Starting phenix.real_space_refine on Wed Feb 14 04:23:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvv_41652/02_2024/8tvv_41652.pdb" } resolution = 3.7 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= -0.001 sd= 0.113 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: 8 Type Number sf(0) Gaussians Zn 8 6.06 5 P 56 5.49 5 Mg 1 5.21 5 S 168 5.16 5 C 18776 2.51 5 N 5295 2.21 5 O 5799 1.98 5 H 28238 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 779": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 847": "OD1" <-> "OD2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A TYR 1154": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1220": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1315": "OE1" <-> "OE2" Residue "A GLU 1337": "OE1" <-> "OE2" Residue "A PHE 1441": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 370": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 1198": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "F ASP 77": "OD1" <-> "OD2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H GLU 45": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Residue "H TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 58341 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 21323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 21323 Classifications: {'peptide': 1366} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1303} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 15603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1041, 15603 Classifications: {'peptide': 1041} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 80} Link IDs: {'PTRANS': 45, 'TRANS': 995} Chain breaks: 10 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 295 Unresolved non-hydrogen angles: 373 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 4, 'TYR:plan': 7, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 8, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 153 Chain: "C" Number of atoms: 4148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 4148 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain: "D" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1581 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 244 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 5, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 103 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3548 Classifications: {'peptide': 215} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 1330 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 75} Chain: "G" Number of atoms: 1762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1762 Classifications: {'peptide': 171} Modifications used: {'COO': 1, 'NH3': 1} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 256 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 121 Chain: "H" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 2090 Classifications: {'peptide': 133} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 2 Chain: "I" Number of atoms: 1666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1666 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 111} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "J" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 1074 Classifications: {'peptide': 65} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1673 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "L" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 752 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "N" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 517 Classifications: {'DNA': 16} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 15} Chain: "T" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 871 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "R" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 394 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" 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} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2440 SG CYS A 167 67.223 89.606 40.914 1.00181.69 S ATOM 935 SG CYS A 70 78.049 44.657 56.257 1.00125.69 S ATOM 1031 SG CYS A 77 77.633 44.781 60.338 1.00120.02 S ATOM 35933 SG CYS B1163 86.446 56.161 51.014 1.00111.14 S ATOM 35969 SG CYS B1166 83.520 58.218 52.255 1.00116.12 S ATOM 36219 SG CYS B1182 83.045 54.625 50.924 1.00117.18 S ATOM 36258 SG CYS B1185 83.698 57.618 48.643 1.00121.28 S ATOM 38234 SG CYS C 86 84.155 12.375 118.360 1.00139.05 S ATOM 38264 SG CYS C 88 81.494 12.586 116.440 1.00147.38 S ATOM 38319 SG CYS C 92 81.152 10.556 119.343 1.00136.76 S ATOM 38363 SG CYS C 95 81.914 14.919 119.412 1.00131.80 S ATOM 51410 SG CYS I 7 32.531 122.159 90.423 1.00229.26 S ATOM 51457 SG CYS I 10 30.858 119.192 88.678 1.00227.52 S ATOM 52513 SG CYS I 78 49.381 115.020 132.562 1.00207.31 S ATOM 52937 SG CYS I 103 51.110 111.537 131.356 1.00204.95 S ATOM 53165 SG CYS J 7 76.530 43.388 131.954 1.00 97.39 S ATOM 53206 SG CYS J 10 79.899 42.997 134.222 1.00100.68 S ATOM 53762 SG CYS J 45 78.530 46.052 133.791 1.00 96.34 S ATOM 53772 SG CYS J 46 76.562 43.312 135.779 1.00100.18 S ATOM 55908 SG CYS L 31 40.654 27.811 108.231 1.00168.80 S ATOM 56203 SG CYS L 51 38.360 30.936 108.993 1.00157.86 S Time building chain proxies: 21.00, per 1000 atoms: 0.36 Number of scatterers: 58341 At special positions: 0 Unit cell: (156.6, 150.8, 165.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 8 29.99 S 168 16.00 P 56 15.00 Mg 1 11.99 O 5799 8.00 N 5295 7.00 C 18776 6.00 H 28238 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 41.77 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 92 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " Number of angles added : 18 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7038 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 41 sheets defined 41.0% alpha, 18.4% beta 22 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 20.