Starting phenix.real_space_refine on Sat Apr 13 03:41:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/04_2024/7m4v_23667_updated.pdb" } resolution = 2.54 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. 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 1 6.06 5 P 2846 5.49 5 Mg 159 5.21 5 S 78 5.16 5 C 42506 2.51 5 N 15878 2.21 5 O 24934 1.98 5 F 2 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 3": "OD1" <-> "OD2" Residue "0 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 167": "OE1" <-> "OE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 98": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 73": "OD1" <-> "OD2" Residue "K GLU 53": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "L PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L GLU 96": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "Q ASP 70": "OD1" <-> "OD2" Residue "R GLU 2": "OE1" <-> "OE2" Residue "S GLU 17": "OE1" <-> "OE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "U GLU 13": "OE1" <-> "OE2" Residue "U ASP 94": "OD1" <-> "OD2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "Y TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 86404 Number of models: 1 Model: "" Number of chains: 48 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2732, 58607 Classifications: {'RNA': 2732} Modifications used: {'5*END': 1, 'rna2p': 3, 'rna2p_pur': 251, 'rna2p_pyr': 147, 'rna3p': 12, 'rna3p_pur': 1311, 'rna3p_pyr': 1008} Link IDs: {'rna2p': 400, 'rna3p': 2331} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 10, 'rna3p': 104} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 942 Classifications: {'peptide': 118} Link IDs: {'TRANS': 117} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 585 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "3" 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: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 237 Unusual residues: {' MG': 157, 'YQM': 2} Classifications: {'undetermined': 159} Link IDs: {None: 158} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "2" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 759 Classifications: {'water': 759} Link IDs: {None: 758} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 114.961 46.345 67.990 1.00 0.00 S ATOM 1398 SG CYS 3 14 111.817 47.613 69.766 1.00 0.00 S ATOM 1503 SG CYS 3 27 113.535 44.443 70.966 1.00 0.00 S Time building chain proxies: 34.16, per 1000 atoms: 0.40 Number of scatterers: 86404 At special positions: 0 Unit cell: (183.168, 204.368, 234.048, 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 1 29.99 S 78 16.00 P 2846 15.00 Mg 159 11.99 F 2 9.00 O 24934 8.00 N 15878 7.00 C 42506 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 34.62 Conformation dependent library (CDL) restraints added in 4.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5690 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 89 helices and 47 sheets defined 26.8% alpha, 19.9% beta 948 base pairs and 1343 stacking pairs defined. Time for finding SS restraints: 38.24 Creating SS restraints... Processing helix chain '1' and resid 9 through 16 Processing helix chain '1' and resid 18 through 22 Processing helix chain '1' and resid 25 through 37 Processing helix chain '2' and resid 8 through 11 No H-bonds generated for 'chain '2' and resid 8 through 11' Processing helix chain '2' and resid 37 through 42 Processing helix chain '2' and resid 51 through 60 removed outlier: 4.312A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Processing helix chain '3' and resid 31 through 33 No H-bonds generated for 'chain '3' and resid 31 through 33' Processing helix chain 'C' and resid 11 through 13 No H-bonds generated for 'chain 'C' and resid 11 through 13' Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 132 through 134 No H-bonds generated for 'chain 'C' and resid 132 through 134' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 264 through 266 No H-bonds generated for 'chain 'C' and resid 264 through 266' Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 63 through 72 removed outlier: 3.679A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 90 No H-bonds generated for 'chain 'D' and resid 87 through 90' Processing helix chain 'D' and resid 124 through 127 No H-bonds generated for 'chain 'D' and resid 124 through 127' Processing helix chain 'E' and resid 15 through 18 No H-bonds generated for 'chain 'E' and resid 15 through 18' Processing helix chain 'E' and resid 24 through 38 Processing helix chain 'E' and resid 97 through 114 Processing helix chain 'E' and resid 130 through 139 Processing helix chain 'E' and resid 154 through 161 Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 189 through 198 Processing helix chain 'F' and resid 6 through 20 removed outlier: 3.582A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 Processing helix chain 'F' and resid 93 through 106 Processing helix chain 'F' and resid 163 through 173 Processing helix chain 'G' and resid 3 through 6 No H-bonds generated for 'chain 'G' and resid 3 through 6' Processing helix chain 'G' and resid 59 through 79 Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.818A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 30 through 33 No H-bonds generated for 'chain 'H' and resid 30 through 33' Processing helix chain 'H' and resid 41 through 59 removed outlier: 5.449A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLU H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 10 No H-bonds generated for 'chain 'I' and resid 8 through 10' Processing helix chain 'I' and resid 25 through 37 removed outlier: 3.972A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 61 No H-bonds generated for 'chain 'I' and resid 59 through 61' Processing helix chain 'I' and resid 68 through 71 No H-bonds generated for 'chain 'I' and resid 68 through 71' Processing helix chain 'I' and resid 89 through 95 removed outlier: 3.508A pdb=" N ALA I 94 " --> pdb=" O GLU I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 106 Processing helix chain 'I' and resid 113 through 121 removed outlier: 3.507A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 135 No H-bonds generated for 'chain 'I' and resid 133 through 135' Processing helix chain 'J' and resid 104 through 106 No H-bonds generated for 'chain 'J' and resid 104 through 106' Processing helix chain 'J' and resid 109 through 117 removed outlier: 3.835A pdb=" N MET J 112 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LYS J 113 " --> pdb=" O GLN J 110 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 