Starting phenix.real_space_refine on Thu Apr 11 15:55:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tvy_41655/04_2024/8tvy_41655_updated.pdb" } resolution = 3.1 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= 0.004 sd= 0.105 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 104 5.49 5 Mg 1 5.21 5 S 209 5.16 5 C 24608 2.51 5 N 6890 2.21 5 O 7716 1.98 5 H 37409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 39": "OE1" <-> "OE2" Residue "A TYR 417": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 1153": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 1297": "OE1" <-> "OE2" Residue "A TYR 1298": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 581": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 908": "OE1" <-> "OE2" Residue "B GLU 1070": "OE1" <-> "OE2" Residue "B TYR 1092": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 1153": "OE1" <-> "OE2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E ASP 74": "OD1" <-> "OD2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 112": "OE1" <-> "OE2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G GLU 35": "OE1" <-> "OE2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 54": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 33": "OE1" <-> "OE2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 76945 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 22822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1448, 22822 Classifications: {'peptide': 1448} Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1380} Chain: "B" Number of atoms: 19184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1207, 19184 Classifications: {'peptide': 1207} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 51, 'TRANS': 1154} Chain: "C" Number of atoms: 4212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 4212 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "D" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 164} Chain breaks: 1 Chain: "E" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3545 Classifications: {'peptide': 215} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, '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: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 2694 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "H" Number of atoms: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2282 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 1947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1947 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "J" Number of atoms: 1164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 1164 Classifications: {'peptide': 70} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "K" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1920 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "L" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 750 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'TRANS': 45} Chain: "M" Number of atoms: 9170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 9170 Classifications: {'peptide': 558} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 23, 'TRANS': 532} Chain breaks: 1 Chain: "N" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 965 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "T" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 947 Unusual residues: {'TTD': 1} Classifications: {'DNA': 45, 'undetermined': 1} Link IDs: {'p': 1, 'rna3p': 43, None: 1} Not linked: pdbres=" DC T 17 " pdbres="TTD T 18 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "R" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 220 Classifications: {'RNA': 10} Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 2} Link IDs: {'rna3p': 9} Chain: "O" Number of atoms: 1091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 1091 Classifications: {'peptide': 71} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 69} 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 1550 SG CYS A 107 67.674 49.357 123.074 1.00100.38 S ATOM 1594 SG CYS A 110 67.888 48.826 127.601 1.00 98.55 S ATOM 947 SG CYS A 67 110.684 69.421 115.678 1.00 76.24 S ATOM 1084 SG CYS A 77 109.439 70.475 114.390 1.00 60.70 S ATOM 41013 SG CYS B1163 102.912 55.038 114.352 1.00 47.04 S ATOM 41049 SG CYS B1166 99.633 56.586 116.134 1.00 56.30 S ATOM 41299 SG CYS B1182 103.245 57.489 117.133 1.00 57.34 S ATOM 41338 SG CYS B1185 101.244 54.222 117.823 1.00 65.27 S ATOM 43341 SG CYS C 86 139.041 108.833 67.274 1.00 66.48 S ATOM 43371 SG CYS C 88 137.183 109.638 70.582 1.00 77.75 S ATOM 43425 SG CYS C 92 138.609 112.326 68.310 1.00 55.78 S ATOM 43469 SG CYS C 95 135.439 110.348 67.442 1.00 53.08 S ATOM 58876 SG CYS I 7 17.904 93.980 98.202 1.00145.63 S ATOM 58922 SG CYS I 10 19.032 94.760 101.368 1.00143.08 S ATOM 59244 SG CYS I 29 20.793 90.905 100.536 1.00155.34 S ATOM 59292 SG CYS I 32 19.783 92.977 102.545 1.00157.21 S ATOM 59929 SG CYS I 75 32.162 103.541 56.446 1.00 92.67 S ATOM 59975 SG CYS I 78 29.592 105.729 56.820 1.00 99.06 S ATOM 60399 SG CYS I 103 33.795 106.342 57.651 1.00 84.57 S ATOM 60439 SG CYS I 106 30.839 107.294 57.921 1.00 90.11 S ATOM 60820 SG CYS J 7 106.375 111.992 55.909 1.00 31.80 S ATOM 61417 SG CYS J 45 105.436 110.908 52.210 1.00 30.43 S ATOM 61427 SG CYS J 46 106.289 113.761 52.617 1.00 31.86 S ATOM 63938 SG CYS L 34 104.479 130.836 95.204 1.00 76.21 S ATOM 64196 SG CYS L 51 105.549 131.511 97.055 1.00 75.01 S Time building chain proxies: 24.67, per 1000 atoms: 0.32 Number of scatterers: 76945 At special positions: 0 Unit cell: (157.76, 153.12, 196.04, 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 209 16.00 P 104 15.00 Mg 1 11.99 O 7716 8.00 N 6890 7.00 C 24608 6.00 H 37409 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 148 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS O 25 " - pdb=" SG CYS O 28 " distance=2.01 Simple disulfide: pdb=" SG CYS O 49 " - pdb=" SG CYS O 52 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 49.54 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb=" ZN B2701 " pdb="ZN ZN B2701 " - pdb=" SG CYS B1185 " pdb="ZN ZN B2701 " - pdb=" SG CYS B1166 " pdb="ZN ZN B2701 " - pdb=" SG CYS B1182 " pdb="ZN ZN B2701 " - pdb=" SG CYS B1163 " pdb=" ZN C3001 " pdb="ZN ZN C3001 " - pdb=" SG CYS C 88 " pdb="ZN ZN C3001 " - pdb=" SG CYS C 92 " pdb="ZN ZN C3001 " - pdb=" SG CYS C 86 " pdb="ZN ZN C3001 " - pdb=" SG CYS C 95 " pdb=" ZN I3901 " pdb="ZN ZN I3901 " - pdb=" SG CYS I 32 " pdb="ZN ZN I3901 " - pdb=" SG CYS I 10 " pdb="ZN ZN I3901 " - pdb=" SG CYS I 29 " pdb="ZN ZN I3901 " - pdb=" SG CYS I 7 " pdb=" ZN I3902 " pdb="ZN ZN I3902 " - pdb=" SG CYS I 78 " pdb="ZN ZN I3902 " - pdb=" SG CYS I 106 " pdb="ZN ZN I3902 " - pdb=" SG CYS I 103 " pdb="ZN ZN I3902 " - pdb=" SG CYS I 75 " pdb=" ZN J4001 " pdb="ZN ZN J4001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J4001 " - pdb=" SG CYS J 46 " pdb="ZN ZN J4001 " - pdb=" SG CYS J 7 " pdb=" ZN L4101 " pdb="ZN ZN L4101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L4101 " - pdb=" SG CYS L 51 " Number of angles added : 24 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8816 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 175 helices and 42 sheets defined 34.1% alpha, 11.1% beta 33 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 34.69 Creating SS restraints... Processing helix chain 'A' and resid 24 through 30 Processing helix chain 'A' and resid 74 through 76 No H-bonds generated for 'chain 'A' and resid 74 through 76' Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.788A pdb=" N ILE A 96 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N ALA A 97 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 204 through 213 Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 261 through 281 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 325 through 328 No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 368 through 371 No H-bonds generated for 'chain 'A' and resid 368 through 371' Processing helix chain 'A' and resid 385 through 394 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 507 through 510 Processing helix chain 'A' and resid 525 through 534 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.721A pdb=" N ASN A 548 " --> pdb=" O ASP A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 581 removed outlier: 3.897A pdb=" N ALA A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 636 Processing helix chain 'A' and resid 639 through 660 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 673 through 698 Processing helix chain 'A' and resid 710 through 736 Processing helix chain 'A' and resid 742 through 748 Processing helix chain 'A' and resid 755 through 762 Processing helix chain 'A' and resid 794 through 796 No H-bonds generated for 'chain 'A' and resid 794 through 796' Processing helix chain 'A' and resid 810 through 844 removed outlier: 4.075A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N GLY A 835 " --> pdb=" O THR A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 870 No H-bonds generated for 'chain 'A' and resid 868 through 870' Processing helix chain 'A' and resid 875 through 877 No H-bonds generated for 'chain 'A' and resid 875 through 877' Processing helix chain 'A' and resid 884 through 886 No H-bonds generated for 'chain 'A' and resid 884 through 886' Processing helix chain 'A' and resid 890 through 897 Processing helix chain 'A' and resid 910 through 912 No H-bonds generated for 'chain 'A' and resid 910 through 912' Processing helix chain 'A' and resid 923 through 946 Processing helix chain 'A' and resid 960 through 971 Processing helix chain 'A' and resid 983 through 996 Processing helix chain 'A' and resid 1005 through 1025 removed outlier: 3.517A pdb=" N VAL A1015 " --> pdb=" O GLN A1011 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N LEU A1017 " --> pdb=" O ASP A1013 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N PHE A1018 " --> pdb=" O ALA A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1032 Processing helix chain 'A' and resid 1039 through 1055 Processing helix chain 'A' and resid 1064 through 1078 Proline residue: A1075 - end of helix removed outlier: 3.905A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1105 Processing helix chain 'A' and resid 1129 through 1138 Processing helix chain 'A' and resid 1143 through 1145 No H-bonds generated for 'chain 'A' and resid 1143 through 1145' Processing helix chain 'A' and resid 1164 through 1174 removed outlier: 4.423A pdb=" N GLU A1168 " --> pdb=" O GLU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1204 Processing helix chain 'A' and resid 1209 through 1219 Processing helix chain 'A' and resid 1257 through 1269 Processing helix chain 'A' and resid 1313 through 1318 removed outlier: 4.640A pdb=" N THR A1318 " --> pdb=" O SER A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1339 Processing helix chain 'A' and resid 1341 through 1357 Processing helix chain 'A' and resid 1365 through 1376 Processing helix chain 'A' and resid 1396 through 1400 Processing helix chain 'A' and resid 1405 through 1415 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1437 through 1439 No H-bonds generated for 'chain 'A' and resid 1437 through 1439' Processing helix chain 'A' and resid 1447 through 1453 removed outlier: 4.245A pdb=" N LYS A1452 " --> pdb=" O GLU A1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 Processing helix chain 'B' and resid 45 through 64 removed outlier: 4.642A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 119 Processing helix chain 'B' and resid 145 through 148 No H-bonds generated for 'chain 'B' and resid 145 through 148' Processing helix chain 'B' and resid 150 through 156 Processing helix chain 'B' and resid 186 through 189 No H-bonds generated for 'chain 'B' and resid 186 through 189' Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 282 through 288 Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 338 Processing helix chain 'B' and resid 349 through 358 Processing helix chain 'B' and resid 368 through 389 removed outlier: 4.857A pdb=" N LYS B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 403 No H-bonds generated for 'chain 'B' and resid 401 through 403' Processing helix chain 'B' and resid 409 through 434 Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.816A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N MET B 444 " --> pdb=" O HIS B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 463 removed outlier: 4.269A pdb=" N LYS B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR B 452 " --> pdb=" O ILE B 448 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE B 453 " --> pdb=" O ASN B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 Processing helix chain 'B' and resid 501 through 505 removed outlier: 3.548A pdb=" N ASP B 505 " --> pdb=" O ILE B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 530 through 532 No H-bonds generated for 'chain 'B' and resid 530 through 532' Processing helix chain 'B' and resid 552 through 561 Processing helix chain 'B' and resid 566 through 568 No H-bonds generated for 'chain 'B' and resid 566 through 568' Processing helix chain 'B' and resid 593 through 606 Processing helix chain 'B' and resid 655 through 669 Processing helix chain 'B' and resid 681 through 686 Processing helix chain 'B' and resid 697 through 699 No H-bonds generated for 'chain 'B' and resid 697 through 699' Processing helix chain 'B' and resid 707 through 710 Processing helix chain 'B' and resid 712 through 716 Processing helix chain 'B' and resid 764 through 775 removed outlier: 4.350A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 812 No H-bonds generated for 'chain 'B' and resid 809 through 812' Processing helix chain 'B' and resid 843 through 846 No H-bonds generated for 'chain 'B' and resid 843 through 846' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 996 through 998 No H-bonds generated for 'chain 'B' and resid 996 through 998' Processing helix chain 'B' and resid 1014 through 1020 removed outlier: 3.607A pdb=" N ILE B1017 " --> pdb=" O PRO B1014 " (cutoff:3.500A) Proline residue: B1018 - end of helix No H-bonds generated for 'chain 'B' and resid 1014 through 1020' Processing helix chain 'B' and resid 1023 through 1038 Processing helix chain 'B' and resid 1052 through 1061 Processing helix chain 'B' and resid 1099 through 1101 No H-bonds generated for 'chain 'B' and resid 1099 through 1101' Processing helix chain 'B' and resid 1132 through 1141 Processing helix chain 'B' and resid 1144 through 1152 Processing helix chain 'B' and resid 1198 through 1209 Processing helix chain 'C' and resid 27 through 39 Processing helix chain 'C' and resid 60 through 68 Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 197 through 200 No H-bonds generated for 'chain 'C' and resid 197 through 200' Processing helix chain 'C' and resid 205 through 209 removed outlier: 4.010A pdb=" N GLU C 208 " --> pdb=" O LYS C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 269 Processing helix chain 'D' and resid 16 through 18 No H-bonds generated for 'chain 'D' and resid 16 through 18' Processing helix chain 'D' and resid 52 through 66 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 140 through 150 Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 174 through 182 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 196 through 199 