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 95 through 104 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.538A pdb=" N ARG A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 143 removed outlier: 3.590A pdb=" N ALA A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 223 Processing helix chain 'A' and resid 230 through 233 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 285 through 305 Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 416 through 423 removed outlier: 6.406A pdb=" N LYS A 419 " --> pdb=" O ARG A 416 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG A 420 " --> pdb=" O TYR A 417 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 421 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.554A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.815A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 582 removed outlier: 3.854A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.536A pdb=" N VAL A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG A 635 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 659 removed outlier: 3.986A pdb=" N LYS A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 669 Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 736 removed outlier: 3.533A pdb=" N GLU A 715 " --> pdb=" O ARG A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 794 through 797 Processing helix chain 'A' and resid 809 through 845 removed outlier: 4.546A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 843 " --> pdb=" O ARG A 839 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 876 No H-bonds generated for 'chain 'A' and resid 874 through 876' Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 922 through 947 removed outlier: 3.561A pdb=" N GLU A 945 " --> pdb=" O LYS A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.036A pdb=" N PHE A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 997 removed outlier: 3.567A pdb=" N ASN A 996 " --> pdb=" O ASP A 992 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1004 through 1015 removed outlier: 3.834A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.554A pdb=" N GLU A1050 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1077 Proline residue: A1075 - end of helix Processing helix chain 'A' and resid 1098 through 1106 Processing helix chain 'A' and resid 1121 through 1125 Processing helix chain 'A' and resid 1127 through 1137 Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1258 through 1271 removed outlier: 3.626A pdb=" N MET A1267 " --> pdb=" O ILE A1263 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A1268 " --> pdb=" O GLU A1264 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.544A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1323 through 1327 Processing helix chain 'A' and resid 1331 through 1340 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.201A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.876A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1395 through 1400 Processing helix chain 'A' and resid 1405 through 1416 Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1436 through 1439 Processing helix chain 'A' and resid 1446 through 1453 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 29 through 42 removed outlier: 3.884A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.889A pdb=" N SER B 50 " --> pdb=" O GLN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 65 Processing helix chain 'B' and resid 113 through 120 Processing helix chain 'B' and resid 179 through 183 removed outlier: 3.955A pdb=" N GLU B 183 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 282 through 289 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 307 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 369 through 391 removed outlier: 3.834A pdb=" N ALA B 375 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG B 384 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU B 385 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 435 removed outlier: 3.621A pdb=" N GLN B 415 " --> pdb=" O PRO B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 464 removed outlier: 3.587A pdb=" N ILE B 448 " --> pdb=" O MET B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 561 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 574 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 671 Processing helix chain 'B' and resid 680 through 688 Processing helix chain 'B' and resid 695 through 699 removed outlier: 3.599A pdb=" N GLU B 699 " --> pdb=" O ALA B 695 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 695 through 699' Processing helix chain 'B' and resid 706 through 710 Processing helix chain 'B' and resid 711 through 716 Processing helix chain 'B' and resid 744 through 749 Processing helix chain 'B' and resid 750 through 756 removed outlier: 3.867A pdb=" N ILE B 755 " --> pdb=" O VAL B 751 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 775 removed outlier: 3.645A pdb=" N ASN B 767 " --> pdb=" O GLN B 763 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 812 Processing helix chain 'B' and resid 843 through 848 Processing helix chain 'B' and resid 1014 through 1017 Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 3.831A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1062 removed outlier: 3.539A pdb=" N HIS B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1102 Processing helix chain 'B' and resid 1121 through 1125 removed outlier: 3.546A pdb=" N ASP B1125 " --> pdb=" O ARG B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1131 through 1142 removed outlier: 3.713A pdb=" N CYS B1137 " --> pdb=" O MET B1133 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET B1138 " --> pdb=" O GLU B1134 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1153 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 removed outlier: 3.578A pdb=" N ALA C 30 " --> pdb=" O ASP C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.718A pdb=" N LEU C 69 " --> pdb=" O HIS C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 116 through 118 No H-bonds generated for 'chain 'C' and resid 116 through 118' Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 239 through 266 Processing helix chain 'D' and resid 51 through 73 Processing helix chain 'D' and resid 118 through 134 Processing helix chain 'D' and resid 138 through 151 removed outlier: 3.902A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 169 removed outlier: 3.696A pdb=" N ALA D 162 " --> pdb=" O GLU D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 183 removed outlier: 3.738A pdb=" N GLN D 179 " --> pdb=" O PHE D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 195 through 200 removed outlier: 3.867A pdb=" N ASN D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 221 removed outlier: 3.741A pdb=" N TYR D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 55 through 59 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 124 Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.735A pdb=" N VAL E 142 " --> pdb=" O ALA E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 168 Processing helix chain 'E' and resid 171 through 175 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 127 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 removed outlier: 3.818A pdb=" N LYS G 27 " --> pdb=" O LYS G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'I' and resid 59 through 65 removed outlier: 4.367A pdb=" N GLY I 63 " --> pdb=" O GLN I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 122 Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 4.081A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 39 through 52 removed outlier: 3.537A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 117 removed outlier: 3.636A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1418 through 1419 Processing sheet with id=AA2, first strand: chain 'A' and resid 82 through 91 removed outlier: 11.022A pdb=" N LEU A 86 " --> pdb=" O PRO A 240 " (cutoff:3.500A) removed outlier: 10.533A pdb=" N LYS A 88 " --> pdb=" O CYS A 238 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N CYS A 238 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA4, first strand: chain 'A' and resid 172 through 177 Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.522A pdb=" N LYS A 343 " --> pdb=" O PHE B1130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 1104 through 1106 removed outlier: 3.687A pdb=" N THR A 351 " --> pdb=" O MET A 487 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 8.366A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.601A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 540 through 542 Processing sheet with id=AA9, first strand: chain 'A' and resid 589 through 590 removed outlier: 6.904A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 766 through 767 Processing sheet with id=AB2, first strand: chain 'A' and resid 849 through 850 Processing sheet with id=AB3, first strand: chain 'A' and resid 878 through 882 Processing sheet with id=AB4, first strand: chain 'A' and resid 1282 through 1292 removed outlier: 4.035A pdb=" N THR A1308 " --> pdb=" O LEU A1116 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.617A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1236 through 1240 removed outlier: 4.677A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS A1240 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR I 44 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.276A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 143 through 147 removed outlier: 5.276A pdb=" N VAL A1443 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY G 59 " --> pdb=" O ILE A1445 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG G 75 " --> pdb=" O LEU G 49 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER G 37 " --> pdb=" O ILE G 45 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 68 through 71 removed outlier: 4.769A pdb=" N ASP B 131 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE B 95 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE B 129 " --> pdb=" O ILE B 95 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL B 97 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY B 127 " --> pdb=" O VAL B 97 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC2, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.561A pdb=" N ASP B 407 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 222 through 227 removed outlier: 3.715A pdb=" N PHE B 226 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 237 " --> pdb=" O PHE B 226 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N LEU B 273 " --> pdb=" O GLN B 278 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN B 278 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 544 through 547 removed outlier: 4.030A pdb=" N ARG B 632 " --> pdb=" O SER B 546 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 650 through 651 Processing sheet with id=AC6, first strand: chain 'B' and resid 564 through 565 removed outlier: 5.489A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ARG B 579 " --> pdb=" O LEU B 624 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ILE B 626 " --> pdb=" O ARG B 579 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE B 581 " --> pdb=" O ILE B 626 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 614 " --> pdb=" O PHE B 627 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.600A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL B 952 " --> pdb=" O LYS L 58 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU L 57 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 804 through 805 removed outlier: 6.000A pdb=" N GLY B1042 " --> pdb=" O THR B 805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.764A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD2, first strand: chain 'B' and resid 1159 through 1163 Processing sheet with id=AD3, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD4, first strand: chain 'C' and resid 7 through 13 removed outlier: 6.755A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 119 through 120 removed outlier: 6.802A pdb=" N GLU C 152 