ILE Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain D residue 144 MET Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 448 ILE Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain F residue 144 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 479 TYR Chi-restraints excluded: chain H residue 144 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 1.9990 chunk 310 optimal weight: 9.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 181 optimal weight: 20.0000 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 0.9980 chunk 92 optimal weight: 20.0000 chunk 272 optimal weight: 0.0970 chunk 285 optimal weight: 10.0000 chunk 300 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 25268 Z= 0.138 Angle : 0.545 11.425 34584 Z= 0.260 Chirality : 0.038 0.285 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.958 20.436 3880 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.10 % Allowed : 13.97 % Favored : 84.93 % 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: 1.59 (0.16), residues: 3340 helix: 2.51 (0.12), residues: 1916 sheet: -1.97 (0.28), residues: 232 loop : -0.76 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 370 HIS 0.001 0.000 HIS E 552 PHE 0.012 0.001 PHE A 429 TYR 0.010 0.001 TYR G 371 ARG 0.002 0.000 ARG A 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 128 time to evaluate : 2.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.9776 (OUTLIER) cc_final: 0.9569 (mmp) REVERT: A 99 MET cc_start: 0.9694 (mtm) cc_final: 0.9409 (mtm) REVERT: A 287 ILE cc_start: 0.9591 (OUTLIER) cc_final: 0.9308 (pt) REVERT: A 332 LEU cc_start: 0.9644 (tp) cc_final: 0.9354 (tt) REVERT: A 431 MET cc_start: 0.9881 (mmm) cc_final: 0.9664 (tpp) REVERT: A 478 MET cc_start: 0.9583 (ppp) cc_final: 0.9254 (ppp) REVERT: A 479 TYR cc_start: 0.9591 (OUTLIER) cc_final: 0.9113 (m-10) REVERT: A 519 MET cc_start: 0.9832 (ttp) cc_final: 0.9457 (mmp) REVERT: B 145 MET cc_start: 0.9167 (mmm) cc_final: 0.8849 (mtp) REVERT: C 92 MET cc_start: 0.9776 (OUTLIER) cc_final: 0.9568 (mmp) REVERT: C 99 MET cc_start: 0.9694 (mtm) cc_final: 0.9410 (mtm) REVERT: C 287 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9308 (pt) REVERT: C 332 LEU cc_start: 0.9644 (tp) cc_final: 0.9355 (tt) REVERT: C 431 MET cc_start: 0.9843 (tpt) cc_final: 0.9520 (tpp) REVERT: C 435 THR cc_start: 0.9513 (OUTLIER) cc_final: 0.9193 (p) REVERT: C 478 MET cc_start: 0.9583 (ppp) cc_final: 0.9254 (ppp) REVERT: C 479 TYR cc_start: 0.9598 (OUTLIER) cc_final: 0.9107 (m-10) REVERT: C 519 MET cc_start: 0.9832 (ttp) cc_final: 0.9458 (mmp) REVERT: D 145 MET cc_start: 0.9167 (mmm) cc_final: 0.8850 (mtp) REVERT: E 92 MET cc_start: 0.9776 (OUTLIER) cc_final: 0.9568 (mmp) REVERT: E 99 MET cc_start: 0.9695 (mtm) cc_final: 0.9411 (mtm) REVERT: E 287 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9310 (pt) REVERT: E 332 LEU cc_start: 0.9644 (tp) cc_final: 0.9355 (tt) REVERT: E 431 MET cc_start: 0.9846 (tpt) cc_final: 0.9527 (tpp) REVERT: E 435 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9123 (p) REVERT: E 478 MET cc_start: 0.9583 (ppp) cc_final: 0.9254 (ppp) REVERT: E 479 TYR cc_start: 0.9598 (OUTLIER) cc_final: 0.9109 (m-10) REVERT: E 519 MET cc_start: 0.9833 (ttp) cc_final: 0.9457 (mmp) REVERT: F 145 MET cc_start: 0.9168 (mmm) cc_final: 0.8850 (mtp) REVERT: G 92 MET cc_start: 0.9777 (OUTLIER) cc_final: 0.9569 (mmp) REVERT: G 99 MET cc_start: 0.9693 (mtm) cc_final: 0.9409 (mtm) REVERT: G 287 ILE cc_start: 0.9592 (OUTLIER) cc_final: 0.9309 (pt) REVERT: G 332 LEU cc_start: 0.9644 (tp) cc_final: 0.9355 (tt) REVERT: G 431 MET cc_start: 0.9843 (tpt) cc_final: 0.9612 (tpp) REVERT: G 435 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9163 (p) REVERT: G 457 MET cc_start: 0.9634 (OUTLIER) cc_final: 0.9416 (ptm) REVERT: G 475 PHE cc_start: 0.9777 (OUTLIER) cc_final: 0.8821 (t80) REVERT: G 478 MET cc_start: 0.9614 (ppp) cc_final: 0.9242 (ppp) REVERT: G 479 TYR cc_start: 0.9545 (OUTLIER) cc_final: 0.8947 (m-10) REVERT: G 519 MET cc_start: 0.9832 (ttp) cc_final: 0.9457 (mmp) REVERT: H 145 MET cc_start: 0.9167 (mmm) cc_final: 0.8850 (mtp) outliers start: 25 outliers final: 4 residues processed: 144 average time/residue: 0.3062 time to fit residues: 77.6697 Evaluate side-chains 144 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 3.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain G residue 92 MET Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 457 MET Chi-restraints excluded: chain G residue 475 PHE Chi-restraints excluded: chain G residue 479 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 30.0000 chunk 319 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 221 optimal weight: 0.0670 chunk 334 optimal weight: 6.9990 chunk 308 optimal weight: 9.9990 chunk 266 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 163 optimal weight: 3.9990 overall best weight: 3.