Starting phenix.real_space_refine (version: 1.21rc1) on Sat Aug 26 20:33:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hv9_0288/08_2023/6hv9_0288_updated.pdb" } resolution = 4.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.035 sd= 0.184 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 54 5.49 5 S 199 5.16 5 C 29962 2.51 5 N 8250 2.21 5 O 9150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 108": "NH1" <-> "NH2" Residue "3 ARG 208": "NH1" <-> "NH2" Residue "3 ARG 224": "NH1" <-> "NH2" Residue "3 ARG 435": "NH1" <-> "NH2" Residue "3 ARG 483": "NH1" <-> "NH2" Residue "3 ARG 557": "NH1" <-> "NH2" Residue "3 ARG 657": "NH1" <-> "NH2" Residue "3 ARG 700": "NH1" <-> "NH2" Residue "3 ARG 734": "NH1" <-> "NH2" Residue "4 ARG 178": "NH1" <-> "NH2" Residue "4 ARG 234": "NH1" <-> "NH2" Residue "4 ARG 373": "NH1" <-> "NH2" Residue "4 ARG 388": "NH1" <-> "NH2" Residue "4 ARG 428": "NH1" <-> "NH2" Residue "4 ARG 557": "NH1" <-> "NH2" Residue "4 ARG 559": "NH1" <-> "NH2" Residue "4 ARG 607": "NH1" <-> "NH2" Residue "4 ARG 681": "NH1" <-> "NH2" Residue "4 ARG 796": "NH1" <-> "NH2" Residue "4 ARG 827": "NH1" <-> "NH2" Residue "5 PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 407": "NH1" <-> "NH2" Residue "5 ARG 460": "NH1" <-> "NH2" Residue "5 ARG 651": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 176": "NH1" <-> "NH2" Residue "6 ARG 190": "NH1" <-> "NH2" Residue "6 ARG 277": "NH1" <-> "NH2" Residue "6 ARG 280": "NH1" <-> "NH2" Residue "6 TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 375": "NH1" <-> "NH2" Residue "6 ARG 446": "NH1" <-> "NH2" Residue "6 ARG 531": "NH1" <-> "NH2" Residue "6 ARG 566": "NH1" <-> "NH2" Residue "6 ARG 594": "NH1" <-> "NH2" Residue "6 ARG 691": "NH1" <-> "NH2" Residue "6 ARG 708": "NH1" <-> "NH2" Residue "6 ARG 790": "NH1" <-> "NH2" Residue "2 ARG 224": "NH1" <-> "NH2" Residue "2 ARG 319": "NH1" <-> "NH2" Residue "2 PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 459": "NH1" <-> "NH2" Residue "2 ARG 489": "NH1" <-> "NH2" Residue "2 ARG 509": "NH1" <-> "NH2" Residue "2 ARG 534": "NH1" <-> "NH2" Residue "2 ARG 656": "NH1" <-> "NH2" Residue "2 ARG 684": "NH1" <-> "NH2" Residue "2 ARG 808": "NH1" <-> "NH2" Residue "2 ARG 824": "NH1" <-> "NH2" Residue "2 ARG 859": "NH1" <-> "NH2" Residue "7 ARG 199": "NH1" <-> "NH2" Residue "7 ARG 213": "NH1" <-> "NH2" Residue "7 ARG 214": "NH1" <-> "NH2" Residue "7 TYR 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 451": "NH1" <-> "NH2" Residue "7 TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 573": "NH1" <-> "NH2" Residue "7 ARG 577": "NH1" <-> "NH2" Residue "7 ARG 606": "NH1" <-> "NH2" Residue "7 ARG 694": "NH1" <-> "NH2" Residue "7 ARG 703": "NH1" <-> "NH2" Residue "7 ARG 718": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 142": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 283": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 117": "NH1" <-> "NH2" Residue "G ARG 226": "NH1" <-> "NH2" Residue "G TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 398": "NH1" <-> "NH2" Residue "G ARG 406": "NH1" <-> "NH2" Residue "G ARG 411": "NH1" <-> "NH2" Residue "G ARG 472": "NH1" <-> "NH2" Residue "G ARG 547": "NH1" <-> "NH2" Residue "G ARG 587": "NH1" <-> "NH2" Residue "B ARG 228": "NH1" <-> "NH2" Residue "B ARG 378": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B PHE 649": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1436": "NH1" <-> "NH2" Residue "A ARG 1572": "NH1" <-> "NH2" Residue "A ARG 1605": "NH1" <-> "NH2" Residue "A ARG 1664": "NH1" <-> "NH2" Residue "A ARG 1678": "NH1" <-> "NH2" Residue "A ARG 1833": "NH1" <-> "NH2" Residue "A TYR 1897": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1905": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 2132": "NH1" <-> "NH2" Residue "A ARG 2151": "NH1" <-> "NH2" Residue "A ARG 2163": "NH1" <-> "NH2" Residue "A ARG 2166": "NH1" <-> "NH2" Residue "A ARG 2172": "NH1" <-> "NH2" Residue "A ARG 2191": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 47617 Number of models: 1 Model: "" Number of chains: 18 Chain: "3" Number of atoms: 4270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4270 Classifications: {'peptide': 558} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 535} Chain breaks: 7 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 76 Chain: "4" Number of atoms: 4543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4543 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 10 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 194 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 6, 'ASN:plan1': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 90 Chain: "5" Number of atoms: 4690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 628, 4690 Classifications: {'peptide': 628} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 603} Chain breaks: 14 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 244 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 185 Chain: "6" Number of atoms: 4307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4307 Classifications: {'peptide': 571} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 62} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 550} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 238 Unresolved non-hydrogen angles: 305 Unresolved non-hydrogen dihedrals: 204 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 6, 'GLU:plan': 6, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 140 Chain: "2" Number of atoms: 4184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4184 Classifications: {'peptide': 549} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 19, 'TRANS': 529} Chain breaks: 10 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 120 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 104 Chain: "7" Number of atoms: 4785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 4785 Classifications: {'peptide': 616} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 586} Chain breaks: 13 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1492 Classifications: {'peptide': 194} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 28} Link IDs: {'CIS': 11, 'PTRANS': 3, 'TRANS': 179} Chain breaks: 2 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 2, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 40 Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1461 Classifications: {'peptide': 181} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 12} Link IDs: {'CIS': 4, 'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'PHE:plan': 2, 'GLN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1262 Classifications: {'peptide': 159} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 9} Link IDs: {'CIS': 3, 'PTRANS': 10, 'TRANS': 145} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1743 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 8, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 5 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 4239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4239 Classifications: {'peptide': 541} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 40} Link IDs: {'CIS': 17, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 508} Chain breaks: 7 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 124 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 81 Chain: "X" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 425 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 433 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Chain: "B" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3661 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 436} Chain breaks: 11 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "A" Number of atoms: 5918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 5918 Classifications: {'peptide': 771} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 92} Link IDs: {'CIS': 4, 'PTRANS': 28, 'TRANS': 738} Chain breaks: 9 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 379 Unresolved non-hydrogen angles: 471 Unresolved non-hydrogen dihedrals: 330 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 11, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 224 Chain: "5" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 46678 SG CYS A2108 141.943 44.627 62.060 1.00194.16 S ATOM 46705 SG CYS A2111 140.563 42.890 62.222 1.00201.20 S ATOM 46814 SG CYS A2130 141.002 43.072 64.673 1.00205.54 S ATOM 46838 SG CYS A2133 143.942 41.763 61.740 1.00208.50 S ATOM 47101 SG CYS A2164 112.564 72.569 89.689 1.00127.78 S ATOM 47124 SG CYS A2167 110.107 72.637 87.810 1.00131.93 S ATOM 47225 SG CYS A2179 109.162 74.225 88.617 1.00116.92 S ATOM 47238 SG CYS A2181 108.509 73.695 90.044 1.00115.72 S Time building chain proxies: 22.26, per 1000 atoms: 0.47 Number of scatterers: 47617 At special positions: 0 Unit cell: (218.04, 169.74, 242.