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR C 53 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N LYS C 154 " --> pdb=" O VAL C 51 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N VAL C 51 " --> pdb=" O LYS C 154 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N THR C 156 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL C 49 " --> pdb=" O THR C 156 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL C 158 " --> pdb=" O ASP C 47 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C 45 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.945A pdb=" N HIS C 131 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 111 through 114 removed outlier: 3.824A pdb=" N CYS C 145 " --> pdb=" O VAL C 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 60 through 61 removed outlier: 5.832A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLY E 108 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE E 135 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE E 110 " --> pdb=" O PHE E 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 152 through 156 removed outlier: 4.459A pdb=" N VAL E 195 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'G' and resid 87 through 95 removed outlier: 3.833A pdb=" N THR G 90 " --> pdb=" O GLN G 102 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N THR G 111 " --> pdb=" O GLY G 161 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 6 through 16 removed outlier: 6.603A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS H 37 " --> pdb=" O GLU H 126 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU H 105 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N PHE H 6 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 15 through 19 Processing sheet with id=AE4, first strand: chain 'I' and resid 70 through 71 removed outlier: 3.644A pdb=" N SER I 71 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN I 83 " --> pdb=" O SER I 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 23 1322 hydrogen bonds defined for protein. 3627 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 55 hydrogen bonds 110 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 22.59 Time building geometry restraints manager: 43.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 28189 1.03 - 1.23: 959 1.23 - 1.43: 11869 1.43 - 1.63: 17668 1.63 - 1.83: 280 Bond restraints: 58965 Sorted by residual: bond pdb=" C1' DG T 7 " pdb=" N9 DG T 7 " ideal model delta sigma weight residual 1.460 1.393 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C1' DA N 42 " pdb=" N9 DA N 42 " ideal model delta sigma weight residual 1.460 1.396 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C1' DG N 47 " pdb=" N9 DG N 47 " ideal model delta sigma weight residual 1.460 1.400 0.060 2.00e-02 2.50e+03 8.86e+00 bond pdb=" O3' DC T 14 " pdb=" P DT T 15 " ideal model delta sigma weight residual 1.607 1.649 -0.042 1.50e-02 4.44e+03 7.95e+00 bond pdb=" C1' DG T 2 " pdb=" N9 DG T 2 " ideal model delta sigma weight residual 1.460 1.409 0.051 2.00e-02 2.50e+03 6.41e+00 ... (remaining 58960 not shown) Histogram of bond angle deviations from ideal: 98.09 - 105.27: 866 105.27 - 112.45: 67498 112.45 - 119.63: 15164 119.63 - 126.81: 22175 126.81 - 133.99: 457 Bond angle restraints: 106160 Sorted by residual: angle pdb=" N PRO G 116 " pdb=" CA PRO G 116 " pdb=" CB PRO G 116 " ideal model delta sigma weight residual 103.25 111.09 -7.84 8.80e-01 1.29e+00 7.93e+01 angle pdb=" N PRO B 877 " pdb=" CA PRO B 877 " pdb=" CB PRO B 877 " ideal model delta sigma weight residual 103.35 111.10 -7.75 8.70e-01 1.32e+00 7.93e+01 angle pdb=" N PRO B 171 " pdb=" CA PRO B 171 " pdb=" CB PRO B 171 " ideal model delta sigma weight residual 103.27 111.09 -7.82 9.00e-01 1.23e+00 7.55e+01 angle pdb=" N PRO G 105 " pdb=" CA PRO G 105 " pdb=" CB PRO G 105 " ideal model delta sigma weight residual 102.17 111.10 -8.93 1.05e+00 9.07e-01 7.24e+01 angle pdb=" N PRO G 127 " pdb=" CA PRO G 127 " pdb=" CB PRO G 127 " ideal model delta sigma weight residual 102.60 111.09 -8.49 1.10e+00 8.26e-01 5.95e+01 ... (remaining 106155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 26820 35.98 - 71.96: 689 71.96 - 107.95: 18 107.95 - 143.93: 0 143.93 - 179.91: 5 Dihedral angle restraints: 27532 sinusoidal: 15161 harmonic: 12371 Sorted by residual: dihedral pdb=" O4' A R 10 " pdb=" C2' A R 10 " pdb=" C1' A R 10 " pdb=" C3' A R 10 " ideal model delta sinusoidal sigma weight residual 25.00 -18.20 43.20 1 8.00e+00 1.56e-02 4.07e+01 dihedral pdb=" O4' C R 13 " pdb=" C1' C R 13 " pdb=" N1 C R 13 " pdb=" C2 C R 13 " ideal model delta sinusoidal sigma weight residual -160.00 -83.09 -76.91 1 1.50e+01 4.44e-03 3.30e+01 dihedral pdb=" C4' A R 10 " pdb=" O4' A R 10 " pdb=" C1' A R 10 " pdb=" C2' A R 10 " ideal model delta sinusoidal sigma weight residual 3.00 -33.46 36.46 1 8.00e+00 1.56e-02 2.94e+01 ... (remaining 27529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 3757 0.048 - 0.096: 686 0.096 - 0.143: 249 0.143 - 0.191: 44 0.191 - 0.239: 9 Chirality restraints: 4745 Sorted by residual: chirality pdb=" C2' C R 3 " pdb=" C3' C R 3 " pdb=" O2' C R 3 " pdb=" C1' C R 3 " both_signs ideal model delta sigma weight residual False -2.75 -2.51 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C2' G R 9 " pdb=" C3' G R 9 " pdb=" O2' G R 9 " pdb=" C1' G R 9 " both_signs ideal model delta sigma weight residual False -2.75 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' A R 10 " pdb=" C4' A R 10 " pdb=" O3' A R 10 " pdb=" C2' A R 10 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 4742 not shown) Planarity restraints: 8573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1106 " 0.281 9.50e-02 1.11e+02 9.48e-02 1.38e+01 pdb=" NE ARG B1106 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B1106 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B1106 " 0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B1106 " 0.002 2.00e-02 2.50e+03 pdb="HH11 ARG B1106 " -0.026 2.00e-02 2.50e+03 pdb="HH12 ARG B1106 