Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 23 02:43:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a57_15161/08_2023/8a57_15161_neut_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 K 1 8.98 5 Zn 2 6.06 5 P 3025 5.49 5 Mg 160 5.21 5 S 85 5.16 5 C 46337 2.51 5 N 17160 2.21 5 O 25990 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 61": "OE1" <-> "OE2" Residue "4 PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 38": "OE1" <-> "OE2" Residue "4 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 50": "OD1" <-> "OD2" Residue "9 GLU 12": "OE1" <-> "OE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 180": "OE1" <-> "OE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 159": "OE1" <-> "OE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 113": "OD1" <-> "OD2" Residue "J ARG 115": "NH1" <-> "NH2" Residue "J PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 140": "OE1" <-> "OE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 40": "OE1" <-> "OE2" Residue "K PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 91": "OE1" <-> "OE2" Residue "P PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 45": "OE1" <-> "OE2" Residue "Q ASP 55": "OD1" <-> "OD2" Residue "R TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R GLU 114": "OE1" <-> "OE2" Residue "S GLU 38": "OE1" <-> "OE2" Residue "S PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 97": "OD1" <-> "OD2" Residue "T ASP 102": "OD1" <-> "OD2" Residue "T PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 63": "OE1" <-> "OE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 114": "OE1" <-> "OE2" Residue "W GLU 14": "OE1" <-> "OE2" Residue "W TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 85": "OD1" <-> "OD2" Residue "X TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 78": "OE1" <-> "OE2" Residue "D GLU 2": "OE1" <-> "OE2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 23": "OE1" <-> "OE2" Residue "D GLU 34": "OE1" <-> "OE2" Residue "D GLU 38": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 65": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ASP 96": "OD1" <-> "OD2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D ASP 136": "OD1" <-> "OD2" Residue "D ASP 138": "OD1" <-> "OD2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D GLU 157": "OE1" <-> "OE2" Residue "D ARG 160": "NH1" <-> "NH2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D GLU 182": "OE1" <-> "OE2" Residue "D GLU 192": "OE1" <-> "OE2" Residue "D TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 219": "OE1" <-> "OE2" Residue "D PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ASP 229": "OD1" <-> "OD2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 241": "OE1" <-> "OE2" Residue "D PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "D TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 291": "OD1" <-> "OD2" Residue "D GLU 302": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 311": "OE1" <-> "OE2" Residue "D TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 326": "OE1" <-> "OE2" Residue "D GLU 328": "OE1" <-> "OE2" Residue "D TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 345": "OE1" <-> "OE2" Residue "D GLU 346": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "D PHE 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 353": "OE1" <-> "OE2" Residue "D GLU 358": "OE1" <-> "OE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D GLU 373": "OE1" <-> "OE2" Residue "D TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 383": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "D GLU 391": "OE1" <-> "OE2" Residue "D GLU 394": "OE1" <-> "OE2" Residue "D GLU 402": "OE1" <-> "OE2" Residue "D GLU 413": "OE1" <-> "OE2" Residue "D TYR 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 90": "OE1" <-> "OE2" Residue "E GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 92760 Number of models: 1 Model: "" Number of chains: 39 Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "2" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 487 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "3" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "4" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 477 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "5" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "6" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 400 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "7" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 357 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "8" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "9" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "A" Number of atoms: 62459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2908, 62459 Classifications: {'RNA': 2908} Modifications used: {'rna2p_pur': 307, 'rna2p_pyr': 142, 'rna3p_pur': 1395, 'rna3p_pyr': 1064} Link IDs: {'rna2p': 448, 'rna3p': 2459} Chain breaks: 2 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 12, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "G" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1582 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1563 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "J" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1365 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1271 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "M" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1117 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1094 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "P" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "Q" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 983 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "R" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "S" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 905 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "T" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "W" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 731 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "X" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 