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 199 16.00 P 54 15.00 O 9150 8.00 N 8250 7.00 C 29962 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.64 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2111 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2133 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2130 " pdb="ZN ZN A2301 " - pdb=" SG CYS A2108 " pdb=" ZN A2302 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2167 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2181 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2164 " pdb="ZN ZN A2302 " - pdb=" SG CYS A2179 " Number of angles added : 12 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11518 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 218 helices and 34 sheets defined 38.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.51 Creating SS restraints... Processing helix chain '3' and resid 20 through 34 Processing helix chain '3' and resid 37 through 57 removed outlier: 3.773A pdb=" N SER 3 41 " --> pdb=" O SER 3 37 " (cutoff:3.500A) Processing helix chain '3' and resid 108 through 116 Processing helix chain '3' and resid 122 through 136 Processing helix chain '3' and resid 262 through 264 No H-bonds generated for 'chain '3' and resid 262 through 264' Processing helix chain '3' and resid 280 through 282 No H-bonds generated for 'chain '3' and resid 280 through 282' Processing helix chain '3' and resid 344 through 355 removed outlier: 3.737A pdb=" N LYS 3 355 " --> pdb=" O ASN 3 351 " (cutoff:3.500A) Processing helix chain '3' and resid 359 through 366 Processing helix chain '3' and resid 375 through 386 Processing helix chain '3' and resid 419 through 425 Processing helix chain '3' and resid 461 through 464 No H-bonds generated for 'chain '3' and resid 461 through 464' Processing helix chain '3' and resid 483 through 492 removed outlier: 4.020A pdb=" N HIS 3 487 " --> pdb=" O ARG 3 483 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU 3 488 " --> pdb=" O VAL 3 484 " (cutoff:3.500A) Processing helix chain '3' and resid 537 through 542 removed outlier: 3.847A pdb=" N SER 3 541 " --> pdb=" O ASP 3 537 " (cutoff:3.500A) Processing helix chain '3' and resid 556 through 569 Processing helix chain '3' and resid 653 through 666 removed outlier: 3.541A pdb=" N ARG 3 657 " --> pdb=" O ILE 3 653 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS 3 658 " --> pdb=" O PRO 3 654 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU 3 665 " --> pdb=" O GLN 3 661 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ARG 3 666 " --> pdb=" O TYR 3 662 " (cutoff:3.500A) Processing helix chain '3' and resid 673 through 688 removed outlier: 3.984A pdb=" N ASN 3 677 " --> pdb=" O GLU 3 674 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL 3 678 " --> pdb=" O ALA 3 675 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL 3 680 " --> pdb=" O ASN 3 677 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN 3 688 " --> pdb=" O ASP 3 685 " (cutoff:3.500A) Processing helix chain '3' and resid 690 through 692 No H-bonds generated for 'chain '3' and resid 690 through 692' Processing helix chain '3' and resid 699 through 715 removed outlier: 3.773A pdb=" N ALA 3 709 " --> pdb=" O LEU 3 705 " (cutoff:3.500A) Processing helix chain '3' and resid 723 through 736 removed outlier: 3.671A pdb=" N ASN 3 731 " --> pdb=" O LYS 3 727 " (cutoff:3.500A) Processing helix chain '4' and resid 187 through 199 Processing helix chain '4' and resid 204 through 209 Processing helix chain '4' and resid 225 through 234 Processing helix chain '4' and resid 246 through 250 Processing helix chain '4' and resid 255 through 263 removed outlier: 3.535A pdb=" N HIS 4 259 " --> pdb=" O GLU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 265 through 284 removed outlier: 3.806A pdb=" N ILE 4 269 " --> pdb=" O PRO 4 265 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N SER 4 270 " --> pdb=" O GLN 4 266 " (cutoff:3.500A) Processing helix chain '4' and resid 293 through 298 Processing helix chain '4' and resid 504 through 513 removed outlier: 3.712A pdb=" N ALA 4 507 " --> pdb=" O GLN 4 504 " (cutoff:3.500A) Processing helix chain '4' and resid 516 through 524 removed outlier: 4.642A pdb=" N TYR 4 519 " --> pdb=" O GLU 4 516 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU 4 522 " --> pdb=" O TYR 4 519 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA 4 523 " --> pdb=" O SER 4 520 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG 4 524 " --> pdb=" O LEU 4 521 " (cutoff:3.500A) Processing helix chain '4' and resid 534 through 544 removed outlier: 3.890A pdb=" N LEU 4 544 " --> pdb=" O ILE 4 540 " (cutoff:3.500A) Processing helix chain '4' and resid 574 through 584 Processing helix chain '4' and resid 620 through 623 No H-bonds generated for 'chain '4' and resid 620 through 623' Processing helix chain '4' and resid 634 through 636 No H-bonds generated for 'chain '4' and resid 634 through 636' Processing helix chain '4' and resid 644 through 650 removed outlier: 3.636A pdb=" N GLU 4 650 " --> pdb=" O GLU 4 647 " (cutoff:3.500A) Processing helix chain '4' and resid 696 through 699 No H-bonds generated for 'chain '4' and resid 696 through 699' Processing helix chain '4' and resid 715 through 731 removed outlier: 4.998A pdb=" N GLU 4 730 " --> pdb=" O ASN 4 726 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASP 4 731 " --> pdb=" O LEU 4 727 " (cutoff:3.500A) Processing helix chain '4' and resid 746 through 756 removed outlier: 3.546A pdb=" N SER 4 752 " --> pdb=" O THR 4 748 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLU 4 756 " --> pdb=" O SER 4 752 " (cutoff:3.500A) Processing helix chain '4' and resid 764 through 779 removed outlier: 3.645A pdb=" N THR 4 768 " --> pdb=" O ALA 4 765 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL 4 775 " --> pdb=" O ARG 4 772 " (cutoff:3.500A) Processing helix chain '4' and resid 795 through 810 removed outlier: 3.619A pdb=" N GLU 4 806 " --> pdb=" O ILE 4 802 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA 4 807 " --> pdb=" O ARG 4 803 " (cutoff:3.500A) Processing helix chain '4' and resid 822 through 836 removed outlier: 3.871A pdb=" N ILE 4 829 " --> pdb=" O ALA 4 825 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA 4 832 " --> pdb=" O LEU 4 828 " (cutoff:3.500A) Processing helix chain '5' and resid 24 through 35 removed outlier: 3.897A pdb=" N ILE 5 28 " --> pdb=" O ASN 5 24 " (cutoff:3.500A) Processing helix chain '5' and resid 46 through 56 removed outlier: 4.175A pdb=" N LEU 5 55 " --> pdb=" O ARG 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 65 through 71 Processing helix chain '5' and resid 74 through 81 Processing helix chain '5' and resid 83 through 104 Proline residue: 5 88 - end of helix removed outlier: 3.553A pdb=" N VAL 5 97 " --> pdb=" O ALA 5 93 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG 5 100 " --> pdb=" O GLN 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 352 through 361 Processing helix chain '5' and resid 366 through 372 Processing helix chain '5' and resid 382 through 391 removed outlier: 4.167A pdb=" N VAL 5 389 " --> pdb=" O LYS 5 385 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS 5 390 " --> pdb=" O LYS 5 386 " (cutoff:3.500A) Processing helix chain '5' and resid 422 through 432 Processing helix chain '5' and resid 458 through 460 No H-bonds generated for 'chain '5' and resid 458 through 460' Processing helix chain '5' and resid 490 through 496 Processing helix chain '5' and resid 528 through 532 removed outlier: 3.824A pdb=" N ASP 5 531 " --> pdb=" O GLY 5 528 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP 5 532 " --> pdb=" O ARG 5 529 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 528 through 532' Processing helix chain '5' and resid 545 through 548 No H-bonds generated for 'chain '5' and resid 545 through 548' Processing helix chain '5' and resid 562 through 576 Processing helix chain '5' and resid 585 through 591 Processing helix chain '5' and resid 596 through 609 removed outlier: 4.249A pdb=" N LEU 5 608 " --> pdb=" O THR 5 604 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS 5 609 " --> pdb=" O TYR 5 605 " (cutoff:3.500A) Processing helix chain '5' and resid 616 through 638 removed outlier: 4.418A pdb=" N GLU 5 620 " --> pdb=" O PRO 5 616 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LYS 