No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 204 through 220 Processing helix chain 'E' and resid 6 through 25 removed outlier: 4.167A pdb=" N ARG E 11 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 36 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 55 through 58 Processing helix chain 'E' and resid 66 through 71 Processing helix chain 'E' and resid 90 through 103 Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.829A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 141 No H-bonds generated for 'chain 'E' and resid 139 through 141' Processing helix chain 'E' and resid 144 through 146 No H-bonds generated for 'chain 'E' and resid 144 through 146' Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 183 through 188 Processing helix chain 'F' and resid 87 through 102 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 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'H' and resid 82 through 86 Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'I' and resid 119 through 121 No H-bonds generated for 'chain 'I' and resid 119 through 121' Processing helix chain 'J' and resid 18 through 26 Processing helix chain 'J' and resid 32 through 38 Processing helix chain 'J' and resid 44 through 51 removed outlier: 4.035A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 62 removed outlier: 4.252A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 9 Processing helix chain 'K' and resid 40 through 52 removed outlier: 4.186A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 83 through 117 removed outlier: 4.611A pdb=" N LEU K 114 " --> pdb=" O ASN K 110 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N ALA K 115 " --> pdb=" O LEU K 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 217 through 225 Processing helix chain 'M' and resid 229 through 231 No H-bonds generated for 'chain 'M' and resid 229 through 231' Processing helix chain 'M' and resid 234 through 249 Processing helix chain 'M' and resid 267 through 272 Processing helix chain 'M' and resid 292 through 296 Processing helix chain 'M' and resid 301 through 314 Processing helix chain 'M' and resid 333 through 341 Processing helix chain 'M' and resid 355 through 368 removed outlier: 3.908A pdb=" N GLN M 360 " --> pdb=" O THR M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 383 through 385 No H-bonds generated for 'chain 'M' and resid 383 through 385' Processing helix chain 'M' and resid 448 through 453 Processing helix chain 'M' and resid 457 through 460 Processing helix chain 'M' and resid 471 through 474 Processing helix chain 'M' and resid 480 through 487 Processing helix chain 'M' and resid 505 through 515 Processing helix chain 'M' and resid 523 through 529 Processing helix chain 'M' and resid 534 through 536 No H-bonds generated for 'chain 'M' and resid 534 through 536' Processing helix chain 'M' and resid 554 through 564 Proline residue: M 563 - end of helix Processing helix chain 'M' and resid 570 through 573 No H-bonds generated for 'chain 'M' and resid 570 through 573' Processing helix chain 'M' and resid 591 through 603 Processing helix chain 'M' and resid 619 through 629 Processing helix chain 'M' and resid 638 through 641 No H-bonds generated for 'chain 'M' and resid 638 through 641' Processing helix chain 'M' and resid 647 through 649 No H-bonds generated for 'chain 'M' and resid 647 through 649' Processing helix chain 'M' and resid 651 through 666 Processing helix chain 'M' and resid 677 through 689 Processing helix chain 'M' and resid 692 through 695 No H-bonds generated for 'chain 'M' and resid 692 through 695' Processing helix chain 'M' and resid 708 through 720 Processing helix chain 'M' and resid 754 through 762 Processing helix chain 'M' and resid 784 through 804 Processing helix chain 'M' and resid 814 through 822 removed outlier: 5.640A pdb=" N ASP M 819 " --> pdb=" O HIS M 815 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER M 822 " --> pdb=" O HIS M 818 " (cutoff:3.500A) Processing helix chain 'O' and resid 66 through 80 Processing sheet with id= A, first strand: chain 'A' and resid 82 through 85 Processing sheet with id= B, first strand: chain 'A' and resid 151 through 153 Processing sheet with id= C, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= D, first strand: chain 'A' and resid 348 through 352 Processing sheet with id= E, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.295A pdb=" N PHE A 468 " --> pdb=" O SER A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.799A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 588 through 591 Processing sheet with id= H, first strand: chain 'A' and resid 879 through 882 Processing sheet with id= I, first strand: chain 'A' and resid 1224 through 1228 removed outlier: 3.557A pdb=" N PHE A1225 " --> pdb=" O ARG A1241 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1283 through 1292 removed outlier: 3.515A pdb=" N ARG A1289 " --> pdb=" O GLU A1301 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 1147 through 1154 removed outlier: 7.007A pdb=" N GLU A1196 " --> pdb=" O ILE A1148 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A1150 " --> pdb=" O ARG A1194 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG A1194 " --> pdb=" O SER A1150 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE A1152 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU A1192 " --> pdb=" O ILE A1152 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 69 through 71 Processing sheet with id= M, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.544A pdb=" N GLY B 168 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 130 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= O, first strand: chain 'B' and resid 203 through 205 Processing sheet with id= P, first strand: chain 'B' and resid 498 through 500 removed outlier: 6.432A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 224 through 227 removed outlier: 6.513A pdb=" N LEU B 258 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL B 237 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL B 256 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU B 239 " --> pdb=" O LEU B 254 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 254 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 580 through 582 removed outlier: 6.474A pdb=" N LEU B 624 " --> pdb=" O PHE B 581 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'B' and resid 793 through 796 removed outlier: 3.646A pdb=" N SER B 853 " --> pdb=" O LYS B 972 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ARG B 969 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N VAL B 949 " --> pdb=" O ARG B 969 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 971 " --> pdb=" O GLY B 947 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N GLY B 947 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 1086 through 1092 removed outlier: 4.248A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B1010 " --> pdb=" O ALA B 826 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 915 through 917 Processing sheet with id= V, first strand: chain 'B' and resid 979 through 981 Processing sheet with id= W, first strand: chain 'B' and resid 1157 through 1163 Processing sheet with id= X, first strand: chain 'B' and resid 839 through 842 removed outlier: 7.619A pdb=" N MET B 841 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THR B 993 " --> pdb=" O MET B 841 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'C' and resid 7 through 13 removed outlier: 7.011A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASN C 231 " --> pdb=" O GLU C 177 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 175 " --> pdb=" O GLU C 233 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'C' and