Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 21 16:22:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_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_23667/08_2023/7m4v_23667_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_23667_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4v_23667/08_2023/7m4v_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-1.21rc1-5044/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: 8 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: 31.40, per 1000 atoms: 0.36 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: 35.58 Conformation dependent library (CDL) restraints added in 3.4 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: 38.64 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: 179.17 Time building geometry restraints manager: 38.44 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 1.038 1.575 -0.537 2.00e-02 2.50e+03 7.22e+02 bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.038 1.575 -0.537 2.00e-02 2.50e+03 7.21e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.948 1.543 0.405 2.00e-02 2.50e+03 4.09e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.948 1.554 0.394 2.00e-02 2.50e+03 3.88e+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 91.39 145.90 -54.51 3.00e+00 1.11e-01 3.30e+02 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C4 6MZ A2026 " ideal model delta sigma weight residual 154.15 106.80 47.35 3.00e+00 1.11e-01 2.49e+02 angle pdb=" C1' 2MA A2499 " pdb=" N9 2MA A2499 " pdb=" C8 2MA A2499 " ideal model delta sigma weight residual 135.36 111.19 24.17 3.00e+00 1.11e-01 6.49e+01 angle pdb=" C1' 2MA A2499 " pdb=" N9 2MA A2499 " pdb=" C4 2MA A2499 " ideal model delta sigma weight residual 116.52 137.94 -21.42 3.00e+00 1.11e-01 5.10e+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 ... (remaining 139766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 47624 35.89 - 71.79: 1602 71.79 - 107.68: 137 107.68 - 143.58: 29 143.58 - 179.47: 38 Dihedral angle restraints: 49430 sinusoidal: 40580 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 49427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 17896 0.185 - 0.370: 16 0.370 - 0.555: 0 0.555 - 0.740: 0 0.740 - 0.925: 1 Chirality restraints: 17913 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=" C1* PSU A2576 " pdb=" O4* PSU A2576 " pdb=" C2* PSU A2576 " pdb=" C5 PSU A2576 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C19 YQM A3202 " pdb=" C05 YQM A3202 " pdb=" C17 YQM A3202 " pdb=" C20 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.68 2.97 -0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 17910 not shown) Planarity restraints: 7129 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 7126 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: 10.440 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: 0.060 Extract box with map and model: 31.300 Check model and map are aligned: 1.380 Set scattering table: 0.650 Process input model: 352.030 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 409.340 ------------------------------------------------------------------------------- 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 0.537 93080 Z= 0.373 Angle : 0.598 54.514 139771 Z= 0.305 Chirality : 0.035 0.925 17913 Planarity : 0.020 0.616 7129 Dihedral : 15.178 179.475 43740 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 % 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 *********************** 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 : 3.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 2.0413 time to fit residues: 1724.0177 Evaluate side-chains 581 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 581 time to evaluate : 3.609 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8712 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN Y 38 GLN Z 41 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 93080 Z= 0.378 Angle : 0.916 27.877 139771 Z= 0.467 Chirality : 0.047 0.374 17913 Planarity : 0.008 0.141 7129 Dihedral : 15.520 178.981 37679 Min Nonbonded Distance : 1.659 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.64 % Favored : 97.17 % Rotamer Outliers : 2.49 % 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: 1.38 (0.18), residues: 818 sheet: 0.24 (0.20), residues: 660 loop : -0.35 (0.14), residues: 1594 *********************** 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 633 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 570 time to evaluate : 3.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 23 residues processed: 588 average time/residue: 2.0182 time to fit residues: 1536.5905 Evaluate side-chains 574 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 551 time to evaluate : 3.543 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 6 residues processed: 17 average time/residue: 1.1522 time to fit residues: 33.2698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 361 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 532 optimal weight: 3.9990 chunk 574 optimal weight: 0.9980 chunk 473 optimal weight: 1.9990 chunk 527 optimal weight: 0.9980 chunk 181 optimal weight: 10.0000 chunk 426 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 S 58 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 93080 Z= 0.154 Angle : 0.659 25.051 139771 Z= 0.355 Chirality : 0.036 0.310 17913 Planarity : 0.006 0.127 7129 Dihedral : 15.110 179.692 37679 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.31 % Favored : 97.53 % Rotamer Outliers : 1.90 % 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: 0.52 (0.15), residues: 3072 helix: 1.65 (0.18), residues: 825 sheet: 0.29 (0.20), residues: 689 loop : -0.28 (0.14), residues: 1558 *********************** 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 602 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 554 time to evaluate : 3.