723 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "Z" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 563 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "D" Number of atoms: 3310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3310 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 10, 'TRANS': 403} Chain: "E" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1032 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 129} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 178 Unusual residues: {' MG': 156, 'PUT': 2, 'SPD': 1} Classifications: {'undetermined': 159} Link IDs: {None: 158} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2093 SG CYS 5 30 196.235 134.602 128.414 1.00104.58 S ATOM 2113 SG CYS 5 33 195.574 134.813 132.392 1.00143.17 S ATOM 2196 SG CYS 5 43 193.640 136.951 130.253 1.00134.80 S ATOM 2218 SG CYS 5 46 196.895 136.348 132.272 1.00150.30 S ATOM 3633 SG CYS 9 11 117.977 98.940 55.085 1.00 66.42 S ATOM 3657 SG CYS 9 14 120.225 97.962 58.270 1.00 62.64 S ATOM 3761 SG CYS 9 27 121.137 100.381 55.435 1.00 56.37 S Time building chain proxies: 33.54, per 1000 atoms: 0.36 Number of scatterers: 92760 At special positions: 0 Unit cell: (217.3, 208.28, 240.26, 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 2 29.99 K 1 19.00 S 85 16.00 P 3025 15.00 Mg 160 11.99 O 25990 8.00 N 17160 7.00 C 46337 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 6 12 " - pdb=" SG CYS 6 36 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.93 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 30 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 33 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 46 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 43 " pdb=" ZN 9 101 " pdb="ZN ZN 9 101 " - pdb=" ND1 HIS 9 32 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 14 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 27 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 11 " Number of angles added : 9 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6460 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 51 sheets defined 26.4% alpha, 19.1% beta 977 base pairs and 1595 stacking pairs defined. Time for finding SS restraints: 44.23 Creating SS restraints... Processing helix chain '1' and resid 51 through 54 No H-bonds generated for 'chain '1' and resid 51 through 54' Processing helix chain '2' and resid 4 through 8 removed outlier: 3.586A pdb=" N ASP 2 8 " --> pdb=" O ASN 2 4 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 4 through 8' Processing helix chain '2' and resid 11 through 33 Processing helix chain '2' and resid 40 through 60 removed outlier: 3.566A pdb=" N ARG 2 44 " --> pdb=" O ALA 2 41 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 25 Processing helix chain '3' and resid 41 through 50 Processing helix chain '5' and resid 10 through 18 Processing helix chain '7' and resid 9 through 16 Processing helix chain '7' and resid 18 through 23 Processing helix chain '7' and resid 25 through 37 Processing helix chain '8' and resid 8 through 11 No H-bonds generated for 'chain '8' and resid 8 through 11' Processing helix chain '8' and resid 38 through 45 Processing helix chain '8' and resid 52 through 62 removed outlier: 5.737A pdb=" N GLN 8 60 " --> pdb=" O LYS 8 56 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N MET 8 61 " --> pdb=" O ARG 8 57 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 8 62 " --> pdb=" O ILE 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 30 through 32 No H-bonds generated for 'chain '9' and resid 30 through 32' Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 132 through 134 No H-bonds generated for 'chain 'G' and resid 132 through 134' Processing helix chain 'G' and resid 198 through 202 removed outlier: 4.258A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 265 through 268 removed outlier: 4.073A pdb=" N LYS G 268 " --> pdb=" O ASN G 265 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 265 through 268' Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 63 through 72 removed outlier: 4.313A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ALA H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'I' and resid 30 through 43 Processing helix chain 'I' and resid 103 through 120 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 163 through 166 No H-bonds generated for 'chain 'I' and resid 163 through 166' Processing helix chain 'I' and resid 178 through 180 No H-bonds generated for 'chain 'I' and resid 178 through 180' Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 196 through 205 removed outlier: 3.601A pdb=" N VAL I 205 " --> pdb=" O LYS I 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 11 Processing helix chain 'J' and resid 14 through 20 Processing helix chain 'J' and resid 48 through 60 removed outlier: 3.637A pdb=" N LEU J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA J 58 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 101 through 105 Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 163 through 173 removed outlier: 3.621A pdb=" N HIS J 167 " --> pdb=" O GLU J 164 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLU J 168 " --> pdb=" O GLU J 165 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU J 170 " --> pdb=" O HIS J 167 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR J 171 " --> pdb=" O GLU J 168 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 80 Processing helix chain 'K' and resid 138 through 151 Processing helix chain 'M' and resid 26 through 38 removed outlier: 6.060A pdb=" N SER M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 114 through 122 removed outlier: 3.669A pdb=" N LYS M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS M 122 " --> pdb=" O GLN M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'N' and resid 104 through 107 Processing helix chain 'N' and resid 112 through 115 No H-bonds generated for 'chain 'N' and resid 112 through 115' Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 57 through 60 No H-bonds generated for 'chain 'O' and resid 57 through 60' Processing helix chain 'O' and