resid 97 through 99 removed outlier: 5.800A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'C' and resid 102 through 104 Processing sheet with id= AB, first strand: chain 'C' and resid 111 through 114 Processing sheet with id= AC, first strand: chain 'D' and resid 36 through 38 Processing sheet with id= AD, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.936A pdb=" N THR E 107 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLU E 81 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE E 109 " --> pdb=" O GLU E 81 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N THR E 131 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N PHE E 110 " --> pdb=" O THR E 131 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLU E 133 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N TYR E 112 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE E 135 " --> pdb=" O TYR E 112 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.855A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N MET E 215 " --> pdb=" O PRO E 176 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE E 178 " --> pdb=" O MET E 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'F' and resid 133 through 137 Processing sheet with id= AG, first strand: chain 'G' and resid 2 through 13 removed outlier: 7.274A pdb=" N PHE G 79 " --> pdb=" O ILE G 45 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ILE G 45 " --> pdb=" O PHE G 79 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 142 through 147 removed outlier: 4.011A pdb=" N VAL G 92 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N CYS G 94 " --> pdb=" O GLY G 98 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N GLY G 98 " --> pdb=" O CYS G 94 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 149 through 152 removed outlier: 4.261A pdb=" N GLY G 149 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 37 through 43 removed outlier: 3.614A pdb=" N GLU H 14 " --> pdb=" O GLU H 27 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA H 29 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N VAL H 12 " --> pdb=" O ALA H 29 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 112 through 114 removed outlier: 4.424A pdb=" N LEU H 125 " --> pdb=" O VAL H 114 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'I' and resid 17 through 19 Processing sheet with id= AM, first strand: chain 'K' and resid 19 through 23 Processing sheet with id= AN, first strand: chain 'M' and resid 317 through 319 removed outlier: 6.396A pdb=" N ARG M 493 " --> pdb=" O GLY M 318 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'M' and resid 725 through 729 removed outlier: 6.623A pdb=" N ALA M 670 " --> pdb=" O PHE M 726 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU M 728 " --> pdb=" O ALA M 670 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LEU M 672 " --> pdb=" O LEU M 728 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG M 744 " --> pdb=" O LEU M 671 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE M 673 " --> pdb=" O ARG M 744 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ILE M 746 " --> pdb=" O PHE M 673 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N SER M 774 " --> pdb=" O ILE M 745 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE M 747 " --> pdb=" O SER M 774 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TYR M 776 " --> pdb=" O ILE M 747 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'O' and resid 35 through 39 removed outlier: 3.810A pdb=" N GLY O 45 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR O 58 " --> pdb=" O GLY O 45 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 32.14 Time building geometry restraints manager: 52.29 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: 37359 1.03 - 1.23: 244 1.23 - 1.42: 16661 1.42 - 1.62: 23294 1.62 - 1.82: 332 Bond restraints: 77890 Sorted by residual: bond pdb=" C2 TTD T 18 " pdb=" N3 TTD T 18 " ideal model delta sigma weight residual 1.510 1.324 0.186 2.00e-02 2.50e+03 8.64e+01 bond pdb=" C2T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.494 1.324 0.170 2.00e-02 2.50e+03 7.24e+01 bond pdb=" C4T TTD T 18 " pdb=" N3T TTD T 18 " ideal model delta sigma weight residual 1.484 1.321 0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" N1 TTD T 18 " pdb=" C2 TTD T 18 " ideal model delta sigma weight residual 1.480 1.326 0.154 2.00e-02 2.50e+03 5.93e+01 bond pdb=" N3 TTD T 18 " pdb=" C4 TTD T 18 " ideal model delta sigma weight residual 1.477 1.327 0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 77885 not shown) Histogram of bond angle deviations from ideal: 64.38 - 79.01: 1 79.01 - 93.64: 4 93.64 - 108.27: 20259 108.27 - 122.90: 111327 122.90 - 137.52: 8814 Bond angle restraints: 140405 Sorted by residual: angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" OP2 DT T 19 " ideal model delta sigma weight residual 108.00 64.38 43.62 3.00e+00 1.11e-01 2.11e+02 angle pdb=" O3' TTD T 18 " pdb=" P DT T 19 " pdb=" OP1 DT T 19 " ideal model delta sigma weight residual 108.00 137.52 -29.52 3.00e+00 1.11e-01 9.69e+01 angle pdb=" C3' TTD T 18 " pdb=" O3' TTD T 18 " pdb=" P DT T 19 " ideal model delta sigma weight residual 120.00 104.94 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" O4P TTD T 18 " pdb=" PB TTD T 18 " pdb=" O5P TTD T 18 " ideal model delta sigma weight residual 106.80 120.32 -13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1R TTD T 18 " pdb=" N1T TTD T 18 " pdb=" C2T TTD T 18 " ideal model delta sigma weight residual 119.94 107.16 12.78 3.00e+00 1.11e-01 1.81e+01 ... (remaining 140400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.81: 34922 30.81 - 61.63: 1454 61.63 - 92.44: 77 92.44 - 123.26: 2 123.26 - 154.07: 2 Dihedral angle restraints: 36457 sinusoidal: 20762 harmonic: 15695 Sorted by residual: dihedral pdb=" CA THR A 44 " pdb=" C THR A 44 " pdb=" N GLN A 45 " pdb=" CA GLN A 45 " ideal model delta harmonic sigma weight residual 180.00 -136.86 -43.14 0 5.00e+00 4.00e-02 7.44e+01 dihedral pdb=" CA GLY O 53 " pdb=" C GLY O 53 " pdb=" N GLN O 54 " pdb=" CA GLN O 54 " ideal model delta harmonic sigma weight residual -180.00 -144.26 -35.74 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CA LYS L 58 " pdb=" C LYS L 58 " pdb=" N ALA L 59 " pdb=" CA ALA L 59 " ideal model delta harmonic sigma weight residual 180.00 146.21 33.79 0 5.00e+00 4.00e-02 4.57e+01 ... (remaining 36454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 4896 0.044 - 0.088: 865 0.088 - 0.132: 389 0.132 - 0.176: 14 0.176 - 0.220: 4 Chirality restraints: 6168 Sorted by residual: chirality pdb=" C6T TTD T 18 " pdb=" C6 TTD T 18 " pdb=" C5T TTD T 18 " pdb=" N1T TTD T 18 " both_signs ideal model delta sigma weight residual False 2.63 2.85 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CB ILE A1445 " pdb=" CA ILE A1445 " pdb=" CG1 ILE A1445 " pdb=" CG2 ILE A1445 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" C3R TTD T 18 " pdb=" C2' TTD T 18 " pdb=" C4R TTD T 18 " pdb=" O3R TTD T 18 " both_signs ideal model delta sigma weight residual False -2.44 -2.64 0.20 2.00e-01 2.50e+01 9.99e-01 ... (remaining 6165 not shown) Planarity restraints: 11273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1R TTD T 18 " 0.453 2.00e-02 2.50e+03 2.91e-01 1.90e+03 pdb=" C2T TTD T 18 " -0.062 2.00e-02 2.50e+03 pdb=" C4T TTD T 18 " 0.104 2.00e-02 2.50e+03 pdb=" C5T TTD T 18 " -0.095 2.00e-02 2.50e+03 pdb=" C6T TTD T 18 " -0.139 2.00e-02 2.50e+03 pdb=" N1T TTD T 18 " -0.347 2.00e-02 2.50e+03 pdb=" N3T TTD T 18 " 0.510 2.00e-02 2.50e+03 pdb=" O2T TTD T 18 " -0.357 2.00e-02 2.50e+03 pdb=" O4T TTD T 18 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' TTD