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 21 residues processed: 571 average time/residue: 2.0557 time to fit residues: 1523.3672 Evaluate side-chains 565 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 544 time to evaluate : 3.644 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 12 residues processed: 9 average time/residue: 1.2104 time to fit residues: 23.3995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 525 optimal weight: 1.9990 chunk 400 optimal weight: 10.0000 chunk 276 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 253 optimal weight: 7.9990 chunk 357 optimal weight: 3.9990 chunk 534 optimal weight: 2.9990 chunk 565 optimal weight: 8.9990 chunk 279 optimal weight: 7.9990 chunk 506 optimal weight: 0.6980 chunk 152 optimal weight: 7.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 3 37 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 S 58 ASN T 38 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 93080 Z= 0.332 Angle : 0.853 22.918 139771 Z= 0.441 Chirality : 0.045 0.364 17913 Planarity : 0.007 0.140 7129 Dihedral : 15.383 179.399 37679 Min Nonbonded Distance : 1.664 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.77 % Favored : 97.07 % Rotamer Outliers : 2.73 % 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: 0.18 (0.14), residues: 3072 helix: 1.33 (0.18), residues: 814 sheet: 0.13 (0.20), residues: 674 loop : -0.47 (0.14), residues: 1584 *********************** 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 620 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 551 time to evaluate : 3.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 38 residues processed: 573 average time/residue: 2.0607 time to fit residues: 1526.6277 Evaluate side-chains 580 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 542 time to evaluate : 3.579 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 14 residues processed: 24 average time/residue: 1.1390 time to fit residues: 45.4055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 470 optimal weight: 5.9990 chunk 320 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 421 optimal weight: 0.5980 chunk 233 optimal weight: 7.9990 chunk 482 optimal weight: 0.7980 chunk 390 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 507 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 overall best weight: 3.4786 ------------------------------------------------------------------------------- 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 3 37 GLN C 25 HIS D 115 GLN D 129 ASN D 176 GLN 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: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1726 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= 0.346 Angle : 0.861 20.885 139771 Z= 0.445 Chirality : 0.045 0.361 17913 Planarity : 0.007 0.140 7129 Dihedral : 15.405 179.679 37679 Min Nonbonded Distance : 1.677 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.23 % Rotamer Outliers : 2.77 % 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: 0.02 (0.14), residues: 3072 helix: 1.20 (0.18), residues: 811 sheet: 0.04 (0.20), residues: 682 loop : -0.57 (0.14), residues: 1579 *********************** 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 632 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 562 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 40 residues processed: 588 average time/residue: 2.0392 time to fit residues: 1554.5752 Evaluate side-chains 585 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 545 time to evaluate : 3.554 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 20 residues processed: 21 average time/residue: 1.0086 time to fit residues: 37.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 111 optimal weight: 5.9990 chunk 331 optimal weight: 2.9990 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 3 4 GLN 3 37 GLN 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 ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.065 93080 Z= 0.430 Angle : 0.962 20.451 139771 Z= 0.489 Chirality : 0.050 0.442 17913 Planarity : 0.008 0.146 7129 Dihedral : 15.562 179.753 37679 Min Nonbonded Distance : 1.624 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.06 % Favored : 96.74 % Rotamer Outliers : 3.04 % 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: -0.19 (0.14), residues: 3072 helix: 1.01 (0.18), residues: 805 sheet: -0.04 (0.20), residues: 682 loop : -0.72 (0.14), residues: 1585 *********************** 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 622 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 545 time to evaluate : 3.987 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 39 residues processed: 574 average time/residue: 2.0500 time to fit residues: 1528.8404 Evaluate side-chains 580 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 541 time to evaluate : 3.555 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 22 residues processed: 18 average time/residue: 0.8994 time to fit residues: 30.6242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 413 optimal weight: 0.5980 chunk 320 optimal weight: 0.6980 chunk 476 optimal weight: 10.0000 chunk 316 optimal weight: 2.9990 chunk 563 optimal weight: 3.9990 chunk 352 optimal weight: 0.9990 chunk 343 optimal weight: 3.9990 chunk 260 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 37 GLN D 129 ASN G 143 GLN I 13 HIS I 63 GLN I 95 HIS K 71 GLN N 66 ASN O 9 GLN R 37 ASN S 58 ASN Y 38 GLN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 93080 Z= 0.208 Angle : 0.717 19.976 139771 Z= 0.382 Chirality : 0.039 0.302 17913 Planarity : 0.006 0.132 7129 Dihedral : 15.199 179.978 37679 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.60 % Favored : 97.23 % Rotamer Outliers : 2.37 % 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: 0.07 (0.14), residues: 3072 helix: 1.40 (0.18), residues: 809 sheet: -0.02 (0.19), residues: 697 loop : -0.59 (0.14), residues: 1566 *********************** 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 602 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 542 time to evaluate : 3.710 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 38 residues processed: 569 average time/residue: 2.0396 time to fit residues: 1510.1205 Evaluate side-chains 570 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 532 time to evaluate : 3.617 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 24 residues processed: 15 average time/residue: 1.3208 time to fit residues: 32.5547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 348 optimal weight: 0.8980 chunk 225 optimal weight: 6.9990 chunk 336 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 358 optimal weight: 0.9980 chunk 384 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 443 optimal weight: 4.