resid 79 through 84 removed outlier: 3.605A pdb=" N ASN O 83 " --> pdb=" O ASP O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 93 through 98 Processing helix chain 'O' and resid 130 through 139 removed outlier: 3.562A pdb=" N GLU O 137 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA O 138 " --> pdb=" O GLU O 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 58 removed outlier: 3.692A pdb=" N TYR P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 124 removed outlier: 4.061A pdb=" N LYS P 124 " --> pdb=" O LEU P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 27 Processing helix chain 'Q' and resid 34 through 53 removed outlier: 4.497A pdb=" N LYS Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 64 Processing helix chain 'Q' and resid 94 through 100 Processing helix chain 'Q' and resid 103 through 106 Processing helix chain 'R' and resid 7 through 19 removed outlier: 3.618A pdb=" N ARG R 17 " --> pdb=" O LYS R 13 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 87 Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'S' and resid 4 through 12 removed outlier: 4.972A pdb=" N SER S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 56 No H-bonds generated for 'chain 'S' and resid 54 through 56' Processing helix chain 'S' and resid 98 through 101 Processing helix chain 'T' and resid 9 through 21 Processing helix chain 'T' and resid 26 through 29 Processing helix chain 'T' and resid 32 through 72 removed outlier: 3.743A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 Processing helix chain 'T' and resid 92 through 101 Processing helix chain 'T' and resid 103 through 116 Processing helix chain 'V' and resid 19 through 29 removed outlier: 4.197A pdb=" N VAL V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU V 28 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE V 29 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 43 Processing helix chain 'V' and resid 47 through 65 removed outlier: 4.400A pdb=" N ILE V 51 " --> pdb=" O SER V 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 18 Processing helix chain 'W' and resid 35 through 46 Processing helix chain 'X' and resid 65 through 67 No H-bonds generated for 'chain 'X' and resid 65 through 67' Processing helix chain 'D' and resid 17 through 30 Processing helix chain 'D' and resid 54 through 66 removed outlier: 3.850A pdb=" N ASP D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 65 " --> pdb=" O LYS D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 removed outlier: 3.683A pdb=" N LEU D 86 " --> pdb=" O GLN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 112 through 136 Proline residue: D 128 - end of helix removed outlier: 4.366A pdb=" N GLN D 133 " --> pdb=" O ARG D 129 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 179 Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.913A pdb=" N LYS D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ARG D 188 " --> pdb=" O ARG D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 266 through 273 removed outlier: 4.407A pdb=" N SER D 272 " --> pdb=" O LYS D 268 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR D 273 " --> pdb=" O ALA D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 278 No H-bonds generated for 'chain 'D' and resid 275 through 278' Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.584A pdb=" N VAL D 307 " --> pdb=" O GLU D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 324 No H-bonds generated for 'chain 'D' and resid 322 through 324' Processing helix chain 'D' and resid 345 through 358 removed outlier: 3.532A pdb=" N GLU D 358 " --> pdb=" O VAL D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 384 removed outlier: 3.573A pdb=" N GLY D 375 " --> pdb=" O PHE D 372 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N GLN D 376 " --> pdb=" O GLU D 373 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N HIS D 384 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 removed outlier: 3.648A pdb=" N LYS D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 27 No H-bonds generated for 'chain 'E' and resid 24 through 27' Processing helix chain 'E' and resid 35 through 38 Processing helix chain 'E' and resid 41 through 44 Processing helix chain 'E' and resid 74 through 79 removed outlier: 3.568A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 110 removed outlier: 3.847A pdb=" N GLU E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 4.638A pdb=" N VAL E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '1' and resid 13 through 18 Processing sheet with id= B, first strand: chain '1' and resid 33 through 41 removed outlier: 6.064A pdb=" N LYS 1 43 " --> pdb=" O VAL 1 40 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '3' and resid 34 through 37 removed outlier: 3.523A pdb=" N GLU 3 5 " --> pdb=" O LYS 3 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain '4' and resid 44 through 48 removed outlier: 3.623A pdb=" N VAL 4 15 " --> pdb=" O LEU 4 46 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE 4 23 " --> pdb=" O PHE 4 14 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '5' and resid 27 through 29 Processing sheet with id= F, first strand: chain '6' and resid 17 through 21 removed outlier: 4.200A pdb=" N TYR 6 17 " --> pdb=" O LEU 6 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '8' and resid 23 through 25 Processing sheet with id= H, first strand: chain '9' and resid 15 through 19 Processing sheet with id= I, first strand: chain 'G' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'G' and resid 34 through 37 removed outlier: 4.020A pdb=" N LEU G 37 " --> pdb=" O ARG G 60 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N ARG G 60 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 101 through 105 removed outlier: 3.646A pdb=" N THR G 80 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASN G 95 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N VAL G 78 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 129 through 131 Processing sheet with id= M, first strand: chain 'G' and resid 181 through 185 removed outlier: 6.345A pdb=" N ARG G 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N