T 18 " 0.090 2.00e-02 2.50e+03 2.22e-01 1.11e+03 pdb=" N1 TTD T 18 " 0.001 2.00e-02 2.50e+03 pdb=" C2 TTD T 18 " 0.040 2.00e-02 2.50e+03 pdb=" O2 TTD T 18 " -0.336 2.00e-02 2.50e+03 pdb=" N3 TTD T 18 " 0.506 2.00e-02 2.50e+03 pdb=" C4 TTD T 18 " 0.072 2.00e-02 2.50e+03 pdb=" O4 TTD T 18 " -0.214 2.00e-02 2.50e+03 pdb=" C5 TTD T 18 " -0.043 2.00e-02 2.50e+03 pdb=" C6 TTD T 18 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A1301 " 0.051 5.00e-02 4.00e+02 7.75e-02 9.61e+00 pdb=" N PRO A1302 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO A1302 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A1302 " 0.042 5.00e-02 4.00e+02 ... (remaining 11270 not shown) Histogram of nonbonded interaction distances: 1.30 - 1.96: 739 1.96 - 2.62: 97181 2.62 - 3.28: 235523 3.28 - 3.94: 303026 3.94 - 4.60: 478468 Nonbonded interactions: 1114937 Sorted by model distance: nonbonded pdb=" HB3 CYS L 34 " pdb="ZN ZN L4101 " model vdw 1.304 1.544 nonbonded pdb=" HB2 CYS A 110 " pdb="ZN ZN A1801 " model vdw 1.306 1.544 nonbonded pdb=" HB2 CYS I 78 " pdb="ZN ZN I3902 " model vdw 1.365 1.544 nonbonded pdb=" O ASP A1446 " pdb=" H SER A1449 " model vdw 1.476 1.850 nonbonded pdb=" O PHE M 512 " pdb=" H PHE M 516 " model vdw 1.482 1.850 ... (remaining 1114932 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: 2.750 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: 0.840 Extract box with map and model: 13.500 Check model and map are aligned: 0.830 Set scattering table: 0.530 Process input model: 234.570 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.210 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: 0.020 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 257.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.005 0.186 40481 Z= 0.284 Angle : 0.616 43.619 55128 Z= 0.315 Chirality : 0.041 0.220 6168 Planarity : 0.006 0.291 6796 Dihedral : 15.606 154.071 15675 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.85 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.13), residues: 4660 helix: 1.05 (0.13), residues: 1620 sheet: -0.87 (0.20), residues: 671 loop : -0.94 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1228 HIS 0.021 0.001 HIS L 53 PHE 0.025 0.001 PHE A 22 TYR 0.034 0.001 TYR B 679 ARG 0.009 0.000 ARG A1281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 4.535 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: symmetry clash revert: 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 487 MET cc_start: 0.9074 (mmm) cc_final: 0.8707 (mmm) REVERT: A 922 ASP cc_start: 0.7240 (m-30) cc_final: 0.6831 (m-30) REVERT: A 1240 CYS cc_start: 0.8335 (m) cc_final: 0.8092 (m) REVERT: A 1265 ASN cc_start: 0.8891 (m110) cc_final: 0.8689 (m110) REVERT: A 1454 MET cc_start: 0.7599 (pmm) cc_final: 0.6124 (tpt) REVERT: B 66 ASP cc_start: 0.7857 (t70) cc_final: 0.7646 (t0) REVERT: B 391 ASP cc_start: 0.7862 (m-30) cc_final: 0.7568 (m-30) REVERT: B 430 ARG cc_start: 0.6761 (mtp180) cc_final: 0.6476 (mtp85) REVERT: C 220 ASP cc_start: 0.8228 (t0) cc_final: 0.7986 (p0) REVERT: D 156 ASP cc_start: 0.8554 (t70) cc_final: 0.8172 (t0) REVERT: D 173 HIS cc_start: 0.7965 (m-70) cc_final: 0.7714 (m-70) REVERT: E 41 ASP cc_start: 0.8500 (t0) cc_final: 0.8297 (t0) REVERT: G 33 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7889 (tm-30) REVERT: M 384 MET cc_start: 0.7605 (pmm) cc_final: 0.7335 (pmm) REVERT: M 559 ASP cc_start: 0.8873 (m-30) cc_final: 0.8642 (m-30) REVERT: O 58 THR cc_start: 0.7919 (t) cc_final: 0.7664 (t) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 1.1006 time to fit residues: 1083.6627 Evaluate side-chains 537 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 537 time to evaluate : 4.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 399 optimal weight: 3.9990 chunk 358 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 370 optimal weight: 0.9990 chunk 143 optimal weight: 0.1980 chunk 225 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 429 optimal weight: 20.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 HIS ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN G 71 ASN ** M 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.0728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 40481 Z= 0.251 Angle : 0.558 7.557 55128 Z= 0.300 Chirality : 0.041 0.200 6168 Planarity : 0.004 0.063 6796 Dihedral : 15.325 154.878 6268 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.51 % Favored : 92.42 % Rotamer: Outliers : 0.56 % Allowed : 5.43 % Favored : 94.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4660 helix: 0.98 (0.13), residues: 1616 sheet: -0.77 (0.20), residues: 660 loop : -0.99 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 31 HIS 0.007 0.001 HIS L 53 PHE 0.024 0.001 PHE B 581 TYR 0.018 0.001 TYR C 114 ARG 0.005 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 548 time to evaluate : 4.560 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 177 ASP cc_start: 0.7859 (t0) cc_final: 0.7522 (p0) REVERT: A 922 ASP cc_start: 0.7133 (m-30) cc_final: 0.6777 (m-30) REVERT: A 1240 CYS cc_start: 0.8466 (m) cc_final: 0.8169 (m) REVERT: A 1265 ASN cc_start: 0.9013 (m110) cc_final: 0.8775 (m110) REVERT: B 391 ASP cc_start: 0.7860 (m-30) cc_final: 0.7581 (m-30) REVERT: B 429 PHE cc_start: 0.8544 (t80) cc_final: 0.8237 (t80) REVERT: B 433 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8093 (mt0) REVERT: C 220 ASP cc_start: 0.8201 (t0) cc_final: 0.7954 (p0) REVERT: D 156 ASP cc_start: 0.8437 (t70) cc_final: 0.8064 (t0) REVERT: E 57 MET cc_start: 0.8457 (mmm) cc_final: 0.8170 (mmp) REVERT: I 36 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7964 (tm-30) REVERT: K 20 LYS cc_start: 0.7980 (mttp) cc_final: 0.7702 (mtmp) REVERT: M 559 ASP cc_start: 0.8866 (m-30) cc_final: 0.8633 (m-30) REVERT: M 568 ARG cc_start: 0.3746 (ttp-170) cc_final: 0.3478 (ttp-170) REVERT: O 48 SER cc_start: 0.8045 (m) cc_final: 0.7774 (p) outliers start: 23 outliers final: 19 residues processed: 557 average time/residue: 1.2298 time to fit residues: 1067.7708 Evaluate side-chains 554 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 534 time to evaluate : 4.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 148 GLU Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 238 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 357 optimal weight: 1.9990 chunk 292 optimal weight: 0.5980 chunk 118 optimal weight: 9.9990 chunk 430 optimal weight: 20.0000 chunk 464 optimal weight: 10.0000 chunk 383 optimal weight: 0.9980 chunk 426 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 345 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS M 313 GLN ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40481 Z= 0.294 Angle : 0.558 8.461 55128 Z= 0.300 Chirality : 0.041 0.174 6168 Planarity : 0.004 0.065 6796 Dihedral : 15.354 155.335 6268 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.62 % Favored : 92.30 % Rotamer: Outliers : 0.77 % Allowed : 6.47 % Favored : 92.