5 621 " --> pdb=" O GLN 5 617 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU 5 622 " --> pdb=" O ALA 5 618 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL 5 627 " --> pdb=" O SER 5 623 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR 5 628 " --> pdb=" O SER 5 624 " (cutoff:3.500A) Processing helix chain '5' and resid 650 through 667 removed outlier: 3.690A pdb=" N ARG 5 658 " --> pdb=" O GLU 5 654 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE 5 659 " --> pdb=" O ALA 5 655 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR 5 660 " --> pdb=" O ILE 5 656 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU 5 661 " --> pdb=" O ILE 5 657 " (cutoff:3.500A) Processing helix chain '5' and resid 674 through 692 removed outlier: 4.242A pdb=" N GLU 5 679 " --> pdb=" O ARG 5 675 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ALA 5 680 " --> pdb=" O HIS 5 676 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE 5 681 " --> pdb=" O VAL 5 677 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG 5 682 " --> pdb=" O ASP 5 678 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP 5 690 " --> pdb=" O ALA 5 686 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA 5 691 " --> pdb=" O SER 5 687 " (cutoff:3.500A) Processing helix chain '5' and resid 717 through 721 Processing helix chain '5' and resid 730 through 738 Processing helix chain '5' and resid 745 through 752 Processing helix chain '5' and resid 761 through 773 removed outlier: 4.065A pdb=" N TYR 5 771 " --> pdb=" O GLY 5 767 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ARG 5 772 " --> pdb=" O GLN 5 768 " (cutoff:3.500A) Processing helix chain '6' and resid 104 through 120 Processing helix chain '6' and resid 135 through 146 Processing helix chain '6' and resid 155 through 161 removed outlier: 4.357A pdb=" N ARG 6 161 " --> pdb=" O HIS 6 157 " (cutoff:3.500A) Processing helix chain '6' and resid 167 through 170 No H-bonds generated for 'chain '6' and resid 167 through 170' Processing helix chain '6' and resid 175 through 192 removed outlier: 3.703A pdb=" N LEU 6 178 " --> pdb=" O TYR 6 175 " (cutoff:3.500A) Proline residue: 6 179 - end of helix removed outlier: 3.956A pdb=" N GLY 6 184 " --> pdb=" O LEU 6 181 " (cutoff:3.500A) Processing helix chain '6' and resid 276 through 278 No H-bonds generated for 'chain '6' and resid 276 through 278' Processing helix chain '6' and resid 281 through 283 No H-bonds generated for 'chain '6' and resid 281 through 283' Processing helix chain '6' and resid 383 through 385 No H-bonds generated for 'chain '6' and resid 383 through 385' Processing helix chain '6' and resid 513 through 520 Processing helix chain '6' and resid 525 through 531 removed outlier: 3.770A pdb=" N ARG 6 531 " --> pdb=" O ASP 6 527 " (cutoff:3.500A) Processing helix chain '6' and resid 542 through 550 Processing helix chain '6' and resid 581 through 591 Processing helix chain '6' and resid 641 through 643 No H-bonds generated for 'chain '6' and resid 641 through 643' Processing helix chain '6' and resid 646 through 657 Processing helix chain '6' and resid 696 through 699 No H-bonds generated for 'chain '6' and resid 696 through 699' Processing helix chain '6' and resid 703 through 708 Processing helix chain '6' and resid 721 through 735 Processing helix chain '6' and resid 748 through 760 removed outlier: 3.949A pdb=" N THR 6 760 " --> pdb=" O LYS 6 756 " (cutoff:3.500A) Processing helix chain '6' and resid 768 through 782 removed outlier: 3.615A pdb=" N GLU 6 775 " --> pdb=" O TYR 6 772 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU 6 779 " --> pdb=" O LYS 6 776 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS 6 782 " --> pdb=" O GLU 6 779 " (cutoff:3.500A) Processing helix chain '6' and resid 797 through 813 removed outlier: 3.810A pdb=" N ALA 6 811 " --> pdb=" O SER 6 807 " (cutoff:3.500A) Processing helix chain '6' and resid 821 through 839 removed outlier: 3.886A pdb=" N VAL 6 838 " --> pdb=" O SER 6 834 " (cutoff:3.500A) Processing helix chain '2' and resid 203 through 210 Processing helix chain '2' and resid 226 through 237 removed outlier: 4.114A pdb=" N ARG 2 232 " --> pdb=" O GLY 2 228 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N THR 2 233 " --> pdb=" O ALA 2 229 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 252 Processing helix chain '2' and resid 255 through 261 Processing helix chain '2' and resid 264 through 280 removed outlier: 3.903A pdb=" N LEU 2 268 " --> pdb=" O PRO 2 264 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS 2 269 " --> pdb=" O GLU 2 265 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU 2 273 " --> pdb=" O LYS 2 269 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL 2 274 " --> pdb=" O ILE 2 270 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 288 No H-bonds generated for 'chain '2' and resid 286 through 288' Processing helix chain '2' and resid 478 through 488 removed outlier: 3.846A pdb=" N PHE 2 484 " --> pdb=" O GLU 2 480 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE 2 487 " --> pdb=" O GLU 2 483 " (cutoff:3.500A) Processing helix chain '2' and resid 493 through 499 removed outlier: 3.791A pdb=" N ILE 2 498 " --> pdb=" O ILE 2 494 " (cutoff:3.500A) Processing helix chain '2' and resid 509 through 520 removed outlier: 3.585A pdb=" N PHE 2 520 " --> pdb=" O ALA 2 516 " (cutoff:3.500A) Processing helix chain '2' and resid 549 through 559 removed outlier: 3.505A pdb=" N LEU 2 553 " --> pdb=" O LYS 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 598 No H-bonds generated for 'chain '2' and resid 595 through 598' Processing helix chain '2' and resid 609 through 611 No H-bonds generated for 'chain '2' and resid 609 through 611' Processing helix chain '2' and resid 614 through 625 Processing helix chain '2' and resid 663 through 666 No H-bonds generated for 'chain '2' and resid 663 through 666' Processing helix chain '2' and resid 671 through 676 Processing helix chain '2' and resid 689 through 703 Processing helix chain '2' and resid 760 through 773 removed outlier: 3.587A pdb=" N THR 2 772 " --> pdb=" O HIS 2 768 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS 2 773 " --> pdb=" O TYR 2 769 " (cutoff:3.500A) Processing helix chain '2' and resid 783 through 796 Processing helix chain '2' and resid 808 through 824 removed outlier: 4.035A pdb=" N LEU 2 814 " --> pdb=" O LEU 2 810 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N SER 2 819 " --> pdb=" O ARG 2 815 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE 2 820 " --> pdb=" O ILE 2 816 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA 2 821 " --> pdb=" O ALA 2 817 " (cutoff:3.500A) Processing helix chain '2' and resid 831 through 848 removed outlier: 4.685A pdb=" N ASP 2 843 " --> pdb=" O LYS 2 839 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER 2 844 " --> pdb=" O VAL 2 840 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA 2 848 " --> pdb=" O SER 2 844 " (cutoff:3.500A) Processing helix chain '2' and resid 851 through 859 removed outlier: 3.687A pdb=" N ARG 2 854 " --> pdb=" O VAL 2 851 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG 2 855 " --> pdb=" O SER 2 852 " (cutoff:3.500A) Processing helix chain '7' and resid 16 through 26 Processing helix chain '7' and resid 62 through 71 Processing helix chain '7' and resid 84 through 95 Processing helix chain '7' and resid 103 through 108 Processing helix chain '7' and resid 112 through 118 removed outlier: 3.808A pdb=" N LEU 7 116 " --> pdb=" O HIS 7 112 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE 7 117 " --> pdb=" O PHE 7 113 " (cutoff:3.500A) Processing helix chain '7' and resid 121 through 123 No H-bonds generated for 'chain '7' and resid 121 through 123' Processing helix chain '7' and resid 127 through 129 No H-bonds generated for 'chain '7' and resid 127 through 129' Processing helix chain '7' and resid 138 through 143 Processing helix chain '7' and resid 209 through 214 Processing helix chain '7' and resid 337 through 339 No H-bonds generated for 'chain '7' and resid 337 through 339' Processing helix chain '7' and resid 395 through 405 removed outlier: 3.759A pdb=" N ARG 7 400 " --> pdb=" O ASP 7 396 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLU 7 403 " --> pdb=" O GLU 7 399 " (cutoff:3.500A) Processing helix chain '7' and resid 410 through 417 removed outlier: 3.592A pdb=" N ALA 7 415 " --> pdb=" O TYR 7 411 " (cutoff:3.500A) Processing helix chain '7' and resid 426 through 437 Processing helix chain '7' and resid 470 through 476 removed outlier: 3.992A pdb=" N CYS 7 474 " --> pdb=" O LEU 7 470 " (cutoff:3.500A) Processing