VAL G 164 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 168 through 175 removed outlier: 5.782A pdb=" N ILE H 108 " --> pdb=" O ASN H 173 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LEU H 199 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL H 27 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N MET H 12 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL H 25 " --> pdb=" O MET H 12 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN H 14 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE H 23 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS H 189 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE H 176 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 80 through 84 removed outlier: 6.162A pdb=" N GLY H 52 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL H 35 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 123 through 126 removed outlier: 6.161A pdb=" N LEU I 192 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU I 126 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE I 194 " --> pdb=" O LEU I 126 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR I 174 " --> pdb=" O ILE I 154 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL I 156 " --> pdb=" O THR I 174 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE I 176 " --> pdb=" O VAL I 156 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 5 through 7 Processing sheet with id= R, first strand: chain 'J' and resid 88 through 91 removed outlier: 4.076A pdb=" N MET J 152 " --> pdb=" O VAL J 132 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL J 132 " --> pdb=" O MET J 152 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL J 154 " --> pdb=" O LEU J 130 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 16 through 19 Processing sheet with id= T, first strand: chain 'K' and resid 42 through 45 Processing sheet with id= U, first strand: chain 'K' and resid 161 through 164 Processing sheet with id= V, first strand: chain 'K' and resid 95 through 98 Processing sheet with id= W, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.464A pdb=" N PHE M 54 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE M 19 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE M 56 " --> pdb=" O ILE M 19 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'M' and resid 74 through 78 Processing sheet with id= Y, first strand: chain 'N' and resid 7 through 9 removed outlier: 6.703A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'O' and resid 75 through 78 Processing sheet with id= AA, first strand: chain 'P' and resid 129 through 133 removed outlier: 3.860A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA P 36 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ILE P 102 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.546A pdb=" N ALA P 89 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 29 through 33 removed outlier: 5.994A pdb=" N ILE Q 131 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N GLU Q 133 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE Q 116 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 70 through 73 removed outlier: 7.057A pdb=" N VAL Q 92 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 93 through 95 removed outlier: 3.560A pdb=" N VAL R 33 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA R 54 " --> pdb=" O ILE R 44 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP R 46 " --> pdb=" O THR R 52 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N THR R 52 " --> pdb=" O ASP R 46 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'S' and resid 83 through 88 removed outlier: 3.791A pdb=" N LYS S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N THR S 25 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG S 37 " --> pdb=" O GLU S 34 " (cutoff:3.500A) removed outlier: 9.197A pdb=" N GLU S 44 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ILE S 64 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N THR S 60 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG S 50 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR S 58 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'U' and resid 10 through 15 removed outlier: 6.913A pdb=" N GLU U 6 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL U 38 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 19 through 22 removed outlier: 3.518A pdb=" N LYS U 64 " --> pdb=" O LYS U 94 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'U' and resid 32 through 35 removed outlier: 6.374A pdb=" N LYS U 61 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE U 97 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'U' and resid 71 through 77 removed outlier: 4.144A pdb=" N TYR U 82 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 7 through 12 removed outlier: 6.455A pdb=" N SER V 113 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL V 76 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 87 through 92 Processing sheet with id= AM, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.884A pdb=" N GLU W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 62 through 65 removed outlier: 4.092A pdb=" N TYR W 68 " --> pdb=" O MET W 65 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'X' and resid 20 through 22 removed outlier: 5.721A pdb=" N LYS X 8 " --> pdb=" O LEU X 71 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU X 70 " --> pdb=" O THR X 79 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU X 77 " --> pdb=" O ASP X 72 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'X' and resid 40 through 45 Processing sheet with id= AQ, first strand: chain 'X' and resid 82 through 86 removed outlier: 3.636A pdb=" N LYS X 86 " --> pdb=" O LYS X 89 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS X 89 " --> pdb=" O LYS X 86 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'X' and resid 23 through 27 removed outlier: 6.792A pdb=" N LEU X 34 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ALA X 26 " --> pdb=" O ARG X 32 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ARG X 32 