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4660 helix: 0.91 (0.13), residues: 1613 sheet: -0.83 (0.20), residues: 668 loop : -1.01 (0.13), residues: 2379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1228 HIS 0.011 0.001 HIS B 572 PHE 0.031 0.002 PHE O 74 TYR 0.022 0.001 TYR O 70 ARG 0.006 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 549 time to evaluate : 4.683 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 175 ARG cc_start: 0.7577 (mmt90) cc_final: 0.7315 (mmp-170) REVERT: A 922 ASP cc_start: 0.7165 (m-30) cc_final: 0.6853 (m-30) REVERT: A 1240 CYS cc_start: 0.8584 (m) cc_final: 0.7976 (m) REVERT: A 1265 ASN cc_start: 0.8991 (m110) cc_final: 0.8753 (m110) REVERT: B 313 MET cc_start: 0.8388 (mtp) cc_final: 0.8059 (mtp) REVERT: B 391 ASP cc_start: 0.7873 (m-30) cc_final: 0.7597 (m-30) REVERT: B 429 PHE cc_start: 0.8569 (t80) cc_final: 0.8230 (t80) REVERT: B 433 GLN cc_start: 0.8395 (OUTLIER) cc_final: 0.8158 (mt0) REVERT: B 884 ARG cc_start: 0.8026 (ptp-170) cc_final: 0.7714 (ptp-170) REVERT: C 220 ASP cc_start: 0.8194 (t0) cc_final: 0.7950 (p0) REVERT: D 156 ASP cc_start: 0.8412 (t70) cc_final: 0.8044 (t0) REVERT: G 99 PHE cc_start: 0.6998 (t80) cc_final: 0.6780 (t80) REVERT: I 36 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8135 (tm-30) REVERT: K 20 LYS cc_start: 0.8001 (mttp) cc_final: 0.7721 (mtmp) REVERT: M 559 ASP cc_start: 0.8876 (m-30) cc_final: 0.8644 (m-30) REVERT: M 568 ARG cc_start: 0.3856 (ttp-170) cc_final: 0.3565 (ttp-170) REVERT: O 48 SER cc_start: 0.8238 (m) cc_final: 0.7923 (p) outliers start: 32 outliers final: 28 residues processed: 562 average time/residue: 1.1621 time to fit residues: 1017.1050 Evaluate side-chains 557 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 528 time to evaluate : 4.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain G residue 31 LEU Chi-restraints excluded: chain G residue 78 VAL Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain M residue 756 THR Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 425 optimal weight: 9.9990 chunk 323 optimal weight: 1.9990 chunk 223 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 288 optimal weight: 0.8980 chunk 431 optimal weight: 9.9990 chunk 457 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 409 optimal weight: 2.9990 chunk 123 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40481 Z= 0.264 Angle : 0.548 8.533 55128 Z= 0.293 Chirality : 0.041 0.164 6168 Planarity : 0.004 0.064 6796 Dihedral : 15.282 155.423 6268 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.49 % Favored : 92.45 % Rotamer: Outliers : 0.85 % Allowed : 7.56 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 4660 helix: 0.91 (0.13), residues: 1618 sheet: -0.84 (0.20), residues: 667 loop : -1.02 (0.13), residues: 2375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.007 0.001 HIS B 110 PHE 0.040 0.001 PHE O 74 TYR 0.016 0.001 TYR C 114 ARG 0.013 0.000 ARG O 84 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 549 time to evaluate : 4.522 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: 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 175 ARG cc_start: 0.7581 (mmt90) cc_final: 0.7306 (mmp-170) REVERT: A 922 ASP cc_start: 0.7206 (m-30) cc_final: 0.6851 (m-30) REVERT: A 1206 ASP cc_start: 0.8544 (t0) cc_final: 0.8342 (t0) REVERT: A 1240 CYS cc_start: 0.8565 (m) cc_final: 0.7967 (m) REVERT: A 1265 ASN cc_start: 0.8973 (m110) cc_final: 0.8727 (m110) REVERT: B 66 ASP cc_start: 0.7868 (t0) cc_final: 0.7526 (t0) REVERT: B 391 ASP cc_start: 0.7864 (m-30) cc_final: 0.7595 (m-30) REVERT: B 429 PHE cc_start: 0.8595 (t80) cc_final: 0.8244 (t80) REVERT: B 433 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8144 (mt0) REVERT: B 572 HIS cc_start: 0.8224 (m90) cc_final: 0.7891 (m90) REVERT: B 884 ARG cc_start: 0.8078 (ptp-170) cc_final: 0.7700 (ptp-170) REVERT: C 220 ASP cc_start: 0.8194 (t0) cc_final: 0.7945 (p0) REVERT: D 156 ASP cc_start: 0.8367 (t70) cc_final: 0.8021 (t0) REVERT: G 33 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8027 (tm-30) REVERT: I 36 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8057 (tm-30) REVERT: M 559 ASP cc_start: 0.8905 (m-30) cc_final: 0.8676 (m-30) REVERT: M 568 ARG cc_start: 0.3883 (ttp-170) cc_final: 0.3486 (ttm170) REVERT: O 48 SER cc_start: 0.8219 (m) cc_final: 0.7937 (p) REVERT: O 74 PHE cc_start: 0.8461 (t80) cc_final: 0.8188 (t80) outliers start: 35 outliers final: 28 residues processed: 561 average time/residue: 1.1411 time to fit residues: 985.8140 Evaluate side-chains 557 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 528 time to evaluate : 4.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain I residue 47 GLU Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain M residue 756 THR Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 380 optimal weight: 0.5980 chunk 259 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 340 optimal weight: 6.9990 chunk 188 optimal weight: 0.9980 chunk 390 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 233 optimal weight: 1.9990 chunk 410 optimal weight: 6.9990 chunk 115 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 427 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS B1193 GLN ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 40481 Z= 0.329 Angle : 0.566 8.840 55128 Z= 0.303 Chirality : 0.042 0.171 6168 Planarity : 0.005 0.064 6796 Dihedral : 15.269 157.219 6268 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 1.16 % Allowed : 8.31 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.13), residues: 4660 helix: 0.84 (0.13), residues: 1616 sheet: -0.89 (0.20), residues: 667 loop : -1.07 (0.13), residues: 2377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 31 HIS 0.007 0.001 HIS A 659 PHE 0.028 0.002 PHE B 581 TYR 0.018 0.001 TYR C 114 ARG 0.006 0.000 ARG A 774 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 536 time to evaluate : 4.543 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8101 (m-80) REVERT: A 175 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7330 (mmp-170) REVERT: A 922 ASP cc_start: 0.7278 (m-30) cc_final: 0.6924 (m-30) REVERT: A 1130 GLN cc_start: 0.7502 (mp10) cc_final: 0.7139 (mp10) REVERT: A 1206 ASP cc_start: 0.8615 (t0) cc_final: 0.8371 (t0) REVERT: A 1240 CYS cc_start: 0.8590 (m) cc_final: 0.7976 (m) REVERT: A 1265 ASN cc_start: 0.8974 (m110) cc_final: 0.8737 (m110) REVERT: B 66 ASP cc_start: 0.7788 (t0) cc_final: 0.7574 (t0) REVERT: B 391 ASP cc_start: 0.7895 (m-30) cc_final: 0.7589 (m-30) REVERT: B 429 PHE cc_start: 0.8591 (t80) cc_final: 0.8237 (t80) REVERT: B 433 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.8149 (mt0) REVERT: B 935 ARG cc_start: 0.7661 (ttm170) cc_final: 0.7360 (ttm170) REVERT: C 220 ASP cc_start: 0.8206 (t0) cc_final: 0.7953 (p0) REVERT: D 156 ASP cc_start: 0.8371 (t70) cc_final: 0.8028 (t0) REVERT: L 42 ARG cc_start: 0.8288 (tpp80) cc_final: 0.8075 (tpp80) REVERT: M 568 ARG cc_start: 0.3776 (ttp-170) cc_final: 0.3399 (ttm170) REVERT: O 48 SER cc_start: 0.8207 (m) cc_final: 0.7941 (p) outliers start: 48 outliers final: 40 residues processed: 563 average time/residue: 1.1539 time to fit residues: 1003.8764 Evaluate side-chains 566 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 524 time to evaluate : 4.