Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 20 01:56:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z1l_14447/10_2023/7z1l_14447_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 7 6.06 5 P 63 5.49 5 Mg 1 5.21 5 S 217 5.16 5 C 26638 2.51 5 N 7293 2.21 5 O 8111 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 221": "OD1" <-> "OD2" Residue "A ASP 330": "OD1" <-> "OD2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 460": "OD1" <-> "OD2" Residue "A TYR 957": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1168": "OD1" <-> "OD2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A GLU 1199": "OE1" <-> "OE2" Residue "A ASP 1204": "OD1" <-> "OD2" Residue "A ASP 1221": "OD1" <-> "OD2" Residue "A PHE 1374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1406": "OD1" <-> "OD2" Residue "B PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1024": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 283": "OE1" <-> "OE2" Residue "C PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "G PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 19": "OE1" <-> "OE2" Residue "J GLU 29": "OE1" <-> "OE2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "K ASP 57": "OD1" <-> "OD2" Residue "K PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ASP 123": "OD1" <-> "OD2" Residue "K ASP 126": "OD1" <-> "OD2" Residue "K ASP 129": "OD1" <-> "OD2" Residue "O GLU 353": "OE1" <-> "OE2" Residue "P PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 306": "OD1" <-> "OD2" Residue "Q ASP 124": "OD1" <-> "OD2" Residue "Q GLU 135": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 42330 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 11228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 11228 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 66, 'TRANS': 1369} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8693 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 41, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2647 Classifications: {'peptide': 334} Link IDs: {'PTRANS': 20, 'TRANS': 313} Chain: "D" Number of atoms: 1185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1185 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 671 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 6, 'TRANS': 76} Chain: "G" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1594 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1084 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 130} Chain breaks: 1 Chain: "I" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 873 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 1 Chain: "K" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 801 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "L" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 358 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1594 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 10, 'TRANS': 185} Chain breaks: 1 Chain: "N" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1196 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 8, 'TRANS': 144} Chain breaks: 2 Chain: "O" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4577 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 20, 'TRANS': 549} Chain breaks: 1 Chain: "P" Number of atoms: 1159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1159 Classifications: {'peptide': 140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 133} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 8, 'TRANS': 114} Chain breaks: 1 Chain: "R" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "S" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 507 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "T" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 597 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '4QM': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'4QM': 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 500 SG CYS A 67 112.986 78.487 107.960 1.00 64.89 S ATOM 518 SG CYS A 70 111.704 75.007 107.000 1.00 64.68 S ATOM 565 SG CYS A 77 110.345 78.145 105.219 1.00 58.96 S ATOM 803 SG CYS A 107 81.459 100.327 137.919 1.00 57.33 S ATOM 826 SG CYS A 110 82.502 97.228 139.918 1.00 59.33 S ATOM 1192 SG CYS A 154 78.799 98.158 139.604 1.00 68.88 S ATOM 1216 SG CYS A 157 81.215 100.181 141.732 1.00 69.42 S ATOM 19494 SG CYS B1095 98.225 69.942 117.054 1.00 56.67 S ATOM 19517 SG CYS B1098 97.720 73.702 117.560 1.00 56.41 S ATOM 19583 SG CYS B1107 101.159 72.310 116.959 1.00 61.02 S ATOM 19603 SG CYS B1110 99.427 71.622 120.263 1.00 62.41 S ATOM 29397 SG CYS I 69 14.357 125.238 101.740 1.00184.32 S ATOM 29647 SG CYS I 100 14.496 124.588 97.349 1.00172.72 S ATOM 29668 SG CYS I 103 16.652 126.696 98.993 1.00175.25 S ATOM 28900 SG CYS I 5 63.049 153.575 108.651 1.00 83.47 S ATOM 28919 SG CYS I 8 66.757 152.775 107.910 1.00 83.37 S ATOM 29047 SG CYS I 26 65.111 150.979 110.772 1.00 86.92 S ATOM 29070 SG CYS I 29 65.583 154.768 110.934 1.00 90.21 S ATOM 29788 SG CYS J 7 92.747 91.347 38.719 1.00 41.91 S ATOM 29811 SG CYS J 10 92.181 88.474 36.191 1.00 43.42 S ATOM 30091 SG CYS J 45 89.337 90.847 37.384 1.00 43.96 S ATOM 30097 SG CYS J 46 92.070 91.863 34.922 1.00 44.15 S ATOM 31154 SG CYS L 31 126.234 110.568 59.006 1.00 77.34 S ATOM 31174 SG CYS L 34 128.057 111.576 55.892 1.00 79.39 S ATOM 31278 SG CYS L 48 130.050 110.991 59.076 1.00 84.50 S ATOM 31301 SG CYS L 51 127.865 114.028 58.831 1.00 84.76 S Time building chain proxies: 21.01, per 1000 atoms: 0.50 Number of scatterers: 42330 At special positions: 0 Unit cell: (147.822, 194.667, 197.79, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 7 29.99 S 217 16.00 P 63 15.00 Mg 1 11.99 O 8111 8.00 N 7293 7.00 C 26638 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.23 Conformation dependent library (CDL) restraints added in 6.