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Z' and resid 59 through 61 Processing sheet with id= AT, first strand: chain 'Z' and resid 74 through 81 removed outlier: 5.798A pdb=" N LYS Z 84 " --> pdb=" O MET Z 80 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'D' and resid 93 through 96 removed outlier: 4.028A pdb=" N LEU D 71 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N ILE D 7 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU D 38 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLY D 9 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ARG D 40 " --> pdb=" O GLY D 9 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'D' and resid 332 through 334 removed outlier: 9.058A pdb=" N ILE D 338 " --> pdb=" O VAL D 315 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N TYR D 317 " --> pdb=" O ILE D 338 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU D 283 " --> pdb=" O ILE D 316 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA D 318 " --> pdb=" O LEU D 283 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS D 285 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASN D 320 " --> pdb=" O HIS D 285 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL D 287 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N VAL D 196 " --> pdb=" O GLN D 249 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LEU D 251 " --> pdb=" O VAL D 196 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N LEU D 198 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR D 253 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 8.885A pdb=" N GLY D 200 " --> pdb=" O THR D 253 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'D' and resid 364 through 371 removed outlier: 3.635A pdb=" N GLU D 389 " --> pdb=" O VAL D 400 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLU D 402 " --> pdb=" O ILE D 387 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N ILE D 387 " --> pdb=" O GLU D 402 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'E' and resid 7 through 12 removed outlier: 3.818A pdb=" N THR E 58 " --> pdb=" O THR E 66 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'E' and resid 97 through 100 removed outlier: 3.531A pdb=" N GLN E 139 " --> pdb=" O VAL E 99 " (cutoff:3.500A) 870 hydrogen bonds defined for protein. 2382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2431 hydrogen bonds 3842 hydrogen bond angles 0 basepair planarities 977 basepair parallelities 1595 stacking parallelities Total time for adding SS restraints: 155.58 Time building geometry restraints manager: 44.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 9043 1.32 - 1.45: 44205 1.45 - 1.58: 41326 1.58 - 1.71: 6045 1.71 - 1.84: 155 Bond restraints: 100774 Sorted by residual: bond pdb=" N3B GNP D 501 " pdb=" PG GNP D 501 " ideal model delta sigma weight residual 1.801 1.625 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" CE1 HIS U 83 " pdb=" NE2 HIS U 83 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.90e+01 bond pdb=" CE1 HIS G 15 " pdb=" NE2 HIS G 15 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" CE1 HIS O 35 " pdb=" NE2 HIS O 35 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.69e+01 bond pdb=" CE1 HIS H 126 " pdb=" NE2 HIS H 126 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.67e+01 ... (remaining 100769 not shown) Histogram of bond angle deviations from ideal: 86.77 - 96.30: 31 96.30 - 105.82: 16128 105.82 - 115.34: 70653 115.34 - 124.87: 50031 124.87 - 134.39: 14201 Bond angle restraints: 151044 Sorted by residual: angle pdb=" O3' A A 731 " pdb=" P U A 732 " pdb=" O5' U A 732 " ideal model delta sigma weight residual 104.00 86.77 17.23 1.50e+00 4.44e-01 1.32e+02 angle pdb=" O3' C A1849 " pdb=" P G A1850 " pdb=" O5' G A1850 " ideal model delta sigma weight residual 104.00 87.21 16.79 1.50e+00 4.44e-01 1.25e+02 angle pdb=" O3' C A1849 " pdb=" C3' C A1849 " pdb=" C2' C A1849 " ideal model delta sigma weight residual 113.70 98.93 14.77 1.50e+00 4.44e-01 9.70e+01 angle pdb=" C3' A A2366 " pdb=" O3' A A2366 " pdb=" P C A2367 " ideal model delta sigma weight residual 120.20 106.27 13.93 1.50e+00 4.44e-01 8.62e+01 angle pdb=" C3' U A 605 " pdb=" O3' U A 605 " pdb=" P G A 606 " ideal model delta sigma weight residual 120.20 106.36 13.84 1.50e+00 4.44e-01 8.51e+01 ... (remaining 151039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 51833 35.97 - 71.95: 1722 71.95 - 107.92: 132 107.92 - 143.90: 12 143.90 - 179.87: 33 Dihedral angle restraints: 53732 sinusoidal: 43685 harmonic: 10047 Sorted by residual: dihedral pdb=" C5' A A 548 " pdb=" C4' A A 548 " pdb=" C3' A A 548 " pdb=" O3' A A 548 " ideal model delta sinusoidal sigma weight residual 147.00 74.57 72.43 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" O4' U A 232 " pdb=" C2' U A 232 " pdb=" C1' U A 232 " pdb=" C3' U A 232 " ideal model delta sinusoidal sigma weight residual 25.00 -43.51 68.51 1 8.00e+00 1.56e-02 9.50e+01 dihedral pdb=" O4' C A 91 " pdb=" C4' C A 91 " pdb=" C3' C A 91 " pdb=" C2' C A 91 " ideal model delta sinusoidal sigma weight residual -35.00 31.53 -66.53 1 8.00e+00 1.56e-02 9.03e+01 ... (remaining 53729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 14121 0.133 - 0.267: 4849 0.267 - 0.400: 265 0.400 - 0.533: 95 0.533 - 0.667: 5 Chirality restraints: 19335 Sorted by residual: chirality pdb=" C3' A A2809 " pdb=" C4' A A2809 " pdb=" O3' A A2809 " pdb=" C2' A A2809 " both_signs ideal model delta sigma weight residual False -2.74 -2.08 -0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" P C A1593 " pdb=" OP1 C A1593 " pdb=" OP2 C A1593 " pdb=" O5' C A1593 " both_signs ideal model delta sigma weight residual True 2.41 -3.04 -0.63 2.00e-01 2.50e+01 9.83e+00 chirality pdb=" P C B 2 " pdb=" OP1 C B 2 " pdb=" OP2 C B 2 " pdb=" O5' C B 2 " both_signs ideal model delta sigma weight residual True 2.41 -3.00 -0.59 2.00e-01 2.50e+01 8.74e+00 ... (remaining 19332 not shown) Planarity restraints: 7861 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 122 " 0.863 9.50e-02 1.11e+02 3.87e-01 9.09e+01 pdb=" NE ARG Q 122 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG Q 122 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 