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 153 optimal weight: 0.6980 chunk 411 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 268 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 379 optimal weight: 0.9980 chunk 211 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 151 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 ASN ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40481 Z= 0.228 Angle : 0.541 8.193 55128 Z= 0.288 Chirality : 0.041 0.195 6168 Planarity : 0.004 0.064 6796 Dihedral : 15.231 158.127 6268 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.25 % Favored : 92.68 % Rotamer: Outliers : 1.14 % Allowed : 8.72 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 4660 helix: 0.95 (0.13), residues: 1613 sheet: -0.87 (0.20), residues: 666 loop : -0.99 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 31 HIS 0.006 0.001 HIS B 363 PHE 0.039 0.001 PHE O 74 TYR 0.018 0.001 TYR C 114 ARG 0.008 0.000 ARG O 84 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 536 time to evaluate : 4.556 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9051 (OUTLIER) cc_final: 0.7960 (m-80) REVERT: A 39 GLU cc_start: 0.6770 (pp20) cc_final: 0.6566 (pp20) REVERT: A 478 TYR cc_start: 0.8945 (m-80) cc_final: 0.8639 (m-80) REVERT: A 922 ASP cc_start: 0.7158 (m-30) cc_final: 0.6830 (m-30) REVERT: A 1130 GLN cc_start: 0.7407 (mp10) cc_final: 0.7179 (mp10) REVERT: A 1206 ASP cc_start: 0.8640 (t0) cc_final: 0.8386 (t0) REVERT: A 1240 CYS cc_start: 0.8566 (m) cc_final: 0.7908 (m) REVERT: A 1265 ASN cc_start: 0.8959 (m110) cc_final: 0.8726 (m110) REVERT: B 66 ASP cc_start: 0.7818 (t0) cc_final: 0.7569 (t0) REVERT: B 391 ASP cc_start: 0.7879 (m-30) cc_final: 0.7574 (m-30) REVERT: B 429 PHE cc_start: 0.8593 (t80) cc_final: 0.8230 (t80) REVERT: B 433 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: B 705 MET cc_start: 0.8732 (tpp) cc_final: 0.8520 (tpp) REVERT: B 935 ARG cc_start: 0.7666 (ttm170) cc_final: 0.7343 (ttm170) REVERT: C 220 ASP cc_start: 0.8187 (t0) cc_final: 0.7951 (p0) REVERT: D 156 ASP cc_start: 0.8378 (t70) cc_final: 0.8049 (t0) REVERT: G 33 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7886 (tm-30) REVERT: I 61 ASP cc_start: 0.8127 (p0) cc_final: 0.7847 (p0) REVERT: L 42 ARG cc_start: 0.8269 (tpp80) cc_final: 0.8040 (tpp80) REVERT: M 568 ARG cc_start: 0.3758 (ttp-170) cc_final: 0.3370 (ttm170) outliers start: 47 outliers final: 42 residues processed: 562 average time/residue: 1.1818 time to fit residues: 1031.7974 Evaluate side-chains 573 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 529 time to evaluate : 4.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 191 LYS Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 441 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 260 optimal weight: 2.9990 chunk 334 optimal weight: 0.8980 chunk 258 optimal weight: 1.9990 chunk 385 optimal weight: 1.9990 chunk 255 optimal weight: 1.9990 chunk 455 optimal weight: 4.9990 chunk 285 optimal weight: 0.0980 chunk 277 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS J 64 ASN ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 40481 Z= 0.276 Angle : 0.548 8.449 55128 Z= 0.292 Chirality : 0.041 0.166 6168 Planarity : 0.005 0.068 6796 Dihedral : 15.205 159.012 6268 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.75 % Favored : 92.19 % Rotamer: Outliers : 1.33 % Allowed : 9.06 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.13), residues: 4660 helix: 0.95 (0.13), residues: 1606 sheet: -0.98 (0.20), residues: 690 loop : -1.02 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1044 HIS 0.008 0.001 HIS B 110 PHE 0.025 0.001 PHE B 581 TYR 0.018 0.001 TYR C 114 ARG 0.010 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 533 time to evaluate : 4.595 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9064 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: A 39 GLU cc_start: 0.6808 (pp20) cc_final: 0.6591 (pp20) REVERT: A 455 MET cc_start: 0.8045 (mtp) cc_final: 0.7506 (mtp) REVERT: A 922 ASP cc_start: 0.7276 (m-30) cc_final: 0.6941 (m-30) REVERT: A 1206 ASP cc_start: 0.8562 (t0) cc_final: 0.8358 (t0) REVERT: A 1240 CYS cc_start: 0.8570 (m) cc_final: 0.7912 (m) REVERT: A 1265 ASN cc_start: 0.8942 (m110) cc_final: 0.8703 (m110) REVERT: B 66 ASP cc_start: 0.7826 (t0) cc_final: 0.7572 (t0) REVERT: B 391 ASP cc_start: 0.7916 (m-30) cc_final: 0.7612 (m-30) REVERT: B 429 PHE cc_start: 0.8617 (t80) cc_final: 0.8288 (t80) REVERT: B 433 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8129 (mt0) REVERT: B 872 GLU cc_start: 0.7273 (tt0) cc_final: 0.7043 (tt0) REVERT: B 935 ARG cc_start: 0.7620 (ttm170) cc_final: 0.7203 (ttm170) REVERT: C 220 ASP cc_start: 0.8198 (t0) cc_final: 0.7957 (p0) REVERT: D 156 ASP cc_start: 0.8464 (t70) cc_final: 0.8107 (t0) REVERT: G 33 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7938 (tm-30) REVERT: L 42 ARG cc_start: 0.8304 (tpp80) cc_final: 0.8078 (tpp80) REVERT: M 568 ARG cc_start: 0.3753 (ttp-170) cc_final: 0.3359 (ttm170) outliers start: 55 outliers final: 46 residues processed: 566 average time/residue: 1.1198 time to fit residues: 974.1614 Evaluate side-chains 575 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 527 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 282 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 272 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 289 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 358 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40481 Z= 0.232 Angle : 0.538 7.949 55128 Z= 0.287 Chirality : 0.040 0.163 6168 Planarity : 0.004 0.069 6796 Dihedral : 15.185 158.782 6268 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.32 % Favored : 92.62 % Rotamer: Outliers : 1.26 % Allowed : 9.30 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.13), residues: 4660 helix: 1.01 (0.13), residues: 1606 sheet: -1.00 (0.20), residues: 701 loop : -0.97 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1228 HIS 0.008 0.001 HIS B 110 PHE 0.022 0.001 PHE B 581 TYR 0.019 0.001 TYR H 116 ARG 0.009 0.000 ARG A 677 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 537 time to evaluate : 4.542 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9045 (OUTLIER) cc_final: 0.7883 (m-80) REVERT: A 39 GLU cc_start: 0.6799 (pp20) cc_final: 0.6574 (pp20) REVERT: A 455 MET cc_start: 0.8001 (mtp) cc_final: 0.7392 (mtp) REVERT: A 478 TYR cc_start: 0.8948 (m-80) cc_final: 0.8644 (m-80) REVERT: A 922 ASP cc_start: 0.7256 (m-30) cc_final: 0.6943 (m-30) REVERT: A 1206 ASP cc_start: 0.8595 (t0) cc_final: 0.8386 (t0) REVERT: A 1240 CYS cc_start: 0.8565 (m) cc_final: 0.7891 (m) REVERT: A 1265 ASN cc_start: 0.8940 (m110) cc_final: 0.8705 (m110) REVERT: B 66 ASP cc_start: 0.7809 (t0) cc_final: 0.7542 (t0) REVERT: B 391 ASP cc_start: 0.7895 (m-30) cc_final: 0.7595 (m-30) REVERT: B 429 PHE cc_start: 0.8623 (t80) cc_final: 0.8301 (t80) REVERT: B 433 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8141 (mt0) REVERT: B 908 GLU cc_start: 0.7410 (tp30) cc_final: 0.7154 (tp30) REVERT: B 935 ARG cc_start: 0.7612 (ttm170) cc_final: 0.7189 (ttm170) REVERT: C 220 ASP cc_start: 0.8186 (t0) cc_final: 0.7947 (p0) REVERT: D 156 ASP cc_start: 0.8496 (t70) cc_final: 0.8148 (t0) REVERT: G 33 GLU cc_start: 0.8255 (tm-30) cc_final: 0.7929 (tm-30) REVERT: L 42 ARG cc_start: 0.8293 (tpp80) cc_final: 0.8062 (tpp80) REVERT: M 568 ARG cc_start: 0.3747 (ttp-170) cc_final: 0.3350 (ttm170) outliers start: 52 outliers final: 46 residues processed: 567 average time/residue: 1.1315 time to fit residues: 986.6474 Evaluate side-chains 574 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 526 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 226 PHE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 414 optimal weight: 9.9990 chunk 436 optimal weight: 4.9990 chunk 398 optimal weight: 2.9990 chunk 424 optimal weight: 10.0000 chunk 255 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 333 optimal weight: 0.0770 chunk 130 optimal weight: 1.9990 chunk 383 optimal weight: 1.9990 chunk 401 optimal weight: 0.8980 chunk 423 optimal weight: 0.7980 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40481 Z= 0.265 Angle : 0.547 9.406 55128 Z= 0.291 Chirality : 0.041 0.165 6168 Planarity : 0.005 0.068 6796 Dihedral : 15.163 158.835 6268 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.60 % Favored : 92.34 % Rotamer: Outliers : 1.40 % Allowed : 9.44 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4660 helix: 0.97 (0.13), residues: 1618 sheet: -0.97 (0.20), residues: 690 loop : -1.01 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1228 HIS 0.008 0.001 HIS B 110 PHE 0.024 0.001 PHE B 581 TYR 0.019 0.001 TYR C 114 ARG 0.009 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 530 time to evaluate : 