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2000 " pdb="ZN ZN A2000 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 67 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 70 " pdb="ZN ZN A2000 " - pdb=" SG CYS A 77 " pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 157 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 110 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 154 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 107 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1095 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1110 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 100 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 69 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 8 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 5 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 26 " pdb=" ZN J 100 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 46 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 100 " - pdb=" SG CYS J 7 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " Number of angles added : 33 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 49 sheets defined 35.3% alpha, 13.0% beta 14 base pairs and 54 stacking pairs defined. Time for finding SS restraints: 16.58 Creating SS restraints... Processing helix chain 'A' and resid 23 through 28 Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 134 through 149 Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 192 through 205 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.349A pdb=" N ARG A 213 " --> pdb=" O GLU A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 284 through 305 Processing helix chain 'A' and resid 309 through 327 Processing helix chain 'A' and resid 329 through 331 No H-bonds generated for 'chain 'A' and resid 329 through 331' Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 363 through 366 No H-bonds generated for 'chain 'A' and resid 363 through 366' Processing helix chain 'A' and resid 396 through 399 No H-bonds generated for 'chain 'A' and resid 396 through 399' Processing helix chain 'A' and resid 413 through 422 Processing helix chain 'A' and resid 451 through 454 No H-bonds generated for 'chain 'A' and resid 451 through 454' Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 558 through 564 Processing helix chain 'A' and resid 573 through 582 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 643 through 645 No H-bonds generated for 'chain 'A' and resid 643 through 645' Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 677 through 685 Processing helix chain 'A' and resid 687 through 707 removed outlier: 3.670A pdb=" N ARG A 703 " --> pdb=" O LYS A 699 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU A 705 " --> pdb=" O CYS A 701 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N GLY A 706 " --> pdb=" O ALA A 702 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASN A 707 " --> pdb=" O ARG A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 747 removed outlier: 3.770A pdb=" N GLU A 728 " --> pdb=" O LYS A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 782 Processing helix chain 'A' and resid 790 through 797 Processing helix chain 'A' and resid 803 through 810 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 858 through 893 removed outlier: 4.372A pdb=" N THR A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA A 880 " --> pdb=" O ALA A 876 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU A 881 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N TYR A 884 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 923 through 925 No H-bonds generated for 'chain 'A' and resid 923 through 925' Processing helix chain 'A' and resid 935 through 945 Processing helix chain 'A' and resid 956 through 972 Proline residue: A 969 - end of helix Processing helix chain 'A' and resid 986 through 988 No H-bonds generated for 'chain 'A' and resid 986 through 988' Processing helix chain 'A' and resid 992 through 994 No H-bonds generated for 'chain 'A' and resid 992 through 994' Processing helix chain 'A' and resid 999 through 1025 Processing helix chain 'A' and resid 1053 through 1059 Processing helix chain 'A' and resid 1064 through 1079 Processing helix chain 'A' and resid 1089 through 1103 Proline residue: A1100 - end of helix Processing helix chain 'A' and resid 1123 through 1130 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 3.572A pdb=" N ARG A1160 " --> pdb=" O VAL A1156 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A1161 " --> pdb=" O VAL A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1196 Processing helix chain 'A' and resid 1202 through 1211 Processing helix chain 'A' and resid 1213 through 1215 No H-bonds generated for 'chain 'A' and resid 1213 through 1215' Processing helix chain 'A' and resid 1255 through 1269 Proline residue: A1268 - end of helix Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1319 through 1326 Processing helix chain 'A' and resid 1328 through 1345 removed outlier: 3.569A pdb=" N TYR A1333 " --> pdb=" O GLU A1329 " (cutoff:3.500A) Processing helix chain 'A' and resid 1352 through 1362 Processing helix chain 'A' and resid 1373 through 1379 removed outlier: 3.562A pdb=" N LYS A1378 " --> pdb=" O PHE A1374 " (cutoff:3.500A) Processing helix chain 'A' and resid 1384 through 1387 No H-bonds generated for 'chain 'A' and resid 1384 through 1387' Processing helix chain 'A' and resid 1392 through 1402 Processing helix chain 'A' and resid 1411 through 1417 Processing helix chain 'A' and resid 1424 through 1426 No H-bonds generated for 'chain 'A' and resid 1424 through 1426' Processing helix chain 'A' and resid 1439 through 1441 No H-bonds generated for 'chain 'A' and resid 1439 through 1441' Processing helix chain 'A' and resid 1447 through 1451 Processing helix chain 'B' and resid 44 through 54 Proline residue: B 49 - end of helix Processing helix chain 'B' and resid 59 through 70 Processing helix chain 'B' and resid 72 through 79 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 277 through 292 removed outlier: 4.920A pdb=" N VAL B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ASN B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 287 " --> pdb=" O PHE B 283 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU B 288 " --> pdb=" O ALA B 284 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU B 289 " --> pdb=" O VAL B 285 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER B 290 " --> pdb=" O ASN B 286 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N SER B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 removed outlier: 4.192A pdb=" N LYS B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 329 Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 380 through 407 removed outlier: 3.885A pdb=" N ASP B 390 " --> pdb=" O LEU B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 421 Processing helix chain 'B' and resid 423 through 438 removed outlier: 5.676A pdb=" N ASN B 428 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE B 429 " --> pdb=" O HIS B 425 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 430 " --> pdb=" O SER B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 Processing helix chain 'B' and resid 491 through 493 No H-bonds generated for 'chain 'B' and resid 491 through 493' Processing helix chain 'B' and resid 527 through 536 Processing helix chain 'B' and resid 549 through 551 No H-bonds generated for 'chain 'B' and resid 549 through 551' Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 624 through 632 Processing helix chain 'B' and resid 637 through 642 Processing helix chain 'B' and resid 651 through 655 Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 691 through 693 No H-bonds generated for 'chain 'B' and resid 691 through 693' Processing helix chain 'B' and resid 696 through 708 removed outlier: 4.473A pdb=" N LYS B 707 " --> pdb=" O CYS B 703 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN B 708 " --> pdb=" O ALA B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 764 through 766 No H-bonds generated for 'chain 'B' and resid 764 through 766' Processing helix chain 'B' and resid 775 through 779 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 946 through 948 No H-bonds generated for 'chain 'B' and resid 946 through 948' Processing helix chain 'B' and resid 955 through 970 Processing helix chain 'B' and resid 984 through 993 Processing helix chain 'B' and resid 1031 through 1033 No H-bonds generated for 'chain 'B' and resid 1031 through 1033' Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1064 through 1073 Processing helix chain 'B' and resid 1076 through 1083 Processing helix chain 'B' and resid 1123 through 1135 Processing helix chain 'C' and resid 33 through 39 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 94 through 102 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 122 through 125 No H-bonds generated for 'chain 'C' and resid 122 through 125' Processing helix chain 'C' and resid 153 through 156 No H-bonds generated for 'chain 'C' and resid 153 through 156' Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 173 through 178 removed outlier: 3.785A pdb=" N THR C 178 " --> pdb=" O GLN C 175 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 241 through 249 Processing helix chain 'C' and resid 278 through 281 Processing helix chain 'C' and resid 283 through 285 No H-bonds generated for 'chain 'C' and resid 283 through 285' Processing helix chain 'C' and resid 310 through 330 Processing helix chain 'D' and resid 13 through 26 Processing helix chain 'D' and resid 31 through 36 Processing helix chain 'D' and resid 53 through 67 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 131 through 137 Processing helix chain 'D' and resid 141 through 144 No H-bonds generated for 'chain 'D' and resid 141 through 144' Processing helix chain 'D' and resid 147 through 158 Processing helix chain 'E' and resid 6 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 39 through 46 Processing helix chain 'E' and resid 55 through 58 No H-bonds generated for 'chain 'E' and resid 55 through 58' Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 91 through 103 Processing helix chain 'E' and resid 118 through 121 No H-bonds generated for 'chain 'E' and resid 118 through 121' Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 103 Processing helix chain 'F' and resid 117 through 126 Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 22 through 34 Processing helix chain 'G' and resid 112 through 114 No H-bonds generated for 'chain 'G' and resid 112 through 114' Processing helix chain 'G' and resid 163 through 174 Processing helix chain 'H' and resid 89 through 92 removed outlier: 3.953A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 92' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 removed outlier: 3.679A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 51 removed outlier: 3.733A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 63 removed outlier: 3.661A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N TYR J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 70 through 82 removed outlier: 4.419A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS K 82 " --> pdb=" O TYR K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 141 removed outlier: 3.675A pdb=" N LYS K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 133 through 139 Processing helix chain 'M' and resid 184 through 198 Processing helix chain 'M' and resid 230 through 239 Processing helix chain 'M' and resid 252 through 262 Processing helix chain 'M' and resid 274 through 279 Processing helix chain 'N' and resid 196 through 199 Processing helix chain 'N' and resid 209 through 211 No H-bonds generated for 'chain 'N' and resid 209 through 211' Processing helix chain 'N' and resid 215 through 224 removed outlier: 3.920A pdb=" N SER N 224 " --> pdb=" O GLN N 220 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 296 Processing helix chain 'N' and resid 353 through 355 No H-bonds generated for 'chain 'N' and resid 353 through 355' Processing helix chain 'O' and resid 28 through 34 Processing helix chain 'O' and resid 44 through 56 Processing helix chain 'O' and resid 59 through 71 Processing helix chain 'O' and resid 76 through 82 Processing helix chain 'O' and resid 88 through 100 Processing helix chain 'O' and resid 124 through 131 Processing helix chain 'O' and resid 133 through 143 Processing helix chain 'O' and resid 150 through 166 Processing helix chain 'O' and resid 171 through 177 removed outlier: 4.177A pdb=" N SER