helix chain '7' and resid 512 through 515 No H-bonds generated for 'chain '7' and resid 512 through 515' Processing helix chain '7' and resid 526 through 528 No H-bonds generated for 'chain '7' and resid 526 through 528' Processing helix chain '7' and resid 531 through 541 Processing helix chain '7' and resid 588 through 593 Processing helix chain '7' and resid 606 through 621 removed outlier: 4.287A pdb=" N GLU 7 610 " --> pdb=" O ARG 7 606 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS 7 611 " --> pdb=" O ASP 7 607 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU 7 612 " --> pdb=" O ASP 7 608 " (cutoff:3.500A) Processing helix chain '7' and resid 635 through 645 Processing helix chain '7' and resid 655 through 671 removed outlier: 3.623A pdb=" N VAL 7 661 " --> pdb=" O ASN 7 657 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN 7 662 " --> pdb=" O ASP 7 658 " (cutoff:3.500A) Processing helix chain '7' and resid 686 through 701 Processing helix chain '7' and resid 710 through 723 removed outlier: 3.727A pdb=" N ALA 7 716 " --> pdb=" O ASP 7 712 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL 7 720 " --> pdb=" O ALA 7 716 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 20 removed outlier: 3.564A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 59 removed outlier: 4.675A pdb=" N GLN C 59 " --> pdb=" O LYS C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 103 removed outlier: 3.971A pdb=" N TYR C 72 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 77 " --> pdb=" O PHE C 73 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 97 " --> pdb=" O ARG C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 144 Processing helix chain 'C' and resid 193 through 202 removed outlier: 3.801A pdb=" N ARG C 198 " --> pdb=" O SER C 194 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLN C 202 " --> pdb=" O ARG C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.489A pdb=" N ASN D 22 " --> pdb=" O PHE D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 95 through 106 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.524A pdb=" N ASN D 128 " --> pdb=" O ARG D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 141 through 162 removed outlier: 4.498A pdb=" N TYR D 162 " --> pdb=" O LYS D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 199 Proline residue: D 183 - end of helix removed outlier: 3.948A pdb=" N ASP D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYS D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 12 Processing helix chain 'E' and resid 48 through 54 removed outlier: 3.922A pdb=" N ILE E 53 " --> pdb=" O TRP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 80 No H-bonds generated for 'chain 'E' and resid 78 through 80' Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 97 through 100 No H-bonds generated for 'chain 'E' and resid 97 through 100' Processing helix chain 'E' and resid 105 through 115 removed outlier: 4.104A pdb=" N LYS E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 139 removed outlier: 4.250A pdb=" N GLU E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 127 " --> pdb=" O VAL E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 167 No H-bonds generated for 'chain 'E' and resid 165 through 167' Processing helix chain 'E' and resid 171 through 191 Processing helix chain 'F' and resid 56 through 72 Processing helix chain 'F' and resid 81 through 108 removed outlier: 4.498A pdb=" N ARG F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU F 99 " --> pdb=" O GLN F 94 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN F 100 " --> pdb=" O SER F 95 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ILE F 101 " --> pdb=" O GLN F 96 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N SER F 102 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU F 106 " --> pdb=" O SER F 102 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP F 107 " --> pdb=" O MET F 103 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N MET F 108 " --> pdb=" O GLY F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 163 removed outlier: 5.740A pdb=" N LEU F 156 " --> pdb=" O ASP F 152 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR F 157 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 197 removed outlier: 3.564A pdb=" N SER F 197 " --> pdb=" O LEU F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 283 through 288 Processing helix chain 'G' and resid 8 through 17 Processing helix chain 'G' and resid 36 through 51 removed outlier: 3.785A pdb=" N ALA G 41 " --> pdb=" O ASP G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 71 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'G' and resid 131 through 134 No H-bonds generated for 'chain 'G' and resid 131 through 134' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 219 through 239 removed outlier: 3.818A pdb=" N GLU G 239 " --> pdb=" O GLY G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 261 Processing helix chain 'G' and resid 267 through 279 Processing helix chain 'G' and resid 287 through 301 removed outlier: 3.787A pdb=" N TYR G 292 " --> pdb=" O ASN G 289 " (cutoff:3.500A) Proline residue: G 293 - end of helix removed outlier: 3.633A pdb=" N ASP G 297 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 339 Processing helix chain 'G' and resid 342 through 348 removed outlier: 4.194A pdb=" N ALA G 346 " --> pdb=" O ASN G 342 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS G 347 " --> pdb=" O TYR G 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 366 removed outlier: 3.802A pdb=" N ARG G 358 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 374 Processing helix chain 'G' and resid 382 through 386 Processing helix chain 'G' and resid 388 through 399 removed outlier: 5.075A pdb=" N ASP G 397 " --> pdb=" O ASP G 393 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ARG G 398 " --> pdb=" O LYS G 394 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TYR G 399 " --> pdb=" O ASN G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 421 through 433 Processing helix chain 'G' and resid 463 through 484 removed outlier: 3.737A pdb=" N TRP G 478 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU G 479 " --> pdb=" O SER G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 516 removed outlier: 4.065A pdb=" N ARG G 494 " --> pdb=" O GLU G 490 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 495 " --> pdb=" O LEU G 491 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN G 500 " --> pdb=" O ILE G 496 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 540 Processing helix chain 'G' and resid 542 through 556 removed outlier: 3.574A pdb=" N CYS G 555 " --> pdb=" O TRP G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 613 Processing helix chain 'G' and resid 634 through 645 Proline residue: G 639 - end of helix Processing helix chain 'B' and resid 14 through 22 Proline residue: B 19 - end of helix Processing helix chain 'B' and resid 35 through 47 removed outlier: 4.348A pdb=" N THR B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 65 removed outlier: 3.724A pdb=" N GLU B 64 " --> pdb=" O LYS B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 89 removed outlier: 3.947A pdb=" N GLN B 89 " --> pdb=" O LYS B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 232 removed outlier: 4.280A pdb=" N PHE B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 219 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG B 221 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN B 232 " --> pdb=" O ARG B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 411 through 426 removed outlier: 3.830A pdb=" N ASP B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 470 Processing helix chain 'B' and resid 510 through 512 No H-bonds generated for 'chain 'B' and resid 510 through 512' Processing helix chain 'B' and resid 514 through 519 Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 599 through 609 Processing helix chain 'B' and resid 627 through 630 No H-bonds generated for 'chain 'B' and resid 627 through 630' Processing helix chain 'A' and resid 1363 through 1369 Proline residue: A1367 - end of helix No H-bonds generated for 'chain 'A' and resid 1363 through 1369' Processing helix chain 'A' and resid 1533 through 1545 removed outlier: 3.963A pdb=" N LYS A1538 " --> pdb=" O GLN A1534 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY A1541 " --> pdb=" O GLU A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1583 removed outlier: 3.929A pdb=" N LEU A1573 " --> pdb=" O LEU A1569 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A1580 " --> pdb=" O GLU