4.529 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9044 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: A 39 GLU cc_start: 0.6818 (pp20) cc_final: 0.6580 (pp20) REVERT: A 455 MET cc_start: 0.8040 (mtp) cc_final: 0.7507 (mtp) REVERT: A 478 TYR cc_start: 0.8957 (m-80) cc_final: 0.8649 (m-80) REVERT: A 922 ASP cc_start: 0.7286 (m-30) cc_final: 0.6966 (m-30) REVERT: A 1240 CYS cc_start: 0.8579 (m) cc_final: 0.7898 (m) REVERT: A 1265 ASN cc_start: 0.8939 (m110) cc_final: 0.8704 (m110) REVERT: B 53 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7500 (tt0) REVERT: B 66 ASP cc_start: 0.7819 (t0) cc_final: 0.7543 (t0) REVERT: B 391 ASP cc_start: 0.7908 (m-30) cc_final: 0.7604 (m-30) REVERT: B 429 PHE cc_start: 0.8629 (t80) cc_final: 0.8305 (t80) REVERT: B 433 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: B 879 ARG cc_start: 0.8514 (mmt180) cc_final: 0.8255 (tpp-160) REVERT: B 908 GLU cc_start: 0.7432 (tp30) cc_final: 0.7192 (tp30) REVERT: C 220 ASP cc_start: 0.8194 (t0) cc_final: 0.7953 (p0) REVERT: D 156 ASP cc_start: 0.8507 (t70) cc_final: 0.8157 (t0) REVERT: G 33 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7940 (tm-30) REVERT: L 42 ARG cc_start: 0.8306 (tpp80) cc_final: 0.8069 (tpp80) REVERT: M 568 ARG cc_start: 0.3730 (ttp-170) cc_final: 0.3334 (ttm170) outliers start: 58 outliers final: 52 residues processed: 566 average time/residue: 1.1510 time to fit residues: 1009.4728 Evaluate side-chains 580 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 525 time to evaluate : 4.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1113 THR Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 790 ASP Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 32 CYS Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 35 SER Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 278 optimal weight: 0.9980 chunk 449 optimal weight: 20.0000 chunk 274 optimal weight: 0.6980 chunk 213 optimal weight: 1.9990 chunk 312 optimal weight: 0.8980 chunk 471 optimal weight: 10.0000 chunk 433 optimal weight: 9.9990 chunk 375 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 289 optimal weight: 1.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 316 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 40481 Z= 0.241 Angle : 0.542 9.123 55128 Z= 0.289 Chirality : 0.041 0.174 6168 Planarity : 0.004 0.067 6796 Dihedral : 15.135 158.380 6268 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.38 % Favored : 92.55 % Rotamer: Outliers : 1.23 % Allowed : 9.93 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.13), residues: 4660 helix: 1.00 (0.13), residues: 1617 sheet: -0.98 (0.20), residues: 691 loop : -0.95 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 201 HIS 0.006 0.001 HIS G 158 PHE 0.022 0.001 PHE B 581 TYR 0.019 0.001 TYR C 114 ARG 0.009 0.000 ARG F 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9320 Ramachandran restraints generated. 4660 Oldfield, 0 Emsley, 4660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 530 time to evaluate : 4.609 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 22 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.7849 (m-80) REVERT: A 39 GLU cc_start: 0.6809 (pp20) cc_final: 0.6578 (pp20) REVERT: A 122 MET cc_start: 0.8242 (ttm) cc_final: 0.8034 (ttm) REVERT: A 455 MET cc_start: 0.8016 (mtp) cc_final: 0.7459 (mtp) REVERT: A 478 TYR cc_start: 0.8950 (m-80) cc_final: 0.8646 (m-80) REVERT: A 922 ASP cc_start: 0.7253 (m-30) cc_final: 0.6971 (m-30) REVERT: A 1240 CYS cc_start: 0.8567 (m) cc_final: 0.7872 (m) REVERT: A 1265 ASN cc_start: 0.8934 (m110) cc_final: 0.8698 (m110) REVERT: B 53 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: B 66 ASP cc_start: 0.7852 (t0) cc_final: 0.7584 (t0) REVERT: B 391 ASP cc_start: 0.7898 (m-30) cc_final: 0.7596 (m-30) REVERT: B 429 PHE cc_start: 0.8682 (t80) cc_final: 0.8365 (t80) REVERT: B 433 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8157 (mt0) REVERT: B 872 GLU cc_start: 0.7248 (tt0) cc_final: 0.6986 (tt0) REVERT: C 220 ASP cc_start: 0.8188 (t0) cc_final: 0.7947 (p0) REVERT: D 156 ASP cc_start: 0.8505 (t70) cc_final: 0.8155 (t0) REVERT: G 33 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7932 (tm-30) REVERT: L 42 ARG cc_start: 0.8237 (tpp80) cc_final: 0.7966 (tpp80) REVERT: M 568 ARG cc_start: 0.3857 (ttp-170) cc_final: 0.3445 (ttm170) outliers start: 51 outliers final: 48 residues processed: 558 average time/residue: 1.1252 time to fit residues: 976.0007 Evaluate side-chains 572 residues out of total 4140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 521 time to evaluate : 4.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 64 ASN Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain A residue 614 PHE Chi-restraints excluded: chain A residue 755 PHE Chi-restraints excluded: chain A residue 1214 GLU Chi-restraints excluded: chain A residue 1287 TYR Chi-restraints excluded: chain A residue 1308 THR Chi-restraints excluded: chain A residue 1454 MET Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 177 LYS Chi-restraints excluded: chain B residue 190 TYR Chi-restraints excluded: chain B residue 310 MET Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 516 ASN Chi-restraints excluded: chain B residue 755 ILE Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 896 ASP Chi-restraints excluded: chain B residue 932 HIS Chi-restraints excluded: chain B residue 953 LEU Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 114 TYR Chi-restraints excluded: chain E residue 54 GLN Chi-restraints excluded: chain E residue 84 ASP Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain G residue 53 ASN Chi-restraints excluded: chain G residue 90 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain H residue 41 ASP Chi-restraints excluded: chain H residue 46 LEU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain K residue 35 PHE Chi-restraints excluded: chain K residue 71 PHE Chi-restraints excluded: chain M residue 304 CYS Chi-restraints excluded: chain M residue 621 ASP Chi-restraints excluded: chain O residue 25 CYS Chi-restraints excluded: chain O residue 28 CYS Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 58 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 298 optimal weight: 9.9990 chunk 399 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 345 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 375 optimal weight: 0.3980 chunk 157 optimal weight: 10.0000 chunk 385 optimal weight: 0.6980 chunk 47 optimal weight: 0.4980 chunk 69 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 316 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 HIS ** M 610 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.177234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.109639 restraints weight = 153727.464| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.27 r_work: 0.3270 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 40481 Z= 0.170 Angle : 0.524 8.733 55128 Z= 0.278 Chirality : 0.040 0.164 6168 Planarity : 0.004 0.071 6796 Dihedral : 15.084 157.799 6268 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.89 % Favored : 93.05 % Rotamer: Outliers : 1.16 % Allowed : 10.24 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.51 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.13), residues: 4660 helix: 1.11 (0.14), residues: 1625 sheet: -0.88 (0.20), residues: 687 loop : -0.91 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 201 HIS 0.009 0.001 HIS B 110 PHE 0.023 0.001 PHE G 109 TYR 0.017 0.001 TYR C 114 ARG 0.010 0.000 ARG B 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18379.60 seconds wall clock time: 317 minutes 9.31 seconds (19029.31 seconds total)