O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 181 through 196 Processing helix chain 'O' and resid 211 through 224 Processing helix chain 'O' and resid 234 through 255 removed outlier: 3.666A pdb=" N LYS O 255 " --> pdb=" O LYS O 251 " (cutoff:3.500A) Processing helix chain 'O' and resid 260 through 262 No H-bonds generated for 'chain 'O' and resid 260 through 262' Processing helix chain 'O' and resid 284 through 302 removed outlier: 3.873A pdb=" N THR O 302 " --> pdb=" O ASN O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 307 through 318 Processing helix chain 'O' and resid 329 through 332 Processing helix chain 'O' and resid 335 through 337 No H-bonds generated for 'chain 'O' and resid 335 through 337' Processing helix chain 'O' and resid 339 through 355 removed outlier: 3.817A pdb=" N GLU O 354 " --> pdb=" O GLU O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 363 through 368 removed outlier: 3.727A pdb=" N ARG O 368 " --> pdb=" O ILE O 364 " (cutoff:3.500A) Processing helix chain 'O' and resid 450 through 461 Processing helix chain 'O' and resid 480 through 500 Proline residue: O 485 - end of helix Processing helix chain 'O' and resid 502 through 513 Processing helix chain 'O' and resid 519 through 525 Processing helix chain 'O' and resid 530 through 543 removed outlier: 3.866A pdb=" N ARG O 542 " --> pdb=" O ALA O 538 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N TYR O 543 " --> pdb=" O SER O 539 " (cutoff:3.500A) Processing helix chain 'O' and resid 570 through 598 Processing helix chain 'O' and resid 600 through 606 Processing helix chain 'O' and resid 615 through 618 No H-bonds generated for 'chain 'O' and resid 615 through 618' Processing helix chain 'O' and resid 621 through 652 removed outlier: 5.231A pdb=" N VAL O 650 " --> pdb=" O SER O 646 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N PHE O 651 " --> pdb=" O LEU O 647 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN O 652 " --> pdb=" O TRP O 648 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 190 Processing helix chain 'P' and resid 194 through 199 Processing helix chain 'P' and resid 218 through 228 Processing helix chain 'P' and resid 237 through 249 Processing helix chain 'P' and resid 265 through 271 removed outlier: 3.656A pdb=" N MET P 271 " --> pdb=" O SER P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 296 through 298 No H-bonds generated for 'chain 'P' and resid 296 through 298' Processing helix chain 'Q' and resid 49 through 66 Processing helix chain 'Q' and resid 108 through 110 No H-bonds generated for 'chain 'Q' and resid 108 through 110' Processing helix chain 'Q' and resid 129 through 131 No H-bonds generated for 'chain 'Q' and resid 129 through 131' Processing helix chain 'Q' and resid 134 through 136 No H-bonds generated for 'chain 'Q' and resid 134 through 136' Processing sheet with id= A, first strand: chain 'A' and resid 15 through 17 Processing sheet with id= B, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= C, first strand: chain 'A' and resid 163 through 166 removed outlier: 4.320A pdb=" N ILE A 178 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 376 through 380 Processing sheet with id= E, first strand: chain 'A' and resid 381 through 383 removed outlier: 6.143A pdb=" N PHE A 498 " --> pdb=" O SER A 382 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 403 through 407 removed outlier: 3.925A pdb=" N TYR A 432 " --> pdb=" O GLU A 463 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N HIS A 465 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ALA A 430 " --> pdb=" O HIS A 465 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 626 through 629 removed outlier: 3.605A pdb=" N ILE A 653 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER A 661 " --> pdb=" O ILE A 653 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ARG A 655 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N ILE A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1140 through 1144 removed outlier: 3.616A pdb=" N ARG A1280 " --> pdb=" O GLU A1296 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 1222 through 1225 removed outlier: 4.459A pdb=" N SER A1182 " --> pdb=" O VAL A1234 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR A1172 " --> pdb=" O ARG A1187 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 82 through 84 removed outlier: 6.301A pdb=" N TYR B 92 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR B 136 " --> pdb=" O TYR B 92 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASP B 132 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE B 98 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR B 130 " --> pdb=" O ILE B 98 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 137 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASN B 140 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 185 through 187 Processing sheet with id= L, first strand: chain 'B' and resid 197 through 200 Processing sheet with id= M, first strand: chain 'B' and resid 205 through 210 removed outlier: 4.577A pdb=" N VAL B 216 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 442 through 444 Processing sheet with id= O, first strand: chain 'B' and resid 538 through 540 removed outlier: 6.910A pdb=" N VAL B 555 " --> pdb=" O ILE B 562 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 564 " --> pdb=" O TYR B 553 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N TYR B 553 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 609 through 613 Processing sheet with id= Q, first strand: chain 'B' and resid 724 through 728 removed outlier: 3.838A pdb=" N ALA B 894 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ARG B 901 " --> pdb=" O ILE B 881 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE B 881 " --> pdb=" O ARG B 901 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 1018 through 1024 removed outlier: 4.231A pdb=" N PHE B1018 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE B 942 " --> pdb=" O ALA B 758 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 846 through 848 Processing sheet with id= T, first strand: chain 'B' and resid 1089 through 