Starting phenix.real_space_refine (version: dev) on Fri Dec 16 11:36:52 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5i_15175/12_2022/8a5i_15175_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "2 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 98": "OD1" <-> "OD2" Residue "G TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 167": "OE1" <-> "OE2" Residue "N ASP 90": "OD1" <-> "OD2" Residue "N PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 80": "OD1" <-> "OD2" Residue "O GLU 105": "OE1" <-> "OE2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 47": "OD1" <-> "OD2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "S PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 97": "OD1" <-> "OD2" Residue "T PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 114": "OE1" <-> "OE2" Residue "W ASP 30": "OD1" <-> "OD2" Residue "W TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 85": "OD1" <-> "OD2" Residue "X TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 78": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 89799 Number of models: 1 Model: "" Number of chains: 56 Chain: "1" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 457 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "2" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 487 Classifications: {'peptide': 59} Link IDs: {'TRANS': 58} Chain: "3" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "4" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 477 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "5" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 425 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 3, 'TRANS': 49} Chain: "6" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 400 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "7" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 357 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "8" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 512 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "9" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 292 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 3, 'TRANS': 32} Chain: "A" Number of atoms: 62459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2908, 62459 Classifications: {'RNA': 2908} Modifications used: {'rna2p_pur': 305, 'rna2p_pyr': 141, 'rna3p_pur': 1397, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 446, 'rna3p': 2461} Chain breaks: 2 Chain: "B" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2430 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 11, 'rna3p_pur': 54, 'rna3p_pyr': 46} Link IDs: {'rna2p': 14, 'rna3p': 99} Chain: "G" Number of atoms: 2108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2108 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 14, 'TRANS': 258} Chain: "H" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1582 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "I" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1563 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "J" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1365 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "K" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1271 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 10, 'TRANS': 154} Chain: "M" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1117 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 925 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1094 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "P" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1055 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 7, 'TRANS': 125} Chain: "Q" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 983 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "R" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 914 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain: "S" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 905 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 5, 'TRANS': 106} Chain: "T" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 939 Classifications: {'peptide': 116} Link IDs: {'TRANS': 115} Chain: "U" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Chain: "V" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "W" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 731 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "X" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 723 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "Z" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 563 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 211 Unusual residues: {' MG': 162, '3QB': 1, 'PUT': 2, 'SPD': 1} