Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 04:32:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2023/5k7l_8215_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2023/5k7l_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_2023/5k7l_8215.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2023/5k7l_8215.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2023/5k7l_8215_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k7l_8215/04_2023/5k7l_8215_updated.pdb" } resolution = 3.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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-1.21rc1-4938/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: 7 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: 7 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: 7 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: 7 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: 14.03, per 1000 atoms: 0.57 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: 11.46 Conformation dependent library (CDL) restraints added in 4.1 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: 3.16 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: 8.26 Time building geometry restraints manager: 12.11 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: 12808 13.29 - 26.58: 1192 26.58 - 39.87: 472 39.87 - 53.16: 108 53.16 - 66.45: 24 Dihedral angle restraints: 14604 sinusoidal: 4728 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 14601 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: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.790 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 66.030 Find NCS groups from input model: 1.760 Set up NCS constraints: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.890 ------------------------------------------------------------------------------- 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 : 13.266 66.453 8204 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 % 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 *********************** 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 : 3.111 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 outliers start: 8 outliers final: 0 residues processed: 172 average time/residue: 0.3545 time to fit residues: 101.0572 Evaluate side-chains 124 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 3.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.3695 ------------------------------------------------------------------------------- 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: 0.8141 moved from start: 0.1758 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= 0.162 Angle : 0.548 7.040 34584 Z= 0.285 Chirality : 0.038 0.140 4100 Planarity : 0.004 0.048 4404 Dihedral : 4.397 20.658 3596 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 3340 helix: 3.28 (0.13), residues: 1920 sheet: -2.42 (0.29), residues: 208 loop : -1.83 (0.17), residues: 1212 *********************** 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 : 3.277 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 outliers start: 41 outliers final: 0 residues processed: 160 average time/residue: 0.3211 time to fit residues: 88.4166 Evaluate side-chains 117 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 2.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 207 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 305 optimal weight: 0.9990 chunk 330 optimal weight: 30.0000 chunk 272 optimal weight: 0.0570 chunk 303 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 245 optimal weight: 4.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25268 Z= 0.169 Angle : 0.508 8.214 34584 Z= 0.262 Chirality : 0.038 0.226 4100 Planarity : 0.003 0.051 4404 Dihedral : 4.016 17.484 3596 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.53 % 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: 1.72 (0.16), residues: 3340 helix: 3.00 (0.12), residues: 1944 sheet: -2.48 (0.29), residues: 200 loop : -1.50 (0.18), residues: 1196 *********************** 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 140 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 140 average time/residue: 0.3102 time to fit residues: 75.1239 Evaluate side-chains 116 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.930 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 6.9990 chunk 229 optimal weight: 30.0000 chunk 158 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 205 optimal weight: 8.9990 chunk 306 optimal weight: 9.9990 chunk 324 optimal weight: 50.0000 chunk 160 optimal weight: 20.0000 chunk 290 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- 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** A 708 HIS ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 246 ASN ** 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 93 ASN E 246 ASN ** 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 93 ASN G 246 ASN ** 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.057 25268 Z= 0.355 Angle : 0.633 8.794 34584 Z= 0.333 Chirality : 0.039 0.189 4100 Planarity : 0.004 0.053 4404 Dihedral : 4.434 17.941 3596 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 1.41 % 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: 1.19 (0.15), residues: 3340 helix: 2.27 (0.12), residues: 1980 sheet: -2.46 (0.30), residues: 200 loop : -1.29 (0.18), residues: 1160 *********************** 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 156 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 124 time to evaluate : 2.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 8 residues processed: 148 average time/residue: 0.2915 time to fit residues: 76.2516 Evaluate side-chains 128 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 120 time to evaluate : 2.906 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2318 time to fit residues: 7.1522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 291 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** ** B 137 ASN ** 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** ** D 137 ASN ** 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** ** F 137 ASN ** 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** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 25268 Z= 0.231 Angle : 0.571 10.945 34584 Z= 0.284 Chirality : 0.038 0.187 4100 Planarity : 0.003 0.053 4404 Dihedral : 4.195 16.186 3596 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 1.23 % 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: 1.38 (0.16), residues: 3340 helix: 2.40 (0.12), residues: 1968 sheet: -2.21 (0.28), residues: 224 loop : -1.12 (0.19), residues: 1148 *********************** 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 152 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 3.333 Fit side-chains outliers start: 28 outliers final: 4 residues processed: 144 average time/residue: 0.3111 time to fit residues: 79.2685 Evaluate side-chains 123 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 3.117 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2186 time to fit residues: 5.8766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 3.9990 chunk 292 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 325 optimal weight: 0.0040 chunk 269 optimal weight: 20.0000 chunk 150 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 107 optimal weight: 0.0050 chunk 170 optimal weight: 9.9990 overall best weight: 0.5806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS C 20 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 583 HIS E 20 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 583 HIS G 20 ASN G 470 ASN ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3670 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= 0.129 Angle : 0.558 10.594 34584 Z= 0.263 Chirality : 0.039 0.274 4100 Planarity : 0.003 0.055 4404 Dihedral : 3.931 16.556 3596 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.53 % 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: 1.37 (0.15), residues: 3340 helix: 2.37 (0.12), residues: 1980 sheet: -2.09 (0.27), residues: 228 loop : -1.15 (0.19), residues: 1132 *********************** 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 140 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 128 time to evaluate : 3.