1095 Processing sheet with id= U, first strand: chain 'B' and resid 126 through 131 removed outlier: 4.321A pdb=" N GLY B 150 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 131 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU B 148 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 771 through 774 removed outlier: 7.682A pdb=" N LEU B 773 " --> pdb=" O GLY B 923 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE B 925 " --> pdb=" O LEU B 773 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'C' and resid 4 through 7 removed outlier: 4.400A pdb=" N LEU C 291 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.652A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.368A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 256 through 258 Processing sheet with id= AA, first strand: chain 'C' and resid 161 through 163 Processing sheet with id= AB, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.030A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.817A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AE, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.779A pdb=" N THR G 47 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE G 77 " --> pdb=" O CYS G 45 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N CYS G 45 " --> pdb=" O PHE G 77 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS G 37 " --> pdb=" O CYS G 45 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 145 through 149 removed outlier: 7.072A pdb=" N LYS G 98 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N CYS G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLY G 96 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE G 108 " --> pdb=" O VAL G 99 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.501A pdb=" N ALA G 127 " --> pdb=" O THR G 122 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 152 through 155 removed outlier: 3.752A pdb=" N ARG G 152 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 50 through 54 removed outlier: 6.781A pdb=" N THR G 71 " --> pdb=" O LEU G 52 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 23 through 29 removed outlier: 5.265A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 12 through 15 removed outlier: 3.597A pdb=" N THR I 15 " --> pdb=" O THR I 23 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR I 23 " --> pdb=" O THR I 15 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 64 through 66 removed outlier: 3.785A pdb=" N TRP I 107 " --> pdb=" O TYR I 98 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 47 through 49 Processing sheet with id= AN, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AO, first strand: chain 'M' and resid 75 through 79 Processing sheet with id= AP, first strand: chain 'M' and resid 87 through 90 Processing sheet with id= AQ, first strand: chain 'M' and resid 180 through 182 removed outlier: 4.449A pdb=" N THR M 147 " --> pdb=" O PHE M 182 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA M 109 " --> pdb=" O ASP M 122 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE M 107 " --> pdb=" O PRO M 124 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'N' and resid 306 through 308 removed outlier: 3.561A pdb=" N THR N 419 " --> pdb=" O ASP N 381 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE N 382 " --> pdb=" O LEU N 371 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU N 371 " --> pdb=" O ILE N 382 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'N' and resid 393 through 395 removed outlier: 3.999A pdb=" N GLY N 410 " --> pdb=" O VAL N 394 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'O' and resid 106 through 110 Processing sheet with id= AU, first strand: chain 'O' and resid 168 through 170 Processing sheet with id= AV, first strand: chain 'O' and resid 547 through 551 Processing sheet with id= AW, first strand: chain 'P' and resid 253 through 257 removed outlier: 3.504A pdb=" N VAL P 256 " --> pdb=" O CYS P 260 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N CYS P 260 " --> pdb=" O VAL P 256 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 36 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 54 stacking parallelities Total time for adding SS restraints: 18.49 Time building geometry restraints manager: 18.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13562 1.34 - 1.46: 9000 1.46 - 1.58: 20182 1.58 - 1.70: 130 1.70 - 1.83: 352 Bond restraints: 43226 Sorted by residual: bond pdb=" C15 4QM C 401 " pdb=" C16 4QM C 401 " ideal model delta sigma weight residual 1.529 1.594 -0.065 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C15 4QM A2003 " pdb=" C16 4QM A2003 " ideal model delta sigma weight residual 1.529 1.593 -0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" C16 4QM A2003 " pdb=" C17 4QM A2003 " ideal model delta sigma weight residual 1.527 1.589 -0.062 2.00e-02 2.50e+03 9.62e+00 bond pdb=" C16 4QM C 401 " pdb=" C17 4QM C 401 " ideal model delta sigma weight residual 1.527 1.589 -0.062 2.00e-02 2.50e+03 9.56e+00 bond pdb=" C19 4QM C 401 " pdb=" C2 4QM C 401 " ideal model delta sigma weight residual 1.551 1.612 -0.061 2.00e-02 2.50e+03 9.16e+00 ... (remaining 43221 not shown) Histogram of bond angle deviations from ideal: 95.29 - 103.06: 392 103.06 - 110.82: 14594 110.82 - 118.59: 20140 118.59 - 126.35: 22865 126.35 - 134.11: 659 Bond angle restraints: 58650 Sorted by residual: angle pdb=" N ILE A 550 " pdb=" CA ILE A 550 " pdb=" C ILE A 550 " ideal model delta sigma weight residual 113.53 108.46 5.07 9.80e-01 1.04e+00 2.68e+01 angle pdb=" C LEU B 293 " pdb=" N ASP B 294 " pdb=" CA ASP B 294 " ideal model delta sigma weight residual 121.54 130.09 -8.55 1.91e+00 2.74e-01 2.01e+01 angle pdb=" C TYR B 164 " pdb=" N ASP B 165 " pdb=" CA ASP B 165 " ideal model delta sigma weight residual 121.54 129.74 -8.20 1.91e+00 2.74e-01 1.84e+01 angle pdb=" C GLN A 555 " pdb=" N ASP A 556 " pdb=" CA ASP A 556 " ideal model delta sigma weight residual 121.54 129.31 -7.77 1.91e+00 2.74e-01 1.65e+01 angle pdb=" C10 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C6 4QM C 401 " ideal model delta sigma weight residual 112.56 100.87 11.69 3.00e+00 1.11e-01 