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG B1106 " 0.013 2.00e-02 2.50e+03 pdb="HH22 ARG B1106 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A1098 " -0.035 5.00e-02 4.00e+02 5.30e-02 4.50e+00 pdb=" N PRO A1099 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1099 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1099 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1122 " -0.185 9.50e-02 1.11e+02 6.18e-02 4.44e+00 pdb=" NE ARG B1122 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG B1122 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B1122 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG B1122 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG B1122 " 0.003 2.00e-02 2.50e+03 pdb="HH12 ARG B1122 " 0.001 2.00e-02 2.50e+03 pdb="HH21 ARG B1122 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG B1122 " -0.001 2.00e-02 2.50e+03 ... (remaining 8570 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.10: 1581 2.10 - 2.73: 102515 2.73 - 3.35: 169860 3.35 - 3.98: 216886 3.98 - 4.60: 339379 Nonbonded interactions: 830221 Sorted by model distance: nonbonded pdb="H2'' DC T 5 " pdb=" H72 DT T 6 " model vdw 1.479 2.440 nonbonded pdb="HE21 GLN B 776 " pdb=" OP1 A R 10 " model vdw 1.505 1.850 nonbonded pdb=" H SER E 157 " pdb=" OE2 GLU E 160 " model vdw 1.540 1.850 nonbonded pdb=" H SER L 41 " pdb=" OD2 ASP L 44 " model vdw 1.543 1.850 nonbonded pdb="HE21 GLN A 767 " pdb=" O GLN A 768 " model vdw 1.545 1.850 ... (remaining 830216 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: 3.360 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: 0.660 Extract box with map and model: 12.840 Check model and map are aligned: 0.670 Set scattering table: 0.420 Process input model: 180.680 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 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:2.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 : 0.004 0.067 30727 Z= 0.256 Angle : 0.625 8.934 41782 Z= 0.389 Chirality : 0.045 0.239 4745 Planarity : 0.004 0.120 5245 Dihedral : 13.416 89.949 11584 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.07 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.14), residues: 3685 helix: 0.70 (0.14), residues: 1299 sheet: -0.88 (0.21), residues: 567 loop : -0.22 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 561 HIS 0.011 0.001 HIS B1104 PHE 0.009 0.001 PHE G 79 TYR 0.021 0.001 TYR E 112 ARG 0.009 0.000 ARG B1122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 271 time to evaluate : 3.664 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 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: A 456 MET cc_start: 0.8699 (mtt) cc_final: 0.8459 (mtm) REVERT: A 526 ASP cc_start: 0.7926 (m-30) cc_final: 0.7512 (m-30) REVERT: A 614 PHE cc_start: 0.6566 (m-10) cc_final: 0.6197 (m-10) REVERT: A 771 GLU cc_start: 0.8662 (mp0) cc_final: 0.8424 (mp0) REVERT: A 873 MET cc_start: 0.8414 (mmm) cc_final: 0.8096 (mmm) REVERT: A 1034 GLU cc_start: 0.8395 (mp0) cc_final: 0.8140 (mp0) REVERT: A 1202 MET cc_start: 0.9547 (mtp) cc_final: 0.9258 (mtp) REVERT: A 1209 MET cc_start: 0.5721 (mtp) cc_final: 0.4815 (mtp) REVERT: B 1009 ASP cc_start: 0.8396 (m-30) cc_final: 0.8104 (m-30) REVERT: D 50 LEU cc_start: 0.9049 (tp) cc_final: 0.8675 (tp) REVERT: E 203 GLU cc_start: 0.8763 (mp0) cc_final: 0.8502 (mp0) REVERT: H 21 ASN cc_start: 0.8900 (m-40) cc_final: 0.8439 (p0) outliers start: 0 outliers final: 0 residues processed: 271 average time/residue: 0.7871 time to fit residues: 346.6985 Evaluate side-chains 215 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 315 optimal weight: 4.9990 chunk 283 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 191 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 293 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 339 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 GLN C 224 GLN G 71 ASN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 30727 Z= 0.410 Angle : 0.610 9.542 41782 Z= 0.339 Chirality : 0.042 0.251 4745 Planarity : 0.005 0.058 5245 Dihedral : 12.528 83.855 4691 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.43 % Favored : 94.49 % Rotamer: Outliers : 0.40 % Allowed : 3.93 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.14), residues: 3685 helix: 0.52 (0.14), residues: 1337 sheet: -0.95 (0.21), residues: 537 loop : -0.43 (0.15), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 681 HIS 0.005 0.001 HIS B1104 PHE 0.021 0.001 PHE A 135 TYR 0.022 0.001 TYR A1328 ARG 0.006 0.001 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 3.690 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 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: A 444 PHE cc_start: 0.9039 (OUTLIER) cc_final: 0.8231 (t80) REVERT: A 1105 LEU cc_start: 0.9272 (mm) cc_final: 0.9041 (mm) REVERT: A 1209 MET cc_start: 0.5355 (mtp) cc_final: 0.4089 (mtp) REVERT: B 841 MET cc_start: 0.8829 (ttt) cc_final: 0.8629 (ttt) REVERT: B 1009 ASP cc_start: 0.8304 (m-30) cc_final: 0.8069 (m-30) REVERT: B 1136 ASP cc_start: 0.7678 (m-30) cc_final: 0.7404 (m-30) REVERT: D 50 LEU cc_start: 0.9034 (tp) cc_final: 0.8784 (tp) REVERT: E 203 GLU cc_start: 0.8794 (mp0) cc_final: 0.8557 (mp0) REVERT: H 21 ASN cc_start: 0.8924 (m-40) cc_final: 0.8400 (p0) REVERT: H 116 TYR cc_start: 0.8812 (m-80) cc_final: 0.8590 (m-80) outliers start: 12 outliers final: 10 residues processed: 234 average time/residue: 0.7738 time to fit residues: 292.9810 Evaluate side-chains 224 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 3.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 1436 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 71 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 188 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 93 optimal weight: 0.0980 chunk 340 optimal weight: 3.9990 chunk 367 optimal weight: 7.9990 chunk 303 optimal weight: 3.9990 chunk 337 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 272 optimal weight: 8.