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 85 GLN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25268 Z= 0.199 Angle : 0.553 10.636 34584 Z= 0.269 Chirality : 0.038 0.250 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.943 20.222 3880 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.83 % Allowed : 14.63 % Favored : 84.53 % 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: 1.44 (0.16), residues: 3340 helix: 2.33 (0.12), residues: 1956 sheet: -2.01 (0.28), residues: 232 loop : -0.83 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 370 HIS 0.003 0.001 HIS A 574 PHE 0.012 0.001 PHE G 241 TYR 0.010 0.001 TYR G 371 ARG 0.003 0.000 ARG C 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6680 Ramachandran restraints generated. 3340 Oldfield, 0 Emsley, 3340 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 2.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9391 (mtm) REVERT: A 287 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9319 (pt) REVERT: A 478 MET cc_start: 0.9564 (ppp) cc_final: 0.9229 (ppp) REVERT: A 479 TYR cc_start: 0.9613 (OUTLIER) cc_final: 0.9052 (m-10) REVERT: A 519 MET cc_start: 0.9836 (ttp) cc_final: 0.9474 (mmp) REVERT: A 568 MET cc_start: 0.9441 (mmm) cc_final: 0.9006 (mmm) REVERT: C 99 MET cc_start: 0.9689 (mtm) cc_final: 0.9392 (mtm) REVERT: C 287 ILE cc_start: 0.9614 (OUTLIER) cc_final: 0.9320 (pt) REVERT: C 431 MET cc_start: 0.9843 (tpt) cc_final: 0.9325 (mmm) REVERT: C 478 MET cc_start: 0.9563 (ppp) cc_final: 0.9228 (ppp) REVERT: C 479 TYR cc_start: 0.9614 (OUTLIER) cc_final: 0.9059 (m-10) REVERT: C 519 MET cc_start: 0.9836 (ttp) cc_final: 0.9474 (mmp) REVERT: C 568 MET cc_start: 0.9442 (mmm) cc_final: 0.9007 (mmm) REVERT: E 99 MET cc_start: 0.9689 (mtm) cc_final: 0.9391 (mtm) REVERT: E 287 ILE cc_start: 0.9614 (OUTLIER) cc_final: 0.9320 (pt) REVERT: E 431 MET cc_start: 0.9845 (tpt) cc_final: 0.9537 (tpp) REVERT: E 435 THR cc_start: 0.9534 (OUTLIER) cc_final: 0.9230 (p) REVERT: E 478 MET cc_start: 0.9562 (ppp) cc_final: 0.9228 (ppp) REVERT: E 479 TYR cc_start: 0.9616 (OUTLIER) cc_final: 0.9061 (m-10) REVERT: E 519 MET cc_start: 0.9836 (ttp) cc_final: 0.9473 (mmp) REVERT: E 568 MET cc_start: 0.9442 (mmm) cc_final: 0.9005 (mmm) REVERT: G 99 MET cc_start: 0.9688 (mtm) cc_final: 0.9391 (mtm) REVERT: G 287 ILE cc_start: 0.9613 (OUTLIER) cc_final: 0.9319 (pt) REVERT: G 431 MET cc_start: 0.9843 (tpt) cc_final: 0.9329 (mmm) REVERT: G 478 MET cc_start: 0.9615 (ppp) cc_final: 0.9276 (ppp) REVERT: G 479 TYR cc_start: 0.9549 (OUTLIER) cc_final: 0.9095 (m-10) REVERT: G 519 MET cc_start: 0.9836 (ttp) cc_final: 0.9472 (mmp) REVERT: G 568 MET cc_start: 0.9443 (mmm) cc_final: 0.9008 (mmm) outliers start: 19 outliers final: 6 residues processed: 135 average time/residue: 0.3046 time to fit residues: 72.3396 Evaluate side-chains 135 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 120 time to evaluate : 2.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 435 THR Chi-restraints excluded: chain C residue 479 TYR Chi-restraints excluded: chain E residue 287 ILE Chi-restraints excluded: chain E residue 434 LEU Chi-restraints excluded: chain E residue 435 THR Chi-restraints excluded: chain E residue 479 TYR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain G residue 435 THR Chi-restraints excluded: chain G residue 448 ILE Chi-restraints excluded: chain G residue 479 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 266 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.030489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.027530 restraints weight = 306359.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.027978 restraints weight = 189631.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.028356 restraints weight = 140943.642| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25268 Z= 0.198 Angle : 0.573 13.691 34584 Z= 0.274 Chirality : 0.038 0.250 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.946 20.800 3880 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.79 % Allowed : 14.81 % Favored : 84.40 % 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: 1.47 (0.16), residues: 3340 helix: 2.36 (0.12), residues: 1936 sheet: -1.99 (0.29), residues: 232 loop : -0.78 (0.19), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 370 HIS 0.003 0.001 HIS A 574 PHE 0.012 0.001 PHE G 241 TYR 0.010 0.001 TYR G 371 ARG 0.003 0.000 ARG C 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3443.55 seconds wall clock time: 65 minutes 24.51 seconds (3924.51 seconds total)