62 No H-bonds generated for 'chain 'K' and resid 59 through 62' Processing helix chain 'K' and resid 82 through 86 Processing helix chain 'K' and resid 94 through 100 Processing helix chain 'K' and resid 131 through 140 Processing helix chain 'L' and resid 44 through 58 Processing helix chain 'L' and resid 111 through 124 removed outlier: 3.636A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 31 Processing helix chain 'M' and resid 38 through 55 removed outlier: 3.745A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 60 through 70 Processing helix chain 'M' and resid 73 through 86 removed outlier: 5.234A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 4 through 22 removed outlier: 4.340A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 60 No H-bonds generated for 'chain 'N' and resid 57 through 60' Processing helix chain 'N' and resid 67 through 84 Processing helix chain 'N' and resid 101 through 112 Processing helix chain 'O' and resid 6 through 15 removed outlier: 3.915A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 59 No H-bonds generated for 'chain 'O' and resid 57 through 59' Processing helix chain 'O' and resid 101 through 104 Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 26 through 29 Processing helix chain 'P' and resid 32 through 71 removed outlier: 3.734A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 76 through 86 Processing helix chain 'P' and resid 92 through 101 Processing helix chain 'P' and resid 103 through 117 Processing helix chain 'R' and resid 14 through 24 removed outlier: 3.778A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 38 Processing helix chain 'R' and resid 42 through 62 removed outlier: 3.917A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN R 62 " --> pdb=" O ALA R 58 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 68 No H-bonds generated for 'chain 'R' and resid 66 through 68' Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'S' and resid 3 through 9 Processing helix chain 'S' and resid 17 through 26 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'T' and resid 65 through 67 No H-bonds generated for 'chain 'T' and resid 65 through 67' Processing helix chain 'U' and resid 18 through 26 Processing helix chain 'U' and resid 48 through 56 Processing helix chain 'U' and resid 59 through 62 No H-bonds generated for 'chain 'U' and resid 59 through 62' Processing helix chain 'W' and resid 53 through 62 Processing helix chain 'W' and resid 64 through 74 Processing helix chain 'X' and resid 3 through 8 removed outlier: 3.678A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 34 Processing helix chain 'X' and resid 41 through 60 Processing helix chain 'Y' and resid 17 through 25 Processing helix chain 'Y' and resid 41 through 53 removed outlier: 3.672A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N TYR Y 52 " --> pdb=" O ASN Y 48 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET Y 53 " --> pdb=" O LYS Y 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 19 removed outlier: 3.518A pdb=" N SER Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain '0' and resid 16 through 22 Processing sheet with id= B, first strand: chain '2' and resid 22 through 24 Processing sheet with id= C, first strand: chain '3' and resid 14 through 19 Processing sheet with id= D, first strand: chain 'C' and resid 34 through 36 Processing sheet with id= E, first strand: chain 'C' and resid 101 through 105 removed outlier: 3.898A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LYS C 95 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N VAL C 78 " --> pdb=" O LYS C 95 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 129 through 131 Processing sheet with id= G, first strand: chain 'C' and resid 181 through 185 removed outlier: 3.660A pdb=" N GLY C 166 " --> pdb=" O ILE C 173 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG C 175 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 172 through 175 removed outlier: 4.547A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG D 14 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL D 23 " --> pdb=" O ARG D 14 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LYS D 193 " --> pdb=" O ILE D 180 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE D 180 " --> pdb=" O LYS D 193 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 79 through 84 removed outlier: 3.824A pdb=" N LEU D 79 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR D 53 " --> pdb=" O LEU D 79 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N THR D 52 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ILE D 35 " --> pdb=" O THR D 52 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 118 through 122 removed outlier: 5.748A pdb=" N LEU D 168 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE D 121 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N GLY D 166 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 2 through 4 Processing sheet with id= L, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.521A pdb=" N VAL E 185 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL E 120 " --> pdb=" O VAL E 185 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N MET E 187 " --> pdb=" O VAL E 120 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 146 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N SER E 188 " --> pdb=" O LEU E 146 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL E 148 " --> pdb=" O SER E 188 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 87 through 92 removed outlier: 6.895A pdb=" N THR F 157 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE F 34 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N THR F 155 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU F 36 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASP F 153 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 16 through 20 Processing sheet with id= O, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= P, first strand: chain 'G' and resid 87 through 90 Processing sheet with id= Q, first strand: chain 'G' and resid 95 through 99 Processing sheet with id= R, first strand: chain 'G' and resid 121 through 124 Processing sheet with id= S, first strand: chain 'H' and resid 18 through 20 Processing sheet with id= T, first strand: chain 'I' and resid 15 through 19 removed outlier: 6.341A pdb=" N TYR I 53 " --> pdb=" O PHE I 16 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL I 18 " --> pdb=" O TYR I 53 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE I 55 " --> pdb=" O VAL I 18 