122 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 122 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 36 " 0.736 9.50e-02 1.11e+02 3.30e-01 6.64e+01 pdb=" NE ARG Q 36 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG Q 36 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 36 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 36 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 1 18 " -0.717 9.50e-02 1.11e+02 3.21e-01 6.32e+01 pdb=" NE ARG 1 18 " 0.046 2.00e-02 2.50e+03 pdb=" CZ ARG 1 18 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG 1 18 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG 1 18 " -0.018 2.00e-02 2.50e+03 ... (remaining 7858 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.61: 1605 2.61 - 3.24: 85700 3.24 - 3.87: 231401 3.87 - 4.51: 309750 4.51 - 5.14: 404113 Nonbonded interactions: 1032569 Sorted by model distance: nonbonded pdb=" ND2 ASN 5 32 " pdb=" SG CYS 5 46 " model vdw 1.972 2.880 nonbonded pdb=" OP1 A A1813 " pdb="MG MG A3079 " model vdw 1.973 2.170 nonbonded pdb=" OP2 A A1036 " pdb="MG MG A3099 " model vdw 1.978 2.170 nonbonded pdb=" OP2 A A1816 " pdb="MG MG A3079 " model vdw 1.978 2.170 nonbonded pdb=" OP1 C A1807 " pdb="MG MG A3132 " model vdw 1.978 2.170 ... (remaining 1032564 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: 2.490 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: 0.110 Extract box with map and model: 16.020 Check model and map are aligned: 1.020 Set scattering table: 0.610 Process input model: 350.090 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.200 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:10.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 382.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 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 : 0.011 0.176 100774 Z= 0.663 Angle : 1.722 17.225 151044 Z= 1.138 Chirality : 0.119 0.667 19335 Planarity : 0.021 0.387 7861 Dihedral : 15.419 179.871 47269 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 1.21 % Allowed : 7.07 % Favored : 91.72 % Rotamer Outliers : 2.49 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 3467 helix: -2.66 (0.12), residues: 967 sheet: -1.71 (0.17), residues: 716 loop : -2.09 (0.13), residues: 1784 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 696 time to evaluate : 3.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 6 residues processed: 750 average time/residue: 2.0588 time to fit residues: 2016.1645 Evaluate side-chains 462 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 456 time to evaluate : 3.805 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 4.1531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 542 optimal weight: 3.9990 chunk 486 optimal weight: 3.9990 chunk 270 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 328 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 503 optimal weight: 7.9990 chunk 194 optimal weight: 20.0000 chunk 305 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 583 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 17 GLN 2 27 ASN 2 39 ASN ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 28 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 31 HIS 8 40 GLN 8 60 GLN G 86 ASN G 114 GLN G 153 GLN H 32 GLN H 87 ASN J 2 ASN J 135 GLN J 172 GLN K 97 GLN K 106 ASN M 118 GLN N 3 GLN N 72 GLN N 109 ASN P 35 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 96 GLN R 58 ASN S 29 HIS S 41 GLN U 101 ASN D 47 ASN D 117 GLN D 119 GLN D 133 GLN D 140 GLN D 285 HIS ** D 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN E 92 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.117 100774 Z= 0.337 Angle : 0.901 11.346 151044 Z= 0.452 Chirality : 0.047 0.470 19335 Planarity : 0.008 0.131 7861 Dihedral : 14.969 179.799 40149 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.12 % Favored : 95.59 % Rotamer Outliers : 3.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3467 helix: -0.76 (0.16), residues: 975 sheet: -0.92 (0.18), residues: 713 loop : -1.35 (0.14), residues: 1779 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 494 time to evaluate : 3.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 48 residues processed: 571 average time/residue: 1.9977 time to fit residues: 1512.3990 Evaluate side-chains 496 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 448 time to evaluate : 3.813 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 12 average time/residue: 1.1137 time to fit residues: 25.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 324 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 485 optimal weight: 8.9990 chunk 396 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 584 optimal weight: 6.9990 chunk 630 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 579 optimal weight: 9.9990 chunk 199 optimal weight: 20.0000 chunk 468 optimal weight: 0.4980 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 3 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 8 31 HIS G 114 GLN H 201 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN K 74 ASN K 137 ASN M 118 GLN N 72 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 203 ASN D 336 ASN D 382 ASN D 398 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.123 100774 Z= 0.304 Angle : 0.827 10.981 151044 Z= 0.421 Chirality : 0.045 0.320 19335 Planarity : 0.007 0.106 7861 Dihedral : 15.038 179.731 40149 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.85 % Favored : 94.95 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.13), residues: 3467 helix: -0.44 (0.16), residues: 991 sheet: -0.86 (0.18), residues: 722 loop : -1.21 (0.14), residues: 1754 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 470 time to evaluate : 3.