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 30727 Z= 0.353 Angle : 0.570 8.188 41782 Z= 0.314 Chirality : 0.042 0.239 4745 Planarity : 0.004 0.062 5245 Dihedral : 12.573 89.592 4691 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.64 % Favored : 94.27 % Rotamer: Outliers : 0.63 % Allowed : 5.25 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3685 helix: 0.65 (0.14), residues: 1336 sheet: -0.93 (0.21), residues: 536 loop : -0.49 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 681 HIS 0.006 0.001 HIS A 92 PHE 0.021 0.001 PHE A 135 TYR 0.022 0.001 TYR A1328 ARG 0.007 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 225 time to evaluate : 3.625 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 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: A 453 MET cc_start: 0.8610 (mmt) cc_final: 0.8385 (mmt) REVERT: A 873 MET cc_start: 0.8951 (mmm) cc_final: 0.8567 (mmm) REVERT: A 1034 GLU cc_start: 0.8567 (mp0) cc_final: 0.8326 (mp0) REVERT: A 1202 MET cc_start: 0.9460 (mtp) cc_final: 0.9011 (mtp) REVERT: A 1209 MET cc_start: 0.5573 (mtp) cc_final: 0.4661 (mtp) REVERT: B 662 MET cc_start: 0.8870 (tmm) cc_final: 0.8566 (tmm) REVERT: B 841 MET cc_start: 0.8772 (ttt) cc_final: 0.8559 (ttt) REVERT: B 1009 ASP cc_start: 0.8326 (m-30) cc_final: 0.8102 (m-30) REVERT: D 50 LEU cc_start: 0.8966 (tp) cc_final: 0.8757 (tp) REVERT: E 58 MET cc_start: 0.9229 (ttm) cc_final: 0.8948 (ttm) REVERT: E 203 GLU cc_start: 0.8737 (mp0) cc_final: 0.8320 (mp0) REVERT: H 21 ASN cc_start: 0.8915 (m-40) cc_final: 0.8396 (p0) outliers start: 19 outliers final: 18 residues processed: 235 average time/residue: 0.7833 time to fit residues: 299.1546 Evaluate side-chains 232 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 3.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 837 ILE Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 336 optimal weight: 3.9990 chunk 255 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 228 optimal weight: 0.9990 chunk 341 optimal weight: 5.9990 chunk 361 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 323 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30727 Z= 0.179 Angle : 0.501 8.697 41782 Z= 0.269 Chirality : 0.041 0.243 4745 Planarity : 0.004 0.060 5245 Dihedral : 12.448 86.388 4691 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.42 % Favored : 95.50 % Rotamer: Outliers : 0.69 % Allowed : 5.87 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.14), residues: 3685 helix: 1.10 (0.14), residues: 1336 sheet: -0.67 (0.22), residues: 529 loop : -0.28 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 681 HIS 0.005 0.001 HIS A 851 PHE 0.020 0.001 PHE A 135 TYR 0.025 0.001 TYR A1328 ARG 0.005 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 234 time to evaluate : 3.625 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 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: A 456 MET cc_start: 0.8613 (mtm) cc_final: 0.8243 (mtm) REVERT: A 676 MET cc_start: 0.8919 (mpp) cc_final: 0.8686 (mmm) REVERT: A 1105 LEU cc_start: 0.9237 (mm) cc_final: 0.8936 (mm) REVERT: A 1202 MET cc_start: 0.9469 (mtp) cc_final: 0.9068 (mtp) REVERT: A 1209 MET cc_start: 0.5568 (mtp) cc_final: 0.4600 (mtp) REVERT: B 662 MET cc_start: 0.8838 (tmm) cc_final: 0.8548 (tmm) REVERT: E 203 GLU cc_start: 0.8700 (mp0) cc_final: 0.8432 (mp0) REVERT: H 21 ASN cc_start: 0.8862 (m-40) cc_final: 0.8397 (p0) outliers start: 21 outliers final: 18 residues processed: 246 average time/residue: 0.7711 time to fit residues: 306.3258 Evaluate side-chains 232 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 3.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain E residue 112 TYR Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 301 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 308 optimal weight: 0.9990 chunk 249 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 324 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 776 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 30727 Z= 0.194 Angle : 0.493 7.108 41782 Z= 0.264 Chirality : 0.040 0.232 4745 Planarity : 0.004 0.057 5245 Dihedral : 12.363 85.227 4691 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 0.79 % Allowed : 6.63 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3685 helix: 1.28 (0.14), residues: 1347 sheet: -0.56 (0.23), residues: 509 loop : -0.29 (0.15), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 31 HIS 0.014 0.001 HIS A 109 PHE 0.018 0.001 PHE A 135 TYR 0.026 0.001 TYR A1328 ARG 0.004 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 3.625 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 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: A 456 MET cc_start: 0.8562 (mtm) cc_final: 0.8202 (mtm) REVERT: A 676 MET cc_start: 0.8894 (mpp) cc_final: 0.8691 (mmm) REVERT: A 873 MET cc_start: 0.8963 (mmm) cc_final: 0.8531 (mmm) REVERT: A 1105 LEU cc_start: 0.9223 (mm) cc_final: 0.8970 (mm) REVERT: A 1202 MET cc_start: 0.9484 (mtp) cc_final: 0.9115 (ttm) REVERT: A 1209 MET cc_start: 0.5517 (mtp) cc_final: 0.4073 (mtp) REVERT: B 662 MET cc_start: 0.8898 (tmm) cc_final: 0.8613 (tmm) REVERT: E 203 GLU cc_start: 0.8708 (mp0) cc_final: 0.8311 (mp0) REVERT: F 85 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8246 (ttm) REVERT: H 21 ASN cc_start: 0.8864 (m-40) cc_final: 0.8413 (p0) outliers start: 24 outliers final: 22 residues processed: 243 average time/residue: 0.7566 time to fit residues: 298.4902 Evaluate side-chains 242 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 219 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1009 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 121 optimal weight: 4.9990 chunk 325 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 89 optimal weight: 30.0000 chunk 361 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 189 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 776 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30727 Z= 0.298 Angle : 0.525 7.654 41782 Z= 0.285 Chirality : 0.041 0.231 4745 Planarity : 0.004 0.085 5245 Dihedral : 12.352 84.591 4691 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.40 % Favored : 94.52 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.14), residues: 3685 helix: 1.23 (0.14), residues: 1350 sheet: -0.60 (0.23), residues: 516 loop : -0.42 (0.15), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 31 HIS 0.007 0.001 HIS A 109 PHE 0.017 0.001 PHE A 135 TYR 0.027 0.001 TYR A1328 ARG 0.005 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 218 time to evaluate : 3.623 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 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: A 456 MET cc_start: 0.8637 (mtm) cc_final: 0.8166 (mtm) REVERT: A 873 MET cc_start: 0.8912 (mmm) cc_final: 0.8483 (mmm) REVERT: B 662 MET cc_start: 0.8925 (tmm) cc_final: 0.8627 (tmm) REVERT: E 58 MET cc_start: 0.9244 (ttm) cc_final: 0.8962 (ttm) REVERT: E 203 GLU cc_start: 0.8697 (mp0) cc_final: 0.8312 (mp0) REVERT: F 85 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8372 (ttm) REVERT: H 21 ASN cc_start: 0.8878 (m-40) cc_final: 0.8441 (p0) outliers start: 29 outliers final: 25 residues processed: 235 average time/residue: 0.7555 time to fit residues: 288.5815 Evaluate side-chains 237 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain J residue 28 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 348 optimal weight: 0.0870 chunk 40 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 264 optimal weight: 1.9990 chunk 204 optimal weight: 0.5980 chunk 304 optimal weight: 0.0770 chunk 202 optimal weight: 1.9990 chunk 360 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 219 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 40 HIS F 100 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30727 Z= 0.149 Angle : 0.485 9.233 41782 Z= 0.256 Chirality : 0.041 0.224 4745 Planarity : 0.003 0.054 5245 Dihedral : 12.270 85.130 4691 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % Favored : 96.26 % Rotamer: Outliers : 0.79 % Allowed : 7.46 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.14), residues: 3685 helix: 1.55 (0.14), residues: 1353 sheet: -0.52 (0.23), residues: 534 loop : -0.23 (0.15), residues: 1798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 31 HIS 0.008 0.001 HIS A 109 PHE 0.016 0.001 PHE A 135 TYR 0.029 0.001 TYR A1328 ARG 0.004 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 233 time to evaluate : 3.643 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 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: A 437 MET cc_start: 0.8498 (mtt) cc_final: 0.8261 (mtt) REVERT: A 456 MET cc_start: 0.8583 (mtm) cc_final: 0.8071 (mtm) REVERT: A 873 MET cc_start: 0.8867 (mmm) cc_final: 0.8444 (mmm) REVERT: A 1105 LEU cc_start: 0.9217 (mm) cc_final: 0.8873 (mm) REVERT: A 1209 MET cc_start: 0.5602 (mtp) cc_final: 0.4081 (mtp) REVERT: B 552 MET cc_start: 0.8732 (mmm) cc_final: 0.8436 (mmm) REVERT: B 662 MET cc_start: 0.8896 (tmm) cc_final: 0.8617 (tmm) REVERT: E 58 MET cc_start: 0.9265 (ttm) cc_final: 0.9053 (ttm) REVERT: E 203 GLU cc_start: 0.8654 (mp0) cc_final: 0.8268 (mp0) REVERT: F 85 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8386 (ttm) REVERT: H 21 ASN cc_start: 0.8836 (m-40) cc_final: 0.8438 (p0) outliers start: 24 outliers final: 22 residues processed: 247 average time/residue: 0.7643 time to fit residues: 308.8498 Evaluate side-chains 240 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 217 time to evaluate : 3.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 223 optimal weight: 2.9990 chunk 143 optimal weight: 30.0000 chunk 215 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 229 optimal weight: 0.9990 chunk 245 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 283 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1104 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30727 Z= 0.293 Angle : 0.521 9.237 41782 Z= 0.281 Chirality : 0.040 0.225 4745 Planarity : 0.004 0.058 5245 Dihedral : 12.280 84.981 4691 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 1.09 % Allowed : 7.49 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3685 helix: 1.45 (0.14), residues: 1351 sheet: -0.65 (0.22), residues: 552 loop : -0.36 (0.15), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.006 0.001 HIS J 53 PHE 0.015 0.001 PHE A 135 TYR 0.029 0.001 TYR A1328 ARG 0.004 0.000 ARG A 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 3.733 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 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: A 456 MET cc_start: 0.8618 (mtm) cc_final: 0.8085 (mtm) REVERT: A 873 MET cc_start: 0.8873 (mmm) cc_final: 0.8438 (mmm) REVERT: A 1034 GLU cc_start: 0.8499 (mp0) cc_final: 0.8280 (mp0) REVERT: A 1105 LEU cc_start: 0.9222 (mm) cc_final: 0.8973 (mm) REVERT: A 1209 MET cc_start: 0.5876 (mtp) cc_final: 0.4316 (mtp) REVERT: B 552 MET cc_start: 0.8784 (mmm) cc_final: 0.8480 (mmm) REVERT: B 662 MET cc_start: 0.8908 (tmm) cc_final: 0.8609 (tmm) REVERT: B 1072 MET cc_start: 0.8452 (mtm) cc_final: 0.8230 (mtm) REVERT: E 58 MET cc_start: 0.9256 (ttm) cc_final: 0.8951 (ttm) REVERT: E 203 GLU cc_start: 0.8692 (mp0) cc_final: 0.8314 (mp0) REVERT: F 85 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8395 (ttm) REVERT: G 54 ILE cc_start: 0.7898 (mm) cc_final: 0.7425 (mt) REVERT: H 21 ASN cc_start: 0.8877 (m-40) cc_final: 0.8473 (p0) outliers start: 33 outliers final: 31 residues processed: 233 average time/residue: 0.7652 time to fit residues: 291.7151 Evaluate side-chains 244 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 212 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 544 ASP Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 754 SER Chi-restraints excluded: chain A residue 758 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain F residue 89 GLU Chi-restraints excluded: chain G residue 12 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 327 optimal weight: 0.0030 chunk 345 optimal weight: 0.0770 chunk 315 optimal weight: 4.9990 chunk 335 optimal weight: 0.2980 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 