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 73 through 77 Processing sheet with id= V, first strand: chain 'J' and resid 7 through 9 removed outlier: 6.695A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N VAL J 24 " --> pdb=" O ILE J 38 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N ILE J 38 " --> pdb=" O VAL J 24 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA J 83 " --> pdb=" O VAL J 63 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'K' and resid 76 through 80 removed outlier: 6.871A pdb=" N ARG K 109 " --> pdb=" O ALA K 77 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N VAL K 79 " --> pdb=" O ARG K 109 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG K 111 " --> pdb=" O VAL K 79 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 129 through 133 removed outlier: 3.552A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ALA L 36 " --> pdb=" O ILE L 102 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE L 102 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.965A pdb=" N ILE L 74 " --> pdb=" O GLU L 91 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N TRP L 93 " --> pdb=" O LYS L 72 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LYS L 72 " --> pdb=" O TRP L 93 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= AA, first strand: chain 'N' and resid 90 through 92 Processing sheet with id= AB, first strand: chain 'O' and resid 86 through 91 removed outlier: 3.687A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N GLU O 47 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE O 67 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR O 63 " --> pdb=" O ILE O 51 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N LYS O 53 " --> pdb=" O ALA O 61 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA O 61 " --> pdb=" O LYS O 53 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 10 through 15 removed outlier: 4.118A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 19 through 23 removed outlier: 3.727A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Q' and resid 32 through 35 removed outlier: 6.410A pdb=" N GLU Q 62 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N ILE Q 98 " --> pdb=" O GLU Q 62 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Q' and resid 72 through 78 removed outlier: 4.321A pdb=" N TYR Q 83 " --> pdb=" O ARG Q 78 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'R' and resid 82 through 87 Processing sheet with id= AH, first strand: chain 'R' and resid 2 through 10 removed outlier: 3.592A pdb=" N GLY R 9 " --> pdb=" O CYS R 101 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N CYS R 101 " --> pdb=" O GLY R 9 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLY R 108 " --> pdb=" O VAL R 71 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N VAL R 71 " --> pdb=" O GLY R 108 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'S' and resid 10 through 13 removed outlier: 6.551A pdb=" N LYS S 32 " --> pdb=" O LYS S 11 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL S 30 " --> pdb=" O PRO S 13 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS S 80 " --> pdb=" O VAL S 33 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LYS S 56 " --> pdb=" O THR S 85 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'S' and resid 66 through 69 Processing sheet with id= AK, first strand: chain 'T' and resid 21 through 23 Processing sheet with id= AL, first strand: chain 'T' and resid 39 through 43 Processing sheet with id= AM, first strand: chain 'T' and resid 81 through 86 Processing sheet with id= AN, first strand: chain 'T' and resid 24 through 28 removed outlier: 6.595A pdb=" N LYS T 33 " --> pdb=" O LEU T 25 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL T 27 " --> pdb=" O ARG T 31 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG T 31 " --> pdb=" O VAL T 27 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'U' and resid 4 through 7 removed outlier: 6.736A pdb=" N ASP U 94 " --> pdb=" O GLN U 79 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N LEU U 81 " --> pdb=" O HIS U 92 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS U 92 " --> pdb=" O LEU U 81 " (cutoff:3.500A) removed outlier: 8.911A pdb=" N ALA U 93 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N PHE U 95 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE U 33 " --> pdb=" O PHE U 95 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ARG U 97 " --> pdb=" O ILE U 33 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N TYR U 35 " --> pdb=" O ARG U 97 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'V' and resid 51 through 53 Processing sheet with id= AQ, first strand: chain 'V' and resid 66 through 72 removed outlier: 3.606A pdb=" N ARG V 77 " --> pdb=" O LYS V 72 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'W' and resid 13 through 18 Processing sheet with id= AS, first strand: chain 'W' and resid 33 through 40 Processing sheet with id= AT, first strand: chain 'Y' and resid 34 through 38 Processing sheet with id= AU, first strand: chain 'Z' and resid 27 through 30 removed outlier: 3.540A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) 809 hydrogen bonds defined for protein. 2292 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2369 hydrogen bonds 3698 hydrogen bond angles 0 basepair planarities 948 basepair parallelities 1343 stacking parallelities Total time for adding SS restraints: 182.23 Time building geometry restraints manager: 37.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 7854 1.31 - 1.43: 41988 1.43 - 1.56: 37391 1.56 - 1.68: 5708 1.68 - 1.81: 139 Bond restraints: 93080 Sorted by residual: bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.575 -0.540 2.00e-02 2.50e+03 7.30e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.575 -0.540 2.00e-02 2.50e+03 7.29e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.951 1.543 0.408 2.00e-02 2.50e+03 4.15e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.554 0.397 2.00e-02 2.50e+03 3.94e+02 bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.12e+02 ... (remaining 93075 not shown) Histogram of bond angle deviations from ideal: 99.80 - 109.02: 36009 109.02 - 118.24: 53264 118.24 - 127.46: 44636 127.46 - 136.68: 5860 136.68 - 145.90: 2 Bond angle restraints: 139771 Sorted by residual: angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 145.90 -19.67 3.00e+00 1.11e-01 4.30e+01 angle pdb=" C2' U A1105 " pdb=" C1' U A1105 " pdb=" N1 U A1105 " ideal model delta sigma weight residual 112.00 121.30 -9.30 1.50e+00 