A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1598 through 1602 removed outlier: 3.581A pdb=" N GLY A1602 " --> pdb=" O THR A1598 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1598 through 1602' Processing helix chain 'A' and resid 1627 through 1630 No H-bonds generated for 'chain 'A' and resid 1627 through 1630' Processing helix chain 'A' and resid 1632 through 1635 No H-bonds generated for 'chain 'A' and resid 1632 through 1635' Processing helix chain 'A' and resid 1637 through 1653 removed outlier: 4.499A pdb=" N GLY A1643 " --> pdb=" O VAL A1639 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A1644 " --> pdb=" O LEU A1640 " (cutoff:3.500A) Processing helix chain 'A' and resid 1669 through 1679 removed outlier: 4.138A pdb=" N LYS A1679 " --> pdb=" O LEU A1675 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1743 Processing helix chain 'A' and resid 1788 through 1799 Processing helix chain 'A' and resid 1808 through 1813 Processing helix chain 'A' and resid 1816 through 1819 No H-bonds generated for 'chain 'A' and resid 1816 through 1819' Processing helix chain 'A' and resid 1832 through 1851 Processing helix chain 'A' and resid 1877 through 1880 No H-bonds generated for 'chain 'A' and resid 1877 through 1880' Processing helix chain 'A' and resid 1882 through 1891 Processing helix chain 'A' and resid 1938 through 1942 Processing helix chain 'A' and resid 1949 through 1955 Processing helix chain 'A' and resid 1958 through 1972 removed outlier: 3.711A pdb=" N TYR A1971 " --> pdb=" O THR A1967 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU A1972 " --> pdb=" O LYS A1968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1998 through 2002 Processing helix chain 'A' and resid 2006 through 2020 Proline residue: A2011 - end of helix removed outlier: 4.406A pdb=" N PHE A2020 " --> pdb=" O VAL A2016 " (cutoff:3.500A) Processing helix chain 'A' and resid 2027 through 2033 removed outlier: 4.526A pdb=" N TYR A2032 " --> pdb=" O LEU A2028 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2059 Proline residue: A2050 - end of helix removed outlier: 3.903A pdb=" N CYS A2059 " --> pdb=" O VAL A2055 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2071 No H-bonds generated for 'chain 'A' and resid 2068 through 2071' Processing helix chain 'A' and resid 2141 through 2159 removed outlier: 3.601A pdb=" N ILE A2159 " --> pdb=" O GLU A2155 " (cutoff:3.500A) Processing helix chain 'A' and resid 2191 through 2208 Processing helix chain 'A' and resid 2211 through 2220 Processing sheet with id= A, first strand: chain '3' and resid 273 through 278 removed outlier: 3.902A pdb=" N ILE 3 274 " --> pdb=" O VAL 3 258 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN 3 254 " --> pdb=" O LEU 3 278 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR 3 257 " --> pdb=" O THR 3 187 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN 3 259 " --> pdb=" O ILE 3 185 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL 3 295 " --> pdb=" O THR 3 325 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '3' and resid 201 through 203 Processing sheet with id= C, first strand: chain '3' and resid 297 through 300 Processing sheet with id= D, first strand: chain '3' and resid 545 through 549 removed outlier: 3.924A pdb=" N PHE 3 547 " --> pdb=" O LEU 3 406 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 193 through 198 removed outlier: 3.686A pdb=" N ARG 3 193 " --> pdb=" O HIS 3 253 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR 3 249 " --> pdb=" O ILE 3 197 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '4' and resid 325 through 328 Processing sheet with id= G, first strand: chain '4' and resid 414 through 419 removed outlier: 3.714A pdb=" N LYS 4 398 " --> pdb=" O ARG 4 334 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG 4 334 " --> pdb=" O LYS 4 398 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N GLN 4 400 " --> pdb=" O VAL 4 332 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL 4 332 " --> pdb=" O GLN 4 400 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 439 through 442 Processing sheet with id= I, first strand: chain '4' and resid 704 through 708 removed outlier: 3.682A pdb=" N ILE 4 564 " --> pdb=" O ILE 4 671 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA 4 673 " --> pdb=" O ILE 4 564 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 4 675 " --> pdb=" O LEU 4 566 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY 4 568 " --> pdb=" O ALA 4 675 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '5' and resid 61 through 64 removed outlier: 4.006A pdb=" N ASN 5 140 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain '5' and resid 326 through 330 removed outlier: 6.595A pdb=" N LYS 5 257 " --> pdb=" O ILE 5 167 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 178 through 182 removed outlier: 3.569A pdb=" N THR 5 190 " --> pdb=" O ILE 5 181 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '5' and resid 436 through 439 removed outlier: 6.188A pdb=" N VAL 5 476 " --> pdb=" O VAL 5 437 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N THR 5 439 " --> pdb=" O VAL 5 476 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N CYS 5 478 " --> pdb=" O THR 5 439 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain '5' and resid 501 through 503 Processing sheet with id= O, first strand: chain '6' and resid 293 through 295 removed outlier: 3.612A pdb=" N THR 6 295 " --> pdb=" O ARG 6 360 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG 6 360 " --> pdb=" O THR 6 295 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN 6 357 " --> pdb=" O LEU 6 381 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU 6 381 " --> pdb=" O GLN 6 357 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain '6' and resid 572 through 574 removed outlier: 6.732A pdb=" N VAL 6 573 " --> pdb=" O ILE 6 678 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA 6 680 " --> pdb=" O VAL 6 573 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLY 6 634 " --> pdb=" O SER 6 677 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU 6 679 " --> pdb=" O GLY 6 634 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N CYS 6 636 " --> pdb=" O LEU 6 679 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ALA 6 681 " --> pdb=" O CYS 6 636 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE 6 638 " --> pdb=" O ALA 6 681 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL 6 596 " --> pdb=" O CYS 6 637 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP 6 639 " --> pdb=" O VAL 6 596 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR 6 598 " --> pdb=" O ASP 6 639 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain '2' and resid 317 through 323 removed outlier: 6.359A pdb=" N ILE 2 429 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ALA 2 453 " --> pdb=" O ILE 2 429 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS 2 431 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE 2 451 " --> pdb=" O LYS 2 431 " (cutoff:3.500A) removed outlier: 10.015A pdb=" N HIS 2 405 " --> pdb=" O THR 2 449 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N ILE 2 451 " --> pdb=" O HIS 2 405 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU 2 407 " --> pdb=" O ILE 2 451 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA 2 453 " --> pdb=" O GLU 2 407 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ILE 2 409 " --> pdb=" O ALA 2 453 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N SER 2 455 " --> pdb=" O ILE 2 409 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN 2 386 " --> pdb=" O LEU 2 410 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain '2' and resid 331 through 334 Processing sheet with id= S, first strand: chain '2' and resid 336 through 338 Processing sheet with id= T, first strand: chain '2' and resid 539 through 542 removed outlier: 6.248A pdb=" N ILE 2 679 " --> pdb=" O LEU 2 540 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N LEU 2 542 " --> pdb=" O ILE 2 679 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N CYS 2 681 " --> pdb=" O LEU 2 542 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain '7' and resid 238 through 243 removed outlier: 3.695A pdb=" N VAL 7 349 " --> pdb=" O GLY 7 243 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE 7 348 " --> pdb=" O HIS 7 384 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 7 380 " --> pdb=" O THR 7 352 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE 7 354 " --> pdb=" O ALA 7 378 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA 7 378 " --> pdb=" O ILE 7 354 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LEU 7 356 " --> pdb=" O LEU 7 376 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LEU 7 376 " --> pdb=" O LEU 7 356 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ALA 7 358 " --> pdb=" O THR 7 374 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N THR 7 374 " --> pdb=" O ALA 7 358 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain '7' and resid 244 through 246 Processing sheet with id= W, first strand: chain '7' and resid 268 through 272 removed outlier: 4.884A pdb=" N ALA 7 259 " --> pdb=" O SER 7 301 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER 7 301 " --> pdb=" O ALA 7 259 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE 7 299 " --> pdb=" O THR 7 261 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain '7' and resid 252 through 257 removed outlier: 3.604A pdb=" N PHE 7 310 " --> pdb=" O LYS 7 252 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LYS 7 306 " --> pdb=" O GLU 7 256 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'D' and resid 68 through 72 Processing sheet with id= Z, first strand: chain 'E' and resid 15 through 17 Processing sheet with id= AA, first strand: chain 'B' and resid 181 through 184 removed outlier: 4.105A pdb=" N SER B 182 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN B 189 " --> pdb=" O ASN B 184 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 282 through 287 Processing sheet with id= AC, first strand: chain 'B' and resid 296 through 300 removed outlier: 4.204A pdb=" N TRP B 296 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL B 305 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP B 300 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 303 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 431 through 433 removed outlier: 3.582A pdb=" N GLU B 674 " --> pdb=" O ILE B 683 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE B 683 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 676 " --> pdb=" O LYS B 681 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'B' and resid 530 through 534 removed outlier: 3.832A pdb=" N ILE B 539 " --> pdb=" O ILE B 532 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 534 " --> pdb=" O GLN B 537 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR B 638 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE B 542 " --> pdb=" O THR B 638 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N VAL B 640 " --> pdb=" O PHE B 542 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'B' and resid 649 through 653 removed outlier: 3.970A pdb=" N TYR B 653 " --> pdb=" O CYS B 656 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N CYS B 656 " --> pdb=" O TYR B 653 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'A' and resid 1501 through 1503 Processing sheet with id= AH, first strand: chain 'A' and resid 1321 through 1327 removed outlier: 6.801A pdb=" N PHE A1339 " --> pdb=" O GLU A1323 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A1325 " --> pdb=" O GLU A1337 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLU A1337 " --> pdb=" O LEU A1325 " (cutoff:3.500A) 1483 hydrogen bonds defined for protein. 4158 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: 15.95 Time building geometry restraints manager: 20.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.26: 7979 1.26 - 1.43: 12016 1.43 - 1.60: 28072 1.60 - 1.78: 92 1.78 - 1.95: 271 Bond restraints: 48430 Sorted by residual: bond pdb=" C GLU 5 269 " pdb=" N MET 5 270 " ideal model delta sigma weight residual 1.339 1.086 0.253 5.57e-02 3.22e+02 2.06e+01 bond pdb=" CB GLU 2 622 " pdb=" CG GLU 2 622 " ideal model delta sigma weight residual 1.520 1.390 0.130 3.00e-02 1.11e+03 1.87e+01 bond pdb=" O5' DT J 3 " pdb=" C5' DT J 3 " ideal model delta sigma weight residual 1.423 1.547 -0.124 3.00e-02 1.11e+03 1.70e+01 bond pdb=" CB VAL 2 397 " pdb=" CG2 VAL 2 397 " ideal model delta sigma weight residual 1.521 1.385 0.136 3.30e-02 9.18e+02 1.69e+01 bond pdb=" CA TYR 4 531 " pdb=" CB TYR 4 531 " ideal model delta sigma weight residual 1.530 1.597 -0.067 1.69e-02 3.50e+03 1.58e+01 ... (remaining 48425 not shown) Histogram of bond angle deviations from ideal: 95.20 - 105.81: 1752 105.81 - 116.42: 31662 116.42 - 127.04: 31546 127.04 - 137.65: 734 137.65 - 148.27: 3 Bond angle restraints: 65697 Sorted by residual: angle pdb=" C VAL F 216 " pdb=" N ASN F 217 " pdb=" CA ASN F 217 " ideal model delta sigma weight residual 122.84 143.44 -20.60 1.81e+00 3.05e-01 1.30e+02 angle pdb=" C ILE G 98 " pdb=" N ASP G 99 " pdb=" CA ASP G 99 " ideal model delta sigma weight residual 121.80 148.27 -26.47 2.44e+00 1.68e-01 1.18e+02 angle pdb=" C LYS F 200 " pdb=" N TYR F 201 " pdb=" CA TYR F 201 " ideal model delta sigma weight residual 121.70 138.87 -17.17 1.80e+00 3.09e-01 9.10e+01 angle pdb=" C SER 5 444 " pdb=" CA SER 5 444 " pdb=" CB SER 5 444 " ideal model delta sigma weight residual 110.45 95.44 15.01 1.73e+00 3.34e-01 7.53e+01 angle pdb=" C ILE C 149 " pdb=" N ASP C 150 " pdb=" CA ASP C 150 " ideal model delta sigma weight residual 121.70 137.10 -15.40 1.80e+00 3.09e-01 7.32e+01 ... (remaining 65692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 28996 35.56 - 71.12: 389 71.12 - 106.68: 29 106.68 - 142.24: 4 142.24 - 177.80: 1 Dihedral angle restraints: 29419 sinusoidal: 11785 harmonic: 17634 Sorted by residual: dihedral pdb=" CA THR F 212 " pdb=" C THR F 212 " pdb=" N GLU F 213 " pdb=" CA GLU F 213 " ideal model delta harmonic sigma weight residual 180.00 53.84 126.16 0 5.00e+00 4.00e-02 6.37e+02 dihedral pdb=" CA VAL F 216 " pdb=" C VAL F 216 " pdb=" N ASN F 217 " pdb=" CA ASN F 217 " ideal model delta harmonic sigma weight residual 180.00 56.50 123.50 0 5.00e+00 4.00e-02 6.10e+02 dihedral pdb=" CA ILE G 98 " pdb=" C ILE G 98 " pdb=" N ASP G 99 " pdb=" CA ASP G 99 " ideal model delta harmonic sigma weight residual 180.00 68.58 111.42 0 5.00e+00 4.00e-02 4.97e+02 ... (remaining 29416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 6664 0.129 - 0.257: 933 0.257 - 0.386: 77 0.386 - 0.514: 5 0.514 - 0.643: 1 Chirality restraints: 7680 Sorted by residual: chirality pdb=" CA ARG B 669 " pdb=" N ARG B 669 " pdb=" C ARG B 669 " pdb=" CB ARG B 669 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.03e+01 chirality pdb=" CA ARG A1664 " pdb=" N ARG A1664 " pdb=" C ARG A1664 " pdb=" CB ARG A1664 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.08e+00 chirality pdb=" CA PHE G 605 " pdb=" N PHE G 605 " pdb=" C PHE G 605 " pdb=" CB PHE G 605 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 7677 not shown) Planarity restraints: 8241 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 523 " -0.219 9.50e-02 1.11e+02 1.24e-01 7.69e+01 pdb=" NE ARG G 523 " 0.063 2.00e-02 2.50e+03 pdb=" CZ ARG G 523 " -0.143 2.00e-02 2.50e+03 pdb=" NH1 ARG G 523 " 0.051 2.00e-02 2.50e+03 pdb=" NH2 ARG G 523 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 212 " -0.035 2.00e-02 2.50e+03 6.89e-02 4.75e+01 pdb=" C THR F 212 " 0.119 2.00e-02 2.50e+03 pdb=" O THR F 212 " -0.044 2.00e-02 2.50e+03 pdb=" N GLU F 213 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 98 " -0.031 2.00e-02 2.50e+03 6.32e-02 3.99e+01 pdb=" C ILE G 98 " 0.109 2.00e-02 2.50e+03 pdb=" O ILE G 98 " -0.041 2.00e-02 2.50e+03 pdb=" N ASP G 99 " -0.038 2.00e-02 2.50e+03 ... (remaining 8238 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 2 2.14 - 2.83: 14278 2.83 - 3.52: 67104 3.52 - 4.21: 105088 4.21 - 4.90: 168223 Nonbonded interactions: 354695 Sorted by model distance: nonbonded pdb=" N CYS A2167 " pdb="ZN ZN A2302 " model vdw 1.447 2.310 nonbonded pdb=" O HIS 3 564 " pdb=" OG1 THR 3 568 " model vdw 2.137 2.440 nonbonded pdb=" O LEU 6 830 " pdb=" OG SER 6 834 " model vdw 2.161 2.440 nonbonded pdb=" O ARG 2 326 " pdb=" OG1 THR 2 389 " model vdw 2.197 2.440 nonbonded pdb=" O LEU A1739 " pdb=" OG1 THR A1743 " model vdw 2.205 2.440 ... (remaining 354690 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.970 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: 0.030 Extract box with map and model: 8.620 Check model and map are aligned: 0.800 Set scattering table: 0.490 Process input model: 121.030 Find NCS groups from input model: 2.520 Set up NCS constraints: 0.170 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 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 : 0.012 0.253 48430 Z= 0.757 Angle : 1.864 26.467 65697 Z= 1.021 Chirality : 0.088 0.643 7680 Planarity : 0.008 0.124 8241 Dihedral : 12.250 177.800 17901 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.90 % Favored : 88.79 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.02 (0.09), residues: 5814 helix: -2.63 (0.08), residues: 2286 sheet: -2.29 (0.19), residues: 610 loop : -2.78 (0.10), residues: 2918 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 979 time to evaluate : 5.