1.52e+01 ... (remaining 58645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.91: 25311 27.91 - 55.83: 891 55.83 - 83.74: 62 83.74 - 111.66: 4 111.66 - 139.57: 1 Dihedral angle restraints: 26269 sinusoidal: 11240 harmonic: 15029 Sorted by residual: dihedral pdb=" CA ASN O 514 " pdb=" C ASN O 514 " pdb=" N LYS O 515 " pdb=" CA LYS O 515 " ideal model delta harmonic sigma weight residual -180.00 -151.39 -28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLN E 179 " pdb=" C GLN E 179 " pdb=" N ARG E 180 " pdb=" CA ARG E 180 " ideal model delta harmonic sigma weight residual 180.00 159.69 20.31 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA PHE B1018 " pdb=" C PHE B1018 " pdb=" N PHE B1019 " pdb=" CA PHE B1019 " ideal model delta harmonic sigma weight residual 180.00 -160.04 -19.96 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 26266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 5786 0.069 - 0.137: 804 0.137 - 0.206: 22 0.206 - 0.275: 6 0.275 - 0.344: 6 Chirality restraints: 6624 Sorted by residual: chirality pdb=" C9 4QM C 401 " pdb=" C20 4QM C 401 " pdb=" C5 4QM C 401 " pdb=" C8 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.61 2.95 -0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" C9 4QM A2003 " pdb=" C20 4QM A2003 " pdb=" C5 4QM A2003 " pdb=" C8 4QM A2003 " both_signs ideal model delta sigma weight residual False 2.61 2.95 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C17 4QM C 401 " pdb=" C16 4QM C 401 " pdb=" C18 4QM C 401 " pdb=" O3 4QM C 401 " both_signs ideal model delta sigma weight residual False 2.39 2.71 -0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 6621 not shown) Planarity restraints: 7322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP P 251 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.97e+00 pdb=" C ASP P 251 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP P 251 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS P 252 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU B 676 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO B 677 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 677 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 677 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 433 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C LEU B 433 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU B 433 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 434 " 0.013 2.00e-02 2.50e+03 ... (remaining 7319 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 421 2.64 - 3.21: 36801 3.21 - 3.77: 65122 3.77 - 4.34: 91790 4.34 - 4.90: 151206 Nonbonded interactions: 345340 Sorted by model distance: nonbonded pdb=" O3' G R 19 " pdb="MG MG A2002 " model vdw 2.079 2.170 nonbonded pdb=" OD1 ASP A 511 " pdb="MG MG A2002 " model vdw 2.092 2.170 nonbonded pdb=" OD1 ASP A 513 " pdb="MG MG A2002 " model vdw 2.132 2.170 nonbonded pdb=" OE2 GLU B 676 " pdb=" OG1 THR B 679 " model vdw 2.169 2.440 nonbonded pdb=" O PHE C 86 " pdb=" OG SER C 203 " model vdw 2.218 2.440 ... (remaining 345335 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.040 Extract box with map and model: 11.390 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 124.960 Find NCS groups from input model: 1.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 152.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 0.003 0.065 43226 Z= 0.222 Angle : 0.652 11.687 58650 Z= 0.341 Chirality : 0.047 0.344 6624 Planarity : 0.005 0.059 7322 Dihedral : 13.457 139.573 16545 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.02 % Allowed : 0.20 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5094 helix: 0.47 (0.12), residues: 1874 sheet: 0.03 (0.21), residues: 656 loop : -0.58 (0.12), residues: 2564 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 556 time to evaluate : 4.531 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 557 average time/residue: 1.6333 time to fit residues: 1111.9297 Evaluate side-chains 450 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 450 time to evaluate : 4.802 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 433 optimal weight: 3.9990 chunk 388 optimal weight: 0.7980 chunk 215 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 262 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 402 optimal weight: 5.9990 chunk 155 optimal weight: 0.0000 chunk 244 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 465 optimal weight: 3.9990 overall best weight: 0.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 GLN A1147 ASN A1262 GLN ** B 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 69 ASN D 130 ASN E 101 GLN G 32 ASN G 69 ASN O 597 GLN P 189 ASN Q 44 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 43226 Z= 0.196 Angle : 0.496 6.998 58650 Z= 0.258 Chirality : 0.042 0.177 6624 Planarity : 0.004 0.049 7322 Dihedral : 9.892 142.461 6239 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.03 % Allowed : 7.93 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.12), residues: 5094 helix: 1.06 (0.12), residues: 1887 sheet: 0.06 (0.20), residues: 667 loop : -0.44 (0.12), residues: 2540 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 484 time to evaluate : 4.827 Fit side-chains outliers start: 47 outliers final: 18 residues processed: 499 average time/residue: 1.5599 time to fit residues: 962.0874 Evaluate side-chains 477 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 459 time to evaluate : 4.876 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 4 residues processed: 14 average time/residue: 0.4603 time to fit residues: 17.9380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 258 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 387 optimal weight: 0.7980 chunk 317 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 466 optimal weight: 4.9990 chunk 504 optimal weight: 6.9990 chunk 415 optimal weight: 6.9990 chunk 462 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 374 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 GLN A1262 GLN B 60 GLN B 595 HIS ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN E 101 GLN E 113 GLN ** J 