4.44e-01 3.84e+01 angle pdb=" C1' 2MG A2441 " pdb=" N9 2MG A2441 " pdb=" C8 2MG A2441 " ideal model delta sigma weight residual 110.07 128.47 -18.40 3.00e+00 1.11e-01 3.76e+01 angle pdb=" O4' U A1105 " pdb=" C1' U A1105 " pdb=" N1 U A1105 " ideal model delta sigma weight residual 108.50 117.53 -9.03 1.50e+00 4.44e-01 3.62e+01 angle pdb=" C1' OMG A2247 " pdb=" N9 OMG A2247 " pdb=" C4 OMG A2247 " ideal model delta sigma weight residual 108.29 126.31 -18.02 3.00e+00 1.11e-01 3.61e+01 ... (remaining 139766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 52386 35.89 - 71.79: 6256 71.79 - 107.68: 715 107.68 - 143.58: 25 143.58 - 179.47: 38 Dihedral angle restraints: 59420 sinusoidal: 50570 harmonic: 8850 Sorted by residual: dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual -160.00 17.56 -177.56 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 715 " pdb=" C1' C A 715 " pdb=" N1 C A 715 " pdb=" C2 C A 715 " ideal model delta sinusoidal sigma weight residual 200.00 37.69 162.31 1 1.50e+01 4.44e-03 8.33e+01 dihedral pdb=" O4' U A 744 " pdb=" C1' U A 744 " pdb=" N1 U A 744 " pdb=" C2 U A 744 " ideal model delta sinusoidal sigma weight residual 200.00 38.65 161.35 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 59417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 17916 0.185 - 0.370: 16 0.370 - 0.555: 2 0.555 - 0.740: 0 0.740 - 0.925: 1 Chirality restraints: 17935 Sorted by residual: chirality pdb=" C1' U A1105 " pdb=" O4' U A1105 " pdb=" C2' U A1105 " pdb=" N1 U A1105 " both_signs ideal model delta sigma weight residual False 2.47 1.54 0.92 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.77 -0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" C05 YQM A3201 " pdb=" C04 YQM A3201 " pdb=" C06 YQM A3201 " pdb=" C19 YQM A3201 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 3.96e+00 ... (remaining 17932 not shown) Planarity restraints: 7125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " -0.065 2.00e-02 2.50e+03 6.16e-01 8.54e+03 pdb=" C4' 7MG A2065 " -0.446 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " -0.682 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " 0.597 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " 0.652 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " 0.176 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " -0.983 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " -0.210 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " 0.961 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " 0.023 2.00e-02 2.50e+03 5.87e-01 7.75e+03 pdb=" C4' 2MG A2441 " 0.449 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " 0.720 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " -0.564 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " -0.226 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " 0.887 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " 0.211 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " -0.914 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2247 " -0.043 2.00e-02 2.50e+03 5.73e-01 7.38e+03 pdb=" C4' OMG A2247 " -0.427 2.00e-02 2.50e+03 pdb=" O4' OMG A2247 " -0.610 2.00e-02 2.50e+03 pdb=" C3' OMG A2247 " 0.596 2.00e-02 2.50e+03 pdb=" O3' OMG A2247 " 0.582 2.00e-02 2.50e+03 pdb=" C2' OMG A2247 " 0.202 2.00e-02 2.50e+03 pdb=" O2' OMG A2247 " -0.930 2.00e-02 2.50e+03 pdb=" C1' OMG A2247 " -0.230 2.00e-02 2.50e+03 pdb=" N9 OMG A2247 " 0.861 2.00e-02 2.50e+03 ... (remaining 7122 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 843 2.43 - 3.04: 47765 3.04 - 3.66: 155293 3.66 - 4.28: 248016 4.28 - 4.90: 329909 Nonbonded interactions: 781826 Sorted by model distance: nonbonded pdb=" OP2 U A1669 " pdb="MG MG A3294 " model vdw 1.808 2.170 nonbonded pdb=" O2' G A 799 " pdb=" OP1 A A 800 " model vdw 1.811 2.440 nonbonded pdb=" OP1 G A 959 " pdb="MG MG A3233 " model vdw 1.825 2.170 nonbonded pdb=" OP2 A A1007 " pdb="MG MG A3322 " model vdw 1.844 2.170 nonbonded pdb=" OP2 G A1355 " pdb="MG MG A3359 " model vdw 1.846 2.170 ... (remaining 781821 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: 9.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.390 Construct map_model_manager: 0.080 Extract box with map and model: 28.280 Check model and map are aligned: 0.930 Set scattering table: 0.590 Process input model: 356.540 Find NCS groups from input model: 1.420 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: 0.010 Load rotamer database and sin/cos tables:9.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 407.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 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 : 0.006 0.540 93080 Z= 0.381 Angle : 0.561 19.674 139771 Z= 0.297 Chirality : 0.035 0.925 17935 Planarity : 0.014 0.616 7125 Dihedral : 23.148 179.475 53730 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.82 (0.15), residues: 3072 helix: 1.80 (0.18), residues: 847 sheet: 0.39 (0.20), residues: 673 loop : -0.01 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 248 HIS 0.014 0.001 HIS 2 30 PHE 0.016 0.001 PHE F 138 TYR 0.011 0.001 TYR F 8 ARG 0.009 0.000 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 653 time to evaluate : 3.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 189 VAL cc_start: 0.8566 (m) cc_final: 0.8331 (t) REVERT: M 110 MET cc_start: 0.8432 (mmm) cc_final: 0.8046 (mmm) REVERT: O 67 ILE cc_start: 0.8564 (mm) cc_final: 0.8212 (mm) REVERT: O 97 ARG cc_start: 0.8562 (ptp-110) cc_final: 0.8351 (ptm160) REVERT: P 91 ASP cc_start: 0.8331 (p0) cc_final: 0.7878 (p0) REVERT: Z 24 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7994 (mt-10) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 2.0334 time to fit residues: 1707.3324 Evaluate side-chains 581 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 493 optimal weight: 4.9990 chunk 443 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 299 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 458 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 278 optimal weight: 6.9990 chunk 341 optimal weight: 2.9990 chunk 531 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 21 HIS C 90 HIS C 243 GLN D 33 ASN D 65 GLN D 137 HIS D 176 GLN G 143 GLN I 63 GLN K 71 GLN M 91 ASN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 13 ASN P 56 GLN R 31 HIS R 37 ASN Y 38 GLN Z 41 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 93080 Z= 0.378 Angle : 0.883 17.354 139771 Z= 0.449 Chirality : 0.047 0.366 17935 Planarity : 0.007 0.144 7125 Dihedral : 23.643 179.139 47669 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.57 % Favored : 97.23 % Rotamer: Outliers : 2.53 % Allowed : 10.31 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.14), residues: 3072 helix: 1.39 (0.18), residues: 818 sheet: 0.23 (0.20), residues: 660 loop : -0.34 (0.14), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 248 HIS 0.015 0.002 HIS M 16 PHE 0.028 0.003 PHE D 121 TYR 0.024 0.003 TYR P 32 ARG 0.011 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 566 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 182 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.6230 (ptp-170) REVERT: D 38 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8396 (mm) REVERT: E 1 MET cc_start: 0.5820 (OUTLIER) cc_final: 0.5429 (ptp) REVERT: I 60 GLU cc_start: 0.7497 (pm20) cc_final: 0.7289 (pm20) REVERT: M 43 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: P 117 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7657 (mp) REVERT: U 79 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6586 (tm-30) REVERT: V 68 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7525 (tppp) outliers start: 64 outliers final: 24 residues processed: 584 average time/residue: 1.9871 time to fit residues: 1502.2574 Evaluate side-chains 580 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 549 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 5 ILE Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 194 LYS Chi-restraints excluded: chain F residue 88 LYS Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 295 optimal weight: 20.0000 chunk 164 optimal weight: 10.0000 chunk 442 optimal weight: 0.9990 chunk 361 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 532 optimal weight: 7.9990 chunk 574 optimal weight: 0.0060 chunk 473 optimal weight: 1.9990 chunk 527 optimal weight: 0.6980 chunk 181 optimal weight: 10.0000 chunk 426 optimal weight: 0.6980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN C 86 ASN D 129 ASN G 143 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 37 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 93080 Z= 0.139 Angle : 0.609 13.401 139771 Z= 0.327 Chirality : 0.036 0.340 17935 Planarity : 0.005 0.125 7125 Dihedral : 23.382 179.718 47669 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.25 % Favored : 97.59 % Rotamer: Outliers : 1.90 % Allowed : 12.92 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % 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: 0.58 (0.15), residues: 3072 helix: 1.70 (0.18), residues: 825 sheet: 0.31 (0.20), residues: 691 loop : -0.24 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 248 HIS 0.006 0.001 HIS M 16 PHE 0.018 0.001 PHE F 138 TYR 0.010 0.001 TYR C 62 ARG 0.008 0.000 ARG F 125 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 557 time to evaluate : 3.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8129 (mtpm) REVERT: C 182 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6413 (ptp-170) REVERT: E 195 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7777 (mt) REVERT: M 43 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6832 (tm-30) REVERT: M 49 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7858 (mt-10) REVERT: P 1 MET cc_start: 0.5399 (OUTLIER) cc_final: 0.4758 (ttt) REVERT: S 56 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7478 (ptpp) outliers start: 48 outliers final: 23 residues processed: 573 average time/residue: 1.9735 time to fit residues: 1466.3484 Evaluate side-chains 573 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 544 time to evaluate : 3.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 195 ILE Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain J residue 112 MET Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 chunk 276 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 357 optimal weight: 0.3980 chunk 534 optimal weight: 10.0000 chunk 565 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 506 optimal weight: 0.5980 chunk 152 optimal weight: 7.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 4 GLN D 33 ASN D 115 GLN D 129 ASN G 143 GLN I 63 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 37 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 93080 Z= 0.290 Angle : 0.767 14.540 139771 Z= 0.397 Chirality : 0.042 0.321 17935 Planarity : 0.006 0.137 7125 Dihedral : 23.478 179.924 47669 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.23 % Rotamer: Outliers : 2.77 % Allowed : 13.91 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.14), residues: 3072 helix: 1.40 (0.18), residues: 823 sheet: 0.16 (0.19), residues: 692 loop : -0.39 (0.14), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.008 0.002 HIS M 16 PHE 0.023 0.002 PHE D 121 TYR 0.020 0.002 TYR P 32 ARG 0.007 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 548 time to evaluate : 3.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.8169 (mtpt) REVERT: C 182 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.6434 (ptp-170) REVERT: F 100 LEU cc_start: 0.5304 (OUTLIER) cc_final: 0.4785 (pt) REVERT: I 60 GLU cc_start: 0.7511 (pm20) cc_final: 0.7295 (pm20) REVERT: M 43 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: M 91 ASN cc_start: 0.8267 (m110) cc_final: 0.8028 (m-40) REVERT: O 67 ILE cc_start: 0.8372 (mm) cc_final: 0.7957 (mm) REVERT: P 1 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5062 (ttt) REVERT: P 117 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7502 (mp) REVERT: S 56 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7496 (ptpp) REVERT: U 79 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6453 (tm-30) REVERT: V 68 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7524 (tppp) outliers start: 70 outliers final: 37 residues processed: 570 average time/residue: 2.0188 time to fit residues: 1488.9970 Evaluate side-chains 585 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 539 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain Y residue 7 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 2.9990 chunk 320 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 421 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 482 optimal weight: 0.5980 chunk 390 optimal weight: 20.0000 chunk 0 optimal weight: 7.9990 chunk 288 optimal weight: 6.9990 chunk 507 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN 3 4 GLN D 115 GLN D 129 ASN D 176 GLN G 143 GLN I 63 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 37 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 93080 Z= 0.297 Angle : 0.780 14.676 139771 Z= 0.405 Chirality : 0.043 0.350 17935 Planarity : 0.006 0.138 7125 Dihedral : 23.522 