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 3 residues processed: 997 average time/residue: 0.6299 time to fit residues: 1027.9895 Evaluate side-chains 460 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 457 time to evaluate : 5.794 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5678 time to fit residues: 10.7157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 507 optimal weight: 6.9990 chunk 455 optimal weight: 5.9990 chunk 252 optimal weight: 10.0000 chunk 155 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 243 optimal weight: 8.9990 chunk 471 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 286 optimal weight: 3.9990 chunk 350 optimal weight: 4.9990 chunk 545 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 46 GLN 3 57 ASN ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 417 GLN 3 493 GLN 3 532 ASN ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 582 HIS 4 651 GLN 4 757 HIS 5 33 ASN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN ** 5 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 574 ASN 5 585 ASN 5 625 ASN ** 6 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 524 HIS 6 653 HIS 6 698 ASN 6 730 HIS 6 750 GLN ** 2 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 290 HIS 2 561 HIS ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 90 ASN 7 107 GLN 7 112 HIS 7 326 HIS 7 455 ASN 7 554 ASN 7 568 ASN 7 620 HIS C 33 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 GLN C 202 GLN ** D 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 GLN D 167 HIS D 172 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS F 160 GLN F 186 HIS G 101 GLN G 138 GLN G 286 GLN ** G 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 575 ASN G 624 ASN B 189 GLN B 397 HIS B 461 ASN B 505 GLN ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 HIS A1369 GLN A1373 ASN A1413 ASN A1703 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1742 ASN A1835 HIS ** A1838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1849 ASN A1938 GLN ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2178 HIS ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.097 48430 Z= 0.314 Angle : 0.869 12.834 65697 Z= 0.457 Chirality : 0.047 0.203 7680 Planarity : 0.006 0.112 8241 Dihedral : 11.490 163.066 6925 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.69 % Favored : 91.18 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.01 (0.10), residues: 5814 helix: -1.19 (0.10), residues: 2284 sheet: -1.95 (0.19), residues: 652 loop : -2.71 (0.11), residues: 2878 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 598 time to evaluate : 5.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 13 outliers final: 3 residues processed: 610 average time/residue: 0.5741 time to fit residues: 585.0857 Evaluate side-chains 406 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 403 time to evaluate : 5.352 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4105 time to fit residues: 9.6461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 303 optimal weight: 40.0000 chunk 169 optimal weight: 0.9990 chunk 454 optimal weight: 3.9990 chunk 371 optimal weight: 9.9990 chunk 150 optimal weight: 0.0020 chunk 546 optimal weight: 6.9990 chunk 590 optimal weight: 9.9990 chunk 486 optimal weight: 0.0000 chunk 542 optimal weight: 0.1980 chunk 186 optimal weight: 9.9990 chunk 438 optimal weight: 20.0000 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 560 HIS 5 571 HIS 5 576 HIS ** 5 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 366 ASN 6 750 GLN 2 238 ASN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS C 25 GLN D 22 ASN D 167 HIS D 169 GLN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 388 HIS B 609 GLN A1369 GLN A1422 ASN A1654 GLN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1837 HIS ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 48430 Z= 0.177 Angle : 0.713 12.198 65697 Z= 0.367 Chirality : 0.044 0.230 7680 Planarity : 0.005 0.079 8241 Dihedral : 10.923 161.820 6925 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.60 % Favored : 92.29 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.10), residues: 5814 helix: -0.47 (0.10), residues: 2294 sheet: -1.77 (0.20), residues: 658 loop : -2.53 (0.11), residues: 2862 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 589 time to evaluate : 6.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 591 average time/residue: 0.5584 time to fit residues: 557.4923 Evaluate side-chains 422 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 5.788 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4318 time to fit residues: 9.2735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 540 optimal weight: 40.0000 chunk 411 optimal weight: 6.9990 chunk 283 optimal weight: 0.6980 chunk 60 optimal weight: 50.0000 chunk 260 optimal weight: 9.9990 chunk 367 optimal weight: 0.9990 chunk 548 optimal weight: 1.9990 chunk 580 optimal weight: 9.9990 chunk 286 optimal weight: 20.0000 chunk 520 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 354 HIS ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 625 ASN 5 685 GLN 6 182 GLN 6 653 HIS 6 658 GLN 6 750 GLN 2 238 ASN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS C 90 GLN D 167 HIS ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN F 100 ASN F 183 HIS G 70 HIS ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN A1422 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 48430 Z= 0.200 Angle : 0.694 11.900 65697 Z= 0.359 Chirality : 0.044 0.237 7680 Planarity : 0.004 0.062 8241 Dihedral : 10.621 163.116 6925 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.38 % Favored : 91.54 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.81 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.11), residues: 5814 helix: -0.21 (0.10), residues: 2306 sheet: -1.78 (0.19), residues: 668 loop : -2.40 (0.11), residues: 2840 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 555 time to evaluate : 5.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 2 outliers final: 1 residues processed: 557 average time/residue: 0.5630 time to fit residues: 534.8603 Evaluate side-chains 406 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 6.196 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4285 time to fit residues: 9.2324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 483 optimal weight: 0.4980 chunk 329 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 chunk 432 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 495 optimal weight: 3.9990 chunk 401 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 296 optimal weight: 9.9990 chunk 521 optimal weight: 0.9990 chunk 146 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 175 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 424 ASN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 5 576 HIS 5 625 ASN 6 182 GLN 6 750 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 48430 Z= 0.191 Angle : 0.668 11.560 65697 Z= 0.347 Chirality : 0.043 0.205 7680 Planarity : 0.004 0.140 8241 Dihedral : 10.431 162.068 6925 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.17 % Favored : 91.74 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.93 (0.11), residues: 5814 helix: -0.00 (0.11), residues: 2311 sheet: -1.61 (0.20), residues: 653 loop : -2.33 (0.11), residues: 2850 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 540 time to evaluate : 5.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 541 average time/residue: 0.5741 time to fit residues: 529.6826 Evaluate side-chains 406 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 5.896 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5268 time to fit residues: 8.7203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 195 optimal weight: 0.1980 chunk 523 optimal weight: 20.0000 chunk 114 optimal weight: 0.3980 chunk 341 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 581 optimal weight: 50.0000 chunk 482 optimal weight: 0.0670 chunk 269 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 305 optimal weight: 2.9990 overall best weight: 1.