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 69 residues processed: 564 average time/residue: 2.0470 time to fit residues: 1528.6873 Evaluate side-chains 487 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 418 time to evaluate : 3.816 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 52 residues processed: 17 average time/residue: 1.2713 time to fit residues: 36.4923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 577 optimal weight: 6.9990 chunk 439 optimal weight: 5.9990 chunk 303 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 392 optimal weight: 7.9990 chunk 586 optimal weight: 6.9990 chunk 620 optimal weight: 0.9990 chunk 306 optimal weight: 9.9990 chunk 555 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN 2 39 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 8 31 HIS G 114 GLN H 32 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 101 ASN U 18 GLN D 47 ASN D 119 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.120 100774 Z= 0.281 Angle : 0.788 11.388 151044 Z= 0.402 Chirality : 0.043 0.314 19335 Planarity : 0.007 0.090 7861 Dihedral : 15.015 179.873 40149 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 4.67 % Favored : 95.13 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.13), residues: 3467 helix: -0.24 (0.16), residues: 989 sheet: -0.80 (0.18), residues: 734 loop : -1.13 (0.14), residues: 1744 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 437 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 152 outliers final: 85 residues processed: 546 average time/residue: 2.0286 time to fit residues: 1463.3497 Evaluate side-chains 499 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 414 time to evaluate : 3.840 Switching outliers to nearest non-outliers outliers start: 85 outliers final: 65 residues processed: 20 average time/residue: 1.2778 time to fit residues: 42.6782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 516 optimal weight: 9.9990 chunk 352 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 462 optimal weight: 0.0570 chunk 256 optimal weight: 20.0000 chunk 529 optimal weight: 6.9990 chunk 428 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 316 optimal weight: 10.0000 chunk 557 optimal weight: 9.9990 chunk 156 optimal weight: 20.0000 overall best weight: 6.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 6 26 ASN 8 31 HIS G 114 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 118 GLN O 126 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 ASN U 18 GLN X 51 ASN D 47 ASN D 119 GLN D 398 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.142 100774 Z= 0.343 Angle : 0.891 12.111 151044 Z= 0.447 Chirality : 0.047 0.353 19335 Planarity : 0.008 0.097 7861 Dihedral : 15.267 179.717 40149 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.88 % Favored : 93.91 % Rotamer Outliers : 5.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.13), residues: 3467 helix: -0.39 (0.16), residues: 979 sheet: -0.94 (0.18), residues: 739 loop : -1.23 (0.13), residues: 1749 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 424 time to evaluate : 3.951 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 166 outliers final: 89 residues processed: 543 average time/residue: 2.0499 time to fit residues: 1471.3024 Evaluate side-chains 493 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 404 time to evaluate : 3.884 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 72 residues processed: 17 average time/residue: 1.2130 time to fit residues: 35.6657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 208 optimal weight: 10.0000 chunk 558 optimal weight: 0.0980 chunk 122 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 621 optimal weight: 9.9990 chunk 515 optimal weight: 8.9990 chunk 287 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 205 optimal weight: 9.9990 chunk 326 optimal weight: 10.0000 overall best weight: 7.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 8 31 HIS G 114 GLN H 66 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN W 54 ASN D 119 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.168 100774 Z= 0.414 Angle : 1.002 13.068 151044 Z= 0.495 Chirality : 0.051 0.369 19335 Planarity : 0.008 0.103 7861 Dihedral : 15.512 179.086 40149 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.54 % Favored : 94.32 % Rotamer Outliers : 5.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.13), residues: 3467 helix: -0.67 (0.16), residues: 978 sheet: -1.07 (0.18), residues: 732 loop : -1.34 (0.13), residues: 1757 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 419 time to evaluate : 3.834 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 156 outliers final: 97 residues processed: 533 average time/residue: 2.0183 time to fit residues: 1426.2397 Evaluate side-chains 512 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 415 time to evaluate : 3.870 Switching outliers to nearest non-outliers outliers start: 97 outliers final: 76 residues processed: 21 average time/residue: 1.3355 time to fit residues: 46.2467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 598 optimal weight: 6.9990 chunk 70 optimal weight: 20.0000 chunk 353 optimal weight: 5.9990 chunk 453 optimal weight: 6.9990 chunk 351 optimal weight: 0.6980 chunk 522 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 618 optimal weight: 0.7980 chunk 387 optimal weight: 0.9980 chunk 377 optimal weight: 2.9990 chunk 285 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN 5 28 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN G 114 GLN H 66 GLN H 152 ASN I 171 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN M 118 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 398 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 100774 Z= 0.153 Angle : 0.603 10.501 151044 Z= 0.319 Chirality : 0.037 0.259 19335 Planarity : 0.005 0.067 7861 Dihedral : 14.804 179.845 40149 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.81 % Favored : 96.02 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.14), residues: 3467 helix: 0.18 (0.17), residues: 984 sheet: -0.68 (0.18), residues: 737 loop : -0.98 (0.14), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 444 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 74 residues processed: 536 average time/residue: 1.9877 time to fit residues: 1426.2023 Evaluate side-chains 478 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 404 time to evaluate : 3.878 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 66 residues processed: 8 average