178.682 47669 Min Nonbonded Distance : 1.709 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.57 % Favored : 97.27 % Rotamer: Outliers : 3.40 % Allowed : 13.83 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % 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: 0.15 (0.14), residues: 3072 helix: 1.35 (0.18), residues: 809 sheet: 0.02 (0.19), residues: 709 loop : -0.48 (0.14), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 248 HIS 0.007 0.002 HIS C 25 PHE 0.021 0.002 PHE D 121 TYR 0.020 0.002 TYR P 32 ARG 0.007 0.001 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 554 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 4 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8199 (mtpt) REVERT: 0 34 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7686 (mtpm) REVERT: 2 59 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: C 182 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.6506 (ptp-170) REVERT: E 1 MET cc_start: 0.5769 (ptp) cc_final: 0.5445 (ptp) REVERT: F 100 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4752 (pt) REVERT: I 23 LYS cc_start: 0.8393 (mttt) cc_final: 0.8192 (mttt) REVERT: L 41 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7515 (ttm170) REVERT: M 43 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7056 (tm-30) REVERT: M 91 ASN cc_start: 0.8296 (m110) cc_final: 0.8030 (m-40) REVERT: O 67 ILE cc_start: 0.8350 (mm) cc_final: 0.7973 (mm) REVERT: P 1 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5090 (ttt) REVERT: P 15 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8269 (ttpp) REVERT: Q 75 ILE cc_start: 0.8546 (OUTLIER) cc_final: 0.8079 (mp) REVERT: S 56 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7535 (ptpp) REVERT: U 79 GLN cc_start: 0.7476 (OUTLIER) cc_final: 0.6504 (tm-30) REVERT: V 68 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7554 (tppp) outliers start: 86 outliers final: 46 residues processed: 588 average time/residue: 2.0090 time to fit residues: 1536.4121 Evaluate side-chains 589 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 530 time to evaluate : 3.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 LYS Chi-restraints excluded: chain 0 residue 18 THR Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain Y residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 190 optimal weight: 5.9990 chunk 509 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 331 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 566 optimal weight: 4.9990 chunk 469 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 187 optimal weight: 5.9990 chunk 297 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN 3 4 GLN C 25 HIS D 129 ASN G 143 GLN I 13 HIS I 63 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 37 ASN Y 38 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 93080 Z= 0.430 Angle : 0.937 17.621 139771 Z= 0.473 Chirality : 0.050 0.409 17935 Planarity : 0.007 0.147 7125 Dihedral : 23.622 179.939 47669 Min Nonbonded Distance : 1.630 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.90 % Favored : 96.91 % Rotamer: Outliers : 3.20 % Allowed : 15.17 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % 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: -0.12 (0.14), residues: 3072 helix: 1.06 (0.18), residues: 807 sheet: -0.00 (0.19), residues: 682 loop : -0.67 (0.14), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 248 HIS 0.009 0.002 HIS C 25 PHE 0.025 0.003 PHE D 121 TYR 0.026 0.003 TYR P 32 ARG 0.009 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 536 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.7863 (mtpm) REVERT: 2 59 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: C 182 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6503 (ptp-170) REVERT: F 100 LEU cc_start: 0.5345 (OUTLIER) cc_final: 0.4811 (pt) REVERT: F 138 PHE cc_start: 0.3773 (OUTLIER) cc_final: 0.3395 (p90) REVERT: I 60 GLU cc_start: 0.7567 (pm20) cc_final: 0.7263 (pm20) REVERT: L 41 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7641 (ttm170) REVERT: M 43 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7110 (tm-30) REVERT: M 91 ASN cc_start: 0.8328 (m110) cc_final: 0.8060 (m-40) REVERT: P 1 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5178 (ttt) REVERT: P 117 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7469 (mp) REVERT: Q 75 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8062 (mp) REVERT: S 56 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7588 (ptpp) REVERT: U 79 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6567 (tm-30) REVERT: V 68 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7579 (tppp) outliers start: 81 outliers final: 50 residues processed: 568 average time/residue: 1.9929 time to fit residues: 1465.3665 Evaluate side-chains 596 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 533 time to evaluate : 3.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 85 ASN Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain P residue 117 LEU Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain Y residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 545 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 413 optimal weight: 0.9990 chunk 320 optimal weight: 3.9990 chunk 476 optimal weight: 9.9990 chunk 316 optimal weight: 3.9990 chunk 563 optimal weight: 6.9990 chunk 352 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 260 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 2 42 GLN D 129 ASN G 143 GLN I 13 HIS I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN R 37 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 93080 Z= 0.303 Angle : 0.785 15.028 139771 Z= 0.407 Chirality : 0.043 0.342 17935 Planarity : 0.006 0.138 7125 Dihedral : 23.503 179.624 47669 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.23 % Rotamer: Outliers : 2.88 % Allowed : 15.88 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % 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: -0.03 (0.14), residues: 3072 helix: 1.21 (0.18), residues: 809 sheet: -0.03 (0.19), residues: 704 loop : -0.63 (0.14), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 248 HIS 0.007 0.001 HIS D 143 PHE 0.022 0.002 PHE D 121 TYR 0.020 0.002 TYR P 32 ARG 0.007 0.001 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 540 time to evaluate : 3.540 Fit side-chains revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7772 (mtpm) REVERT: 2 59 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7658 (ttt180) REVERT: 3 8 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7833 (mttm) REVERT: C 182 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.6518 (ptp-170) REVERT: D 210 ILE cc_start: 0.8373 (pp) cc_final: 0.8081 (pp) REVERT: F 100 LEU cc_start: 0.5319 (OUTLIER) cc_final: 0.4750 (pt) REVERT: F 138 PHE cc_start: 0.3724 (OUTLIER) cc_final: 0.3364 (p90) REVERT: G 63 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.6910 (ptp) REVERT: I 60 GLU cc_start: 0.7526 (pm20) cc_final: 0.7221 (pm20) REVERT: L 41 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7424 (ttm170) REVERT: L 85 ASN cc_start: 0.7642 (m-40) cc_final: 0.7434 (m-40) REVERT: L 134 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7371 (ttp-170) REVERT: M 43 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7058 (tm-30) REVERT: M 91 ASN cc_start: 0.8291 (m110) cc_final: 0.8062 (m-40) REVERT: P 1 MET cc_start: 0.5780 (OUTLIER) cc_final: 0.5035 (ttt) REVERT: Q 75 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8004 (mp) REVERT: S 56 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7518 (ptpp) REVERT: U 79 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: V 68 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7546 (tppp) outliers start: 73 outliers final: 51 residues processed: 566 average time/residue: 2.1026 time to fit residues: 1548.1722 Evaluate side-chains 598 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 532 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 88 GLU Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain Y residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 336 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 358 optimal weight: 8.9990 chunk 384 optimal weight: 30.0000 chunk 278 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 443 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN D 129 ASN I 13 HIS I 95 HIS K 71 GLN N 66 ASN O 9 GLN R 37 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 93080 Z= 0.464 Angle : 0.976 18.719 139771 Z= 0.490 Chirality : 0.051 0.403 17935 Planarity : 0.008 0.148 7125 Dihedral : 23.629 179.828 47669 Min Nonbonded Distance : 1.601 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % Rotamer: Outliers : 3.36 % Allowed : 15.65 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.14), residues: 3072 helix: 0.91 (0.18), residues: 805 sheet: -0.08 (0.20), residues: 676 loop : -0.78 (0.14), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 248 HIS 0.010 0.002 HIS D 143 PHE 0.026 0.003 PHE D 121 TYR 0.027 0.004 TYR P 32 ARG 0.009 0.001 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 532 time to evaluate : 3.493 Fit side-chains revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7845 (mtpm) REVERT: 2 59 ARG cc_start: 0.8393 (OUTLIER) cc_final: 0.7761 (ttt180) REVERT: 3 8 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7863 (mttm) REVERT: C 182 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6472 (ptp-170) REVERT: D 210 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8204 (pp) REVERT: F 100 LEU cc_start: 0.5328 (OUTLIER) cc_final: 0.4765 (pt) REVERT: F 138 PHE cc_start: 0.3767 (OUTLIER) cc_final: 0.3412 (p90) REVERT: G 63 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7049 (ptp) REVERT: L 41 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: L 134 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7398 (ttp-170) REVERT: M 43 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: M 91 ASN cc_start: 0.8336 (m110) cc_final: 0.8128 (m-40) REVERT: P 1 MET cc_start: 0.5939 (OUTLIER) cc_final: 0.5182 (ttt) REVERT: Q 75 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8090 (mp) REVERT: S 56 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7594 (ptpp) REVERT: U 79 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.6571 (tm-30) REVERT: V 68 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7596 (tppp) outliers start: 85 outliers final: 56 residues processed: 565 average time/residue: 2.0134 time to fit residues: 1472.8666 Evaluate side-chains 602 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 530 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 8 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 104 ILE Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 27 LYS Chi-restraints excluded: chain G residue 63 MET Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 88 ASN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 113 LYS Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 64 ILE Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain O residue 83 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 75 ILE Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 70 LYS Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 32 VAL Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 79 GLN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Chi-restraints excluded: chain Y residue 7 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 0.0970 chunk 540 optimal weight: 0.9990 chunk 492 optimal weight: 6.9990 chunk 525 optimal weight: 4.9990 chunk 316 optimal weight: 0.9990 chunk 228 optimal weight: 5.9990 chunk 412 optimal weight: 0.6980 chunk 161 optimal weight: 8.9990 chunk 474 optimal weight: 7.9990 chunk 496 optimal weight: 3.9990 chunk 523 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN C 46 ASN C 198 GLN D 129 ASN G 143 GLN I 13 HIS I 95 HIS K 71 GLN N 66 ASN O 9 GLN R 37 ASN Z 52 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.103 93080 Z= 0.136 Angle : 0.601 13.364 139771 Z= 0.323 Chirality : 0.036 0.353 17935 Planarity : 0.005 0.122 7125 Dihedral : 23.318 179.449 47669 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.15 % Favored : 97.72 % Rotamer: Outliers : 2.09 % Allowed : 17.15 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % 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: 0.26 (0.15), residues: 3072 helix: 1.56 (0.18), residues: 815 sheet: 0.12 (0.19), residues: 701 loop : -0.50 (0.15), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 248 HIS 0.004 0.001 HIS I 47 PHE 0.017 0.001 PHE F 138 TYR 0.010 0.001 TYR Q 2 ARG 0.008 0.000 ARG Q 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 544 time to evaluate : 3.627 Fit side-chains revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.7551 (mtpm) REVERT: 1 1 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6770 (mtp) REVERT: 2 59 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7446 (ttt180) REVERT: C 182 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6594 (ptp-170) REVERT: D 210 ILE cc_start: 0.8175 (pp) cc_final: 0.7897 (pp) REVERT: F 100 LEU cc_start: 0.5308 (OUTLIER) cc_final: 0.4729 (pt) REVERT: F 138 PHE cc_start: 0.3670 (OUTLIER) cc_final: 0.3341 (p90) REVERT: L 41 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7167 (ttm170) REVERT: L 134 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7330 (ttp-170) REVERT: M 49 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7912 (mt-10) REVERT: M 91 ASN cc_start: 0.8247 (m110) cc_final: 0.8023 (m-40) REVERT: O 67 ILE cc_start: 0.8311 (mm) cc_final: 0.8009 (mm) REVERT: P 1 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.4698 (ttt) REVERT: S 56 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7463 (ptpp) REVERT: V 68 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7512 (tppp) outliers start: 53 outliers final: 30 residues processed: 568 average time/residue: 2.0722 time to fit residues: 1521.7276 Evaluate side-chains 570 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 529 time to evaluate : 3.