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43226 Z= 0.332 Angle : 0.538 6.749 58650 Z= 0.279 Chirality : 0.044 0.179 6624 Planarity : 0.004 0.051 7322 Dihedral : 10.063 143.272 6239 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.43 % Allowed : 10.41 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.12), residues: 5094 helix: 1.10 (0.12), residues: 1892 sheet: -0.06 (0.20), residues: 683 loop : -0.43 (0.12), residues: 2519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 483 time to evaluate : 5.200 Fit side-chains outliers start: 65 outliers final: 28 residues processed: 510 average time/residue: 1.5787 time to fit residues: 996.6731 Evaluate side-chains 491 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 463 time to evaluate : 4.841 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 10 residues processed: 18 average time/residue: 0.5683 time to fit residues: 23.8891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 461 optimal weight: 4.9990 chunk 350 optimal weight: 3.9990 chunk 242 optimal weight: 0.0170 chunk 51 optimal weight: 0.9990 chunk 222 optimal weight: 0.9990 chunk 313 optimal weight: 1.9990 chunk 468 optimal weight: 3.9990 chunk 495 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 443 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 GLN A1262 GLN A1284 ASN B 595 HIS B 702 GLN ** C 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 69 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 113 GLN G 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43226 Z= 0.175 Angle : 0.477 9.041 58650 Z= 0.249 Chirality : 0.041 0.172 6624 Planarity : 0.003 0.047 7322 Dihedral : 9.938 142.691 6239 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.34 % Allowed : 12.10 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.12), residues: 5094 helix: 1.35 (0.12), residues: 1888 sheet: 0.04 (0.21), residues: 649 loop : -0.34 (0.12), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 481 time to evaluate : 4.534 Fit side-chains outliers start: 61 outliers final: 25 residues processed: 511 average time/residue: 1.4606 time to fit residues: 927.1302 Evaluate side-chains 487 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 462 time to evaluate : 4.917 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 13 residues processed: 14 average time/residue: 0.4641 time to fit residues: 17.8694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 412 optimal weight: 8.9990 chunk 281 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 369 optimal weight: 7.9990 chunk 204 optimal weight: 4.9990 chunk 423 optimal weight: 7.9990 chunk 342 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 253 optimal weight: 3.9990 chunk 445 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 HIS A 828 GLN A1262 GLN A1284 ASN B 595 HIS B 702 GLN C 200 GLN C 234 ASN D 64 ASN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 113 GLN J 53 HIS ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** N 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.096 43226 Z= 0.748 Angle : 0.718 9.751 58650 Z= 0.368 Chirality : 0.053 0.246 6624 Planarity : 0.005 0.055 7322 Dihedral : 10.383 143.726 6239 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.11 % Allowed : 13.01 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 5094 helix: 0.66 (0.12), residues: 1914 sheet: -0.28 (0.20), residues: 696 loop : -0.63 (0.12), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 491 time to evaluate : 4.652 Fit side-chains outliers start: 96 outliers final: 55 residues processed: 544 average time/residue: 1.5564 time to fit residues: 1049.9978 Evaluate side-chains 524 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 469 time to evaluate : 5.064 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 33 residues processed: 23 average time/residue: 0.7249 time to fit residues: 31.8434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 166 optimal weight: 0.7980 chunk 446 optimal weight: 0.0970 chunk 98 optimal weight: 0.9980 chunk 291 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 496 optimal weight: 1.9990 chunk 412 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 164 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A1262 GLN A1284 ASN B 427 ASN B 595 HIS B1148 GLN D 51 ASN D 64 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 101 GLN E 113 GLN M 89 GLN N 392 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43226 Z= 0.188 Angle : 0.514 10.732 58650 Z= 0.267 Chirality : 0.042 0.227 6624 Planarity : 0.004 0.050 7322 Dihedral : 10.102 142.878 6239 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 14.70 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.12), residues: 5094 helix: 1.16 (0.12), residues: 1899 sheet: -0.03 (0.21), residues: 658 loop : -0.44 (0.12), residues: 2537 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 483 time to evaluate : 4.851 Fit side-chains outliers start: 83 outliers final: 43 residues processed: 537 average time/residue: 1.5609 time to fit residues: 1043.7241 Evaluate side-chains 507 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 464 time to evaluate : 4.793 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 34 residues processed: 11 average time/residue: 0.4015 time to fit residues: 15.0257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 478 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 362 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 417 optimal weight: 5.9990 chunk 277 optimal weight: 0.8980 chunk 494 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 828 GLN A1262 GLN A1284 ASN B 595 HIS D 64 ASN ** D 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 101 GLN E 113 GLN G 36 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 43226 Z= 0.373 Angle : 0.567 11.285 58650 Z= 0.292 Chirality : 0.044 0.246 6624 Planarity : 0.004 0.048 7322 Dihedral : 10.168 143.333 6239 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.78 % Allowed : 15.82 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.12), residues: 5094 helix: 1.11 (0.12), residues: 1892 sheet: -0.12 (0.20), residues: 694 loop : -0.46 (0.12), residues: 2508 