time/residue: 1.0630 time to fit residues: 17.8957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 382 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 369 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 393 optimal weight: 4.9990 chunk 421 optimal weight: 9.9990 chunk 305 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 486 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 8 31 HIS G 114 GLN H 66 GLN H 87 ASN J 2 ASN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN K 74 ASN N 72 GLN O 126 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.184 100774 Z= 0.456 Angle : 1.055 12.614 151044 Z= 0.515 Chirality : 0.053 0.379 19335 Planarity : 0.009 0.106 7861 Dihedral : 15.481 178.351 40149 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.68 % Favored : 94.09 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3467 helix: -0.55 (0.16), residues: 977 sheet: -0.98 (0.18), residues: 734 loop : -1.24 (0.13), residues: 1756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 416 time to evaluate : 3.947 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 88 residues processed: 515 average time/residue: 2.0197 time to fit residues: 1384.0582 Evaluate side-chains 497 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 409 time to evaluate : 3.856 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 71 residues processed: 17 average time/residue: 1.3203 time to fit residues: 37.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 562 optimal weight: 6.9990 chunk 592 optimal weight: 3.9990 chunk 540 optimal weight: 6.9990 chunk 576 optimal weight: 0.9990 chunk 347 optimal weight: 2.9990 chunk 251 optimal weight: 9.9990 chunk 452 optimal weight: 0.7980 chunk 176 optimal weight: 10.0000 chunk 521 optimal weight: 3.9990 chunk 545 optimal weight: 8.9990 chunk 574 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 114 GLN H 66 GLN I 171 GLN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN M 118 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN D 47 ASN D 119 GLN D 398 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 100774 Z= 0.161 Angle : 0.623 10.533 151044 Z= 0.328 Chirality : 0.037 0.267 19335 Planarity : 0.005 0.068 7861 Dihedral : 14.826 179.646 40149 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.87 % Favored : 95.96 % Rotamer Outliers : 3.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3467 helix: 0.13 (0.17), residues: 983 sheet: -0.68 (0.19), residues: 732 loop : -0.97 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 422 time to evaluate : 3.994 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 71 residues processed: 502 average time/residue: 1.9848 time to fit residues: 1328.4355 Evaluate side-chains 479 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 408 time to evaluate : 3.794 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 65 residues processed: 6 average time/residue: 1.0886 time to fit residues: 14.6343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 378 optimal weight: 9.9990 chunk 609 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 423 optimal weight: 3.9990 chunk 639 optimal weight: 7.9990 chunk 588 optimal weight: 0.7980 chunk 509 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 chunk 393 optimal weight: 0.7980 chunk 312 optimal weight: 10.0000 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 114 GLN H 66 GLN J 2 ASN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN M 118 GLN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN U 101 ASN D 119 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 100774 Z= 0.221 Angle : 0.697 10.940 151044 Z= 0.361 Chirality : 0.040 0.284 19335 Planarity : 0.006 0.071 7861 Dihedral : 14.900 179.636 40149 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 4.79 % Favored : 95.04 % Rotamer Outliers : 3.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 3467 helix: 0.06 (0.16), residues: 985 sheet: -0.65 (0.19), residues: 739 loop : -0.98 (0.14), residues: 1743 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6934 Ramachandran restraints generated. 3467 Oldfield, 0 Emsley, 3467 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 406 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 76 residues processed: 485 average time/residue: 2.0121 time to fit residues: 1303.1517 Evaluate side-chains 479 residues out of total 2969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 403 time to evaluate : 4.689 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 66 residues processed: 10 average time/residue: 1.1893 time to fit residues: 23.2151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 642 random chunks: chunk 404 optimal weight: 6.9990 chunk 542 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 469 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 510 optimal weight: 6.9990 chunk 213 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 64 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 27 ASN ** 5 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 22 ASN 8 31 HIS G 70 ASN G 114 GLN H 66 GLN J 2 ASN ** J 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 51 ASN M 118 GLN O 126 ASN ** Q 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 18 GLN U 101 ASN D 14 GLN D 119 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.184657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.154034 restraints weight = 78858.759| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.85 r_work: 0.3392 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 2.44 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.146 100774 Z= 0.340 Angle : 0.883 12.058 151044 Z= 0.442 Chirality : 0.047 0.340 19335 Planarity : 0.007 0.096 7861 Dihedral : 15.259 179.596 40149 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.34 % Favored : 94.49 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.13), residues: 3467 helix: -0.31 (0.16), residues: 981 sheet: -0.79 (0.19), residues: 729 loop : -1.11 (0.14), residues: 1757 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23919.51 seconds wall clock time: 421 minutes 27.40 seconds (25287.40 seconds total)