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 411 ASN 5 576 HIS 5 625 ASN 6 182 GLN 6 653 HIS 6 750 GLN ** 7 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 326 HIS C 39 ASN ** E 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN B 609 GLN ** A1657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1865 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 48430 Z= 0.165 Angle : 0.652 11.027 65697 Z= 0.335 Chirality : 0.043 0.206 7680 Planarity : 0.004 0.062 8241 Dihedral : 10.284 162.225 6925 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.88 % Favored : 92.05 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.11), residues: 5814 helix: 0.15 (0.11), residues: 2312 sheet: -1.46 (0.20), residues: 662 loop : -2.27 (0.11), residues: 2840 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 529 time to evaluate : 5.703 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 TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 530 average time/residue: 0.5624 time to fit residues: 511.2519 Evaluate side-chains 393 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 5.260 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.6828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 560 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 331 optimal weight: 6.9990 chunk 424 optimal weight: 0.2980 chunk 329 optimal weight: 9.9990 chunk 489 optimal weight: 0.5980 chunk 324 optimal weight: 0.0000 chunk 579 optimal weight: 5.9990 chunk 362 optimal weight: 20.0000 chunk 353 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 450 GLN ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 576 HIS 5 625 ASN 6 182 GLN 6 750 GLN ** 2 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 89 GLN 7 326 HIS E 133 GLN ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 231 HIS ** B 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1657 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2143 GLN A2145 HIS ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 48430 Z= 0.154 Angle : 0.650 11.409 65697 Z= 0.330 Chirality : 0.043 0.189 7680 Planarity : 0.004 0.061 8241 Dihedral : 10.147 162.678 6925 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.07 % Favored : 92.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.57 (0.11), residues: 5814 helix: 0.33 (0.11), residues: 2310 sheet: -1.37 (0.20), residues: 646 loop : -2.17 (0.11), residues: 2858 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 5.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.5648 time to fit residues: 522.1979 Evaluate side-chains 406 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 406 time to evaluate : 6.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.4490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 358 optimal weight: 7.9990 chunk 231 optimal weight: 1.9990 chunk 345 optimal weight: 20.0000 chunk 174 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 368 optimal weight: 9.9990 chunk 394 optimal weight: 5.9990 chunk 286 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 455 optimal weight: 10.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 185 ASN 5 424 GLN 5 576 HIS 5 625 ASN 6 182 GLN 6 750 GLN 2 531 HIS 7 89 GLN 7 326 HIS F 225 ASN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1838 ASN ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.4486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 48430 Z= 0.197 Angle : 0.675 9.571 65697 Z= 0.347 Chirality : 0.043 0.236 7680 Planarity : 0.004 0.101 8241 Dihedral : 10.160 162.072 6925 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.10 % Favored : 91.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.11), residues: 5814 helix: 0.36 (0.11), residues: 2306 sheet: -1.40 (0.19), residues: 690 loop : -2.18 (0.11), residues: 2818 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 5.698 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 TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 506 average time/residue: 0.5860 time to fit residues: 514.4841 Evaluate side-chains 385 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 5.539 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 526 optimal weight: 8.9990 chunk 554 optimal weight: 7.9990 chunk 506 optimal weight: 20.0000 chunk 539 optimal weight: 0.9980 chunk 324 optimal weight: 50.0000 chunk 235 optimal weight: 10.0000 chunk 423 optimal weight: 6.9990 chunk 165 optimal weight: 10.0000 chunk 487 optimal weight: 0.9990 chunk 510 optimal weight: 0.0870 chunk 537 optimal weight: 1.9990 overall best weight: 2.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 231 ASN ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 424 GLN 5 576 HIS 5 625 ASN 6 182 GLN 6 750 GLN 7 90 ASN 7 326 HIS ** E 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 48430 Z= 0.172 Angle : 0.665 10.878 65697 Z= 0.339 Chirality : 0.043 0.191 7680 Planarity : 0.004 0.065 8241 Dihedral : 10.121 159.922 6925 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.46 % Favored : 92.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.11), residues: 5814 helix: 0.38 (0.11), residues: 2311 sheet: -1.38 (0.19), residues: 689 loop : -2.17 (0.11), residues: 2814 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 505 time to evaluate : 5.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. 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: 0 outliers final: 0 residues processed: 505 average time/residue: 0.5532 time to fit residues: 485.2209 Evaluate side-chains 379 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 5.786 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 354 optimal weight: 8.9990 chunk 570 optimal weight: 20.0000 chunk 348 optimal weight: 0.9980 chunk 270 optimal weight: 7.9990 chunk 396 optimal weight: 7.9990 chunk 598 optimal weight: 5.9990 chunk 551 optimal weight: 0.4980 chunk 476 optimal weight: 30.0000 chunk 49 optimal weight: 5.9990 chunk 368 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 57 ASN 3 175 HIS ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 259 HIS 4 582 HIS ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 625 ASN 6 182 GLN 6 750 GLN 2 627 GLN 7 326 HIS G 231 HIS ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1838 ASN ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.079 48430 Z= 0.255 Angle : 0.731 10.706 65697 Z= 0.378 Chirality : 0.045 0.217 7680 Planarity : 0.005 0.081 8241 Dihedral : 10.288 158.626 6925 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.15 % Favored : 90.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.74 (0.11), residues: 5814 helix: 0.17 (0.11), residues: 2320 sheet: -1.55 (0.19), residues: 722 loop : -2.24 (0.11), residues: 2772 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11628 Ramachandran restraints generated. 5814 Oldfield, 0 Emsley, 5814 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 476 time to evaluate : 5.865 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 TARDY: cannot create tardy model for: "MET 6 656 " (corrupted residue). Skipping it. 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: 0 outliers final: 0 residues processed: 476 average time/residue: 0.5847 time to fit residues: 481.9330 Evaluate side-chains 371 residues out of total 5444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 371 time to evaluate : 5.913 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.7767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 601 random chunks: chunk 378 optimal weight: 3.9990 chunk 507 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 439 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 132 optimal weight: 0.9990 chunk 477 optimal weight: 60.0000 chunk 199 optimal weight: 2.9990 chunk 490 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 87 optimal weight: 30.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 284 ASN 5 625 ASN 6 735 HIS 6 750 GLN 2 626 GLN 7 326 HIS ** B 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 648 GLN ** A1723 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.088508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.071159 restraints weight = 320281.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.071397 restraints weight = 253946.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.071786 restraints weight = 198285.057| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6826 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 48430 Z= 0.204 Angle : 0.684 16.474 65697 Z= 0.350 Chirality : 0.044 0.188 7680 Planarity : 0.004 0.069 8241 Dihedral : 10.257 159.196 6925 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.17 % Favored : 91.78 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.43 % Cis-general : 0.83 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.67 (0.11), residues: 5814 helix: 0.25 (0.11), residues: 2323 sheet: -1.54 (0.19), residues: 719 loop : -2.22 (0.11), residues: 2772 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9974.17 seconds wall clock time: 182 minutes 26.73 seconds (10946.73 seconds total)