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 471 time to evaluate : 4.819 Fit side-chains outliers start: 81 outliers final: 56 residues processed: 520 average time/residue: 1.5308 time to fit residues: 989.8162 Evaluate side-chains 526 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 470 time to evaluate : 4.415 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 39 residues processed: 21 average time/residue: 0.7692 time to fit residues: 29.8628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 305 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 295 optimal weight: 0.9990 chunk 148 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 314 optimal weight: 1.9990 chunk 336 optimal weight: 2.9990 chunk 244 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 388 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 828 GLN A1262 GLN A1284 ASN B 595 HIS B 702 GLN D 64 ASN D 133 HIS E 32 GLN E 101 GLN E 113 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43226 Z= 0.196 Angle : 0.509 11.217 58650 Z= 0.264 Chirality : 0.041 0.244 6624 Planarity : 0.003 0.051 7322 Dihedral : 10.060 142.866 6239 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.56 % Allowed : 16.30 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.12), residues: 5094 helix: 1.32 (0.12), residues: 1888 sheet: -0.03 (0.21), residues: 660 loop : -0.36 (0.12), residues: 2546 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 484 time to evaluate : 4.982 Fit side-chains outliers start: 71 outliers final: 49 residues processed: 535 average time/residue: 1.5198 time to fit residues: 1014.7928 Evaluate side-chains 523 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 474 time to evaluate : 5.265 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 41 residues processed: 10 average time/residue: 0.6573 time to fit residues: 17.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 449 optimal weight: 6.9990 chunk 473 optimal weight: 6.9990 chunk 432 optimal weight: 0.9980 chunk 460 optimal weight: 3.9990 chunk 277 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 361 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 416 optimal weight: 6.9990 chunk 435 optimal weight: 0.9980 chunk 459 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN D 64 ASN ** D 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 32 GLN E 101 GLN E 113 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 43226 Z= 0.346 Angle : 0.560 12.121 58650 Z= 0.288 Chirality : 0.044 0.241 6624 Planarity : 0.004 0.053 7322 Dihedral : 10.132 143.083 6239 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.65 % Allowed : 16.39 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.12), residues: 5094 helix: 1.19 (0.12), residues: 1896 sheet: -0.07 (0.20), residues: 680 loop : -0.43 (0.12), residues: 2518 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 469 time to evaluate : 5.118 Fit side-chains outliers start: 75 outliers final: 53 residues processed: 521 average time/residue: 1.5395 time to fit residues: 1001.6433 Evaluate side-chains 523 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 470 time to evaluate : 4.505 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 45 residues processed: 10 average time/residue: 0.6181 time to fit residues: 16.2585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 302 optimal weight: 3.9990 chunk 487 optimal weight: 0.8980 chunk 297 optimal weight: 0.7980 chunk 231 optimal weight: 0.4980 chunk 338 optimal weight: 0.3980 chunk 511 optimal weight: 5.9990 chunk 470 optimal weight: 0.6980 chunk 406 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 249 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN D 64 ASN D 133 HIS E 32 GLN E 101 GLN E 113 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Q 44 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 43226 Z= 0.176 Angle : 0.507 12.117 58650 Z= 0.262 Chirality : 0.041 0.224 6624 Planarity : 0.003 0.055 7322 Dihedral : 10.026 142.822 6239 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.19 % Allowed : 17.05 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.12), residues: 5094 helix: 1.39 (0.12), residues: 1892 sheet: -0.02 (0.21), residues: 642 loop : -0.33 (0.12), residues: 2560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10188 Ramachandran restraints generated. 5094 Oldfield, 0 Emsley, 5094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 477 time to evaluate : 4.889 Fit side-chains outliers start: 54 outliers final: 48 residues processed: 524 average time/residue: 1.4907 time to fit residues: 979.1530 Evaluate side-chains 516 residues out of total 4559 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 468 time to evaluate : 4.922 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 44 residues processed: 8 average time/residue: 0.4661 time to fit residues: 13.5859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 513 random chunks: chunk 323 optimal weight: 2.9990 chunk 433 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 375 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 chunk 407 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 418 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1262 GLN A1284 ASN B 702 GLN D 64 ASN D 69 ASN ** D 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 HIS E 32 GLN E 101 GLN E 113 GLN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 298 ASN Q 44 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.077527 restraints weight = 68631.648| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.03 r_work: 0.3023 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 43226 Z= 0.471 Angle : 0.602 11.856 58650 Z= 0.310 Chirality : 0.046 0.258 6624 Planarity : 0.004 0.056 7322 Dihedral : 10.224 143.128 6239 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.49 % Allowed : 16.85 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.12), residues: 5094 helix: 1.05 (0.12), residues: 1908 sheet: -0.12 (0.20), residues: 697 loop : -0.45 (0.12), residues: 2489 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15637.69 seconds wall clock time: 279 minutes 30.26 seconds (16770.26 seconds total)