263 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 chunk 317 optimal weight: 8.9990 chunk 334 optimal weight: 0.9990 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1048 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30727 Z= 0.139 Angle : 0.483 9.255 41782 Z= 0.254 Chirality : 0.041 0.222 4745 Planarity : 0.003 0.052 5245 Dihedral : 12.219 85.597 4691 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.74 % Favored : 96.17 % Rotamer: Outliers : 0.66 % Allowed : 7.85 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.14), residues: 3685 helix: 1.76 (0.14), residues: 1345 sheet: -0.46 (0.23), residues: 533 loop : -0.15 (0.15), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 31 HIS 0.006 0.001 HIS B1104 PHE 0.015 0.001 PHE A 135 TYR 0.027 0.001 TYR A1328 ARG 0.004 0.000 ARG E 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 232 time to evaluate : 3.625 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 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: A 456 MET cc_start: 0.8593 (mtm) cc_final: 0.8044 (mtm) REVERT: A 1105 LEU cc_start: 0.9189 (mm) cc_final: 0.8850 (mm) REVERT: A 1209 MET cc_start: 0.5595 (mtp) cc_final: 0.4058 (mtp) REVERT: B 552 MET cc_start: 0.8763 (mmm) cc_final: 0.8443 (mmm) REVERT: B 662 MET cc_start: 0.8908 (tmm) cc_final: 0.8688 (tmm) REVERT: E 58 MET cc_start: 0.9254 (ttm) cc_final: 0.8999 (ttm) REVERT: E 203 GLU cc_start: 0.8623 (mp0) cc_final: 0.8247 (mp0) REVERT: F 85 MET cc_start: 0.8980 (OUTLIER) cc_final: 0.8374 (ttm) REVERT: H 21 ASN cc_start: 0.8828 (m-40) cc_final: 0.8443 (p0) outliers start: 20 outliers final: 18 residues processed: 243 average time/residue: 0.7686 time to fit residues: 304.5460 Evaluate side-chains 238 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 219 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 220 optimal weight: 2.9990 chunk 355 optimal weight: 1.9990 chunk 216 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 342 optimal weight: 4.9990 chunk 296 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 229 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 30727 Z= 0.209 Angle : 0.493 9.028 41782 Z= 0.261 Chirality : 0.040 0.220 4745 Planarity : 0.004 0.055 5245 Dihedral : 12.201 85.703 4691 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.45 % Favored : 95.47 % Rotamer: Outliers : 0.76 % Allowed : 7.92 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.14), residues: 3685 helix: 1.74 (0.14), residues: 1352 sheet: -0.45 (0.23), residues: 533 loop : -0.20 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.004 0.001 HIS J 53 PHE 0.014 0.001 PHE A 135 TYR 0.030 0.001 TYR A1328 ARG 0.012 0.000 ARG A 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7370 Ramachandran restraints generated. 3685 Oldfield, 0 Emsley, 3685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 3.716 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 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: A 456 MET cc_start: 0.8610 (mtm) cc_final: 0.8068 (mtm) REVERT: A 1105 LEU cc_start: 0.9231 (mm) cc_final: 0.8927 (mm) REVERT: A 1209 MET cc_start: 0.5813 (mtp) cc_final: 0.4279 (mtp) REVERT: B 552 MET cc_start: 0.8767 (mmm) cc_final: 0.8445 (mmm) REVERT: B 662 MET cc_start: 0.8941 (tmm) cc_final: 0.8713 (tmm) REVERT: B 1072 MET cc_start: 0.8472 (mtm) cc_final: 0.8261 (mtm) REVERT: E 58 MET cc_start: 0.9281 (ttm) cc_final: 0.9001 (ttm) REVERT: E 203 GLU cc_start: 0.8670 (mp0) cc_final: 0.8314 (mp0) REVERT: F 85 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8481 (ttm) REVERT: H 21 ASN cc_start: 0.8868 (m-40) cc_final: 0.8494 (p0) outliers start: 23 outliers final: 21 residues processed: 234 average time/residue: 0.7834 time to fit residues: 300.3998 Evaluate side-chains 237 residues out of total 3292 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 215 time to evaluate : 3.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 444 PHE Chi-restraints excluded: chain A residue 605 MET Chi-restraints excluded: chain A residue 666 ILE Chi-restraints excluded: chain A residue 826 ASP Chi-restraints excluded: chain A residue 884 ASP Chi-restraints excluded: chain A residue 975 HIS Chi-restraints excluded: chain A residue 1389 PHE Chi-restraints excluded: chain B residue 236 HIS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 1061 GLU Chi-restraints excluded: chain C residue 38 ILE Chi-restraints excluded: chain E residue 2 ASP Chi-restraints excluded: chain F residue 85 MET Chi-restraints excluded: chain F residue 86 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 55 ASP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain K residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 374 random chunks: chunk 235 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 273 optimal weight: 30.0000 chunk 43 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 297 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 305 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.079900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060561 restraints weight = 401949.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.062827 restraints weight = 169217.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.064259 restraints weight = 101995.755| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30727 Z= 0.209 Angle : 0.495 8.737 41782 Z= 0.264 Chirality : 0.040 0.220 4745 Planarity : 0.004 0.056 5245 Dihedral : 12.199 85.628 4691 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.86 % Allowed : 7.79 % Favored : 91.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.14), residues: 3685 helix: 1.76 (0.14), residues: 1347 sheet: -0.48 (0.22), residues: 549 loop : -0.20 (0.15), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 31 HIS 0.005 0.001 HIS A 851 PHE 0.014 0.001 PHE A 135 TYR 0.029 0.001 TYR A1328 ARG 0.007 0.000 ARG A 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8162.05 seconds wall clock time: 143 minutes 37.42 seconds (8617.42 seconds total)