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 2 residues processed: 140 average time/residue: 0.3174 time to fit residues: 78.3467 Evaluate side-chains 130 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 128 time to evaluate : 3.208 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2164 time to fit residues: 4.8165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 30.0000 chunk 36 optimal weight: 20.0000 chunk 185 optimal weight: 10.0000 chunk 237 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 273 optimal weight: 10.0000 chunk 181 optimal weight: 40.0000 chunk 323 optimal weight: 50.0000 chunk 202 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 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** ** D 137 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** ** F 137 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** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 25268 Z= 0.396 Angle : 0.686 9.740 34584 Z= 0.355 Chirality : 0.039 0.188 4100 Planarity : 0.004 0.054 4404 Dihedral : 4.408 16.693 3596 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer Outliers : 0.97 % 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: 1.13 (0.15), residues: 3340 helix: 2.07 (0.12), residues: 1968 sheet: -2.47 (0.28), residues: 224 loop : -0.91 (0.20), residues: 1148 *********************** 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 : 2.953 Fit side-chains outliers start: 22 outliers final: 8 residues processed: 134 average time/residue: 0.3149 time to fit residues: 74.7564 Evaluate side-chains 123 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 115 time to evaluate : 3.077 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2422 time to fit residues: 8.0226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 205 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 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** ** D 137 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** ** F 137 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** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4389 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= 0.218 Angle : 0.590 13.065 34584 Z= 0.289 Chirality : 0.038 0.240 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.241 18.786 3596 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.53 % 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: 1.27 (0.16), residues: 3340 helix: 2.25 (0.12), residues: 1956 sheet: -2.38 (0.28), residues: 224 loop : -0.96 (0.19), residues: 1160 *********************** 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 130 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 4 residues processed: 130 average time/residue: 0.3186 time to fit residues: 73.5788 Evaluate side-chains 122 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2284 time to fit residues: 6.2428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 8.9990 chunk 310 optimal weight: 8.9990 chunk 283 optimal weight: 6.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 236 optimal weight: 30.0000 chunk 92 optimal weight: 8.9990 chunk 272 optimal weight: 6.9990 chunk 285 optimal weight: 5.9990 chunk 300 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 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** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 470 ASN ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 ASN ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 25268 Z= 0.295 Angle : 0.630 12.404 34584 Z= 0.315 Chirality : 0.039 0.190 4100 Planarity : 0.004 0.055 4404 Dihedral : 4.383 19.516 3596 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3340 helix: 2.08 (0.12), residues: 1960 sheet: -2.35 (0.28), residues: 220 loop : -0.94 (0.19), residues: 1160 *********************** 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 121 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 2.986 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 121 average time/residue: 0.3112 time to fit residues: 67.0573 Evaluate side-chains 116 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 3.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.1453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 194 optimal weight: 0.2980 chunk 151 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 308 optimal weight: 0.6980 chunk 266 optimal weight: 30.0000 chunk 27 optimal weight: 0.0570 chunk 205 optimal weight: 4.9990 chunk 163 optimal weight: 0.8980 overall best weight: 1.1900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 ASN A 85 GLN A 246 ASN ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 ASN C 85 GLN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 20 ASN ** E 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 ASN ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 25268 Z= 0.135 Angle : 0.585 12.853 34584 Z= 0.276 Chirality : 0.038 0.298 4100 Planarity : 0.003 0.055 4404 Dihedral : 4.069 20.901 3596 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer Outliers : 0.04 % 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: 1.52 (0.15), residues: 3340 helix: 2.49 (0.12), residues: 1904 sheet: -2.05 (0.30), residues: 220 loop : -0.83 (0.18), residues: 1216 ********************** 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 129 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.3191 time to fit residues: 72.2574 Evaluate side-chains 121 residues out of total 2996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 3.089 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2055 time to fit residues: 4.2338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 1.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 245 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 266 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 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** ** D 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 137 ASN ** 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 = 0.3040 r_free = 0.3040 target = 0.030825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.027805 restraints weight = 301670.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.028284 restraints weight = 183760.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.028646 restraints weight = 134357.446| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 25268 Z= 0.220 Angle : 0.616 12.545 34584 Z= 0.293 Chirality : 0.038 0.247 4100 Planarity : 0.003 0.055 4404 Dihedral : 4.060 19.987 3596 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 3340 helix: 2.37 (0.12), residues: 1952 sheet: -2.12 (0.29), residues: 220 loop : -0.89 (0.19), residues: 1168 =============================================================================== Job complete usr+sys time: 3137.40 seconds wall clock time: 59 minutes 36.84 seconds (3576.84 seconds total)