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 37 GLN D 129 ASN I 95 HIS K 71 GLN O 9 GLN P 71 GLN R 37 ASN S 58 ASN X 25 GLN Y 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.060 93080 Z= 0.373 Angle : 0.891 19.786 139771 Z= 0.458 Chirality : 0.046 0.379 17913 Planarity : 0.008 0.143 7129 Dihedral : 15.398 179.791 37679 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.93 % Favored : 96.88 % Rotamer Outliers : 2.37 % 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: -0.10 (0.14), residues: 3072 helix: 1.14 (0.18), residues: 805 sheet: -0.02 (0.19), residues: 687 loop : -0.68 (0.14), residues: 1580 *********************** 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 598 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 538 time to evaluate : 3.620 Fit side-chains revert: symmetry clash outliers start: 60 outliers final: 41 residues processed: 568 average time/residue: 2.0220 time to fit residues: 1494.7585 Evaluate side-chains 577 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 536 time to evaluate : 3.578 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 24 residues processed: 19 average time/residue: 0.9071 time to fit residues: 32.4287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 512 optimal weight: 0.9980 chunk 540 optimal weight: 2.9990 chunk 492 optimal weight: 2.9990 chunk 525 optimal weight: 6.9990 chunk 316 optimal weight: 0.7980 chunk 228 optimal weight: 6.9990 chunk 412 optimal weight: 0.9990 chunk 161 optimal weight: 8.9990 chunk 474 optimal weight: 5.9990 chunk 496 optimal weight: 3.9990 chunk 523 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN 3 37 GLN D 129 ASN G 143 GLN I 95 HIS K 71 GLN N 66 ASN O 9 GLN R 37 ASN S 58 ASN Y 38 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 93080 Z= 0.196 Angle : 0.700 19.459 139771 Z= 0.374 Chirality : 0.038 0.294 17913 Planarity : 0.006 0.131 7129 Dihedral : 15.119 179.584 37679 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.73 % Favored : 97.14 % Rotamer Outliers : 1.86 % 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: 0.10 (0.14), residues: 3072 helix: 1.42 (0.18), residues: 813 sheet: 0.02 (0.19), residues: 696 loop : -0.59 (0.14), residues: 1563 *********************** 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 589 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 542 time to evaluate : 3.895 Fit side-chains revert: symmetry clash outliers start: 47 outliers final: 35 residues processed: 569 average time/residue: 2.0566 time to fit residues: 1523.4325 Evaluate side-chains 572 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 537 time to evaluate : 3.639 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 26 residues processed: 11 average time/residue: 1.4618 time to fit residues: 26.4507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 339 optimal weight: 5.9990 chunk 263 optimal weight: 6.9990 chunk 386 optimal weight: 30.0000 chunk 582 optimal weight: 0.0050 chunk 536 optimal weight: 8.9990 chunk 464 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 358 optimal weight: 5.9990 chunk 284 optimal weight: 7.9990 overall best weight: 4.6002 ------------------------------------------------------------------------------- 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 63 GLN I 95 HIS K 71 GLN N 66 ASN O 9 GLN P 71 GLN R 37 ASN S 58 ASN T 38 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1995 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= 0.447 Angle : 0.972 19.398 139771 Z= 0.492 Chirality : 0.050 0.403 17913 Planarity : 0.008 0.146 7129 Dihedral : 15.468 179.490 37679 Min Nonbonded Distance : 1.614 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.03 % Favored : 96.81 % Rotamer Outliers : 1.74 % 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: -0.21 (0.14), residues: 3072 helix: 1.05 (0.18), residues: 799 sheet: -0.07 (0.20), residues: 675 loop : -0.76 (0.14), residues: 1598 ********************** 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 584 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 540 time to evaluate : 4.036 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 36 residues processed: 567 average time/residue: 2.0724 time to fit residues: 1525.4538 Evaluate side-chains 572 residues out of total 2531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 536 time to evaluate : 3.642 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 27 residues processed: 11 average time/residue: 1.0155 time to fit residues: 21.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 585 random chunks: chunk 368 optimal weight: 0.9980 chunk 494 optimal weight: 0.6980 chunk 142 optimal weight: 5.9990 chunk 427 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 464 optimal weight: 3.9990 chunk 194 optimal weight: 7.9990 chunk 477 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 95 HIS K 71 GLN N 66 ASN O 9 GLN R 37 ASN S 58 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.159024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.122917 restraints weight = 713894.433| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.43 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 93080 Z= 0.210 Angle : 0.718 19.203 139771 Z= 0.383 Chirality : 0.039 0.305 17913 Planarity : 0.006 0.133 7129 Dihedral : 15.137 179.040 37679 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.86 % Favored : 97.01 % Rotamer Outliers : 1.70 % 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: 0.02 (0.14), residues: 3072 helix: 1.38 (0.18), residues: 800 sheet: -0.05 (0.19), residues: 696 loop : -0.64 (0.14), residues: 1576 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21499.47 seconds wall clock time: 377 minutes 54.32 seconds (22674.32 seconds total)