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 265 LYS Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain N residue 66 ASN Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 68 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 345 optimal weight: 4.9990 chunk 555 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 386 optimal weight: 20.0000 chunk 582 optimal weight: 7.9990 chunk 536 optimal weight: 10.0000 chunk 464 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 358 optimal weight: 0.7980 chunk 284 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 4 GLN C 46 ASN D 129 ASN I 63 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 56 GLN P 71 GLN R 37 ASN T 38 ASN Z 52 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 93080 Z= 0.373 Angle : 0.862 16.431 139771 Z= 0.439 Chirality : 0.046 0.368 17935 Planarity : 0.007 0.142 7125 Dihedral : 23.500 179.421 47669 Min Nonbonded Distance : 1.648 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.90 % Favored : 96.94 % Rotamer: Outliers : 2.13 % Allowed : 17.70 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % 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: -0.06 (0.14), residues: 3072 helix: 1.21 (0.18), residues: 806 sheet: -0.03 (0.19), residues: 687 loop : -0.65 (0.14), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 248 HIS 0.008 0.002 HIS D 143 PHE 0.023 0.003 PHE D 121 TYR 0.024 0.003 TYR P 32 ARG 0.008 0.001 ARG Q 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6144 Ramachandran restraints generated. 3072 Oldfield, 0 Emsley, 3072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 537 time to evaluate : 3.535 Fit side-chains revert: symmetry clash REVERT: 0 34 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7745 (mtpm) REVERT: 2 59 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7741 (ttt180) REVERT: C 182 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6474 (ptp-170) REVERT: D 210 ILE cc_start: 0.8387 (pp) cc_final: 0.8081 (pp) REVERT: F 100 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4842 (pt) REVERT: F 138 PHE cc_start: 0.3627 (OUTLIER) cc_final: 0.3328 (p90) REVERT: L 41 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7602 (ttm170) REVERT: L 134 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7410 (ttp-170) REVERT: M 43 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: M 91 ASN cc_start: 0.8318 (m110) cc_final: 0.8093 (m-40) REVERT: O 66 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7964 (pttm) REVERT: O 67 ILE cc_start: 0.8338 (mm) cc_final: 0.8011 (mm) REVERT: P 1 MET cc_start: 0.5886 (OUTLIER) cc_final: 0.5105 (ttt) REVERT: S 56 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7559 (ptpp) REVERT: V 68 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7567 (tppp) outliers start: 54 outliers final: 34 residues processed: 559 average time/residue: 2.0750 time to fit residues: 1498.1454 Evaluate side-chains 577 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 531 time to evaluate : 3.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 34 LYS Chi-restraints excluded: chain 1 residue 1 MET Chi-restraints excluded: chain 2 residue 59 ARG Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain C residue 38 LYS Chi-restraints excluded: chain C residue 182 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 138 PHE Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain F residue 170 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 17 VAL Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain K residue 75 LYS Chi-restraints excluded: chain K residue 118 ILE Chi-restraints excluded: chain L residue 26 THR Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 43 GLU Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain O residue 66 LYS Chi-restraints excluded: chain O residue 68 SER Chi-restraints excluded: chain O residue 69 SER Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 6 ARG Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 28 VAL Chi-restraints excluded: chain S residue 52 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain U residue 46 LEU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain V residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 5.9990 chunk 494 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 464 optimal weight: 5.9990 chunk 194 optimal weight: 7.9990 chunk 477 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 4 GLN D 129 ASN I 63 GLN I 95 HIS K 71 GLN ** N 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN P 71 GLN R 37 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.155123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.118482 restraints weight = 709037.034| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 4.52 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 93080 Z= 0.438 Angle : 0.945 18.450 139771 Z= 0.477 Chirality : 0.050 0.392 17935 Planarity : 0.008 0.147 7125 Dihedral : 23.601 179.867 47669 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.16 % Favored : 96.68 % Rotamer: Outliers : 2.33 % Allowed : 17.58 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.10 % Cis-general : 0.00 % Twisted Proline : 1.10 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.14), residues: 3072 helix: 0.96 (0.18), residues: 800 sheet: -0.11 (0.20), residues: 673 loop : -0.81 (0.14), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 248 HIS 0.010 0.002 HIS D 143 PHE 0.025 0.003 PHE D 121 TYR 0.026 0.003 TYR P 32 ARG 0.009 0.001 ARG C 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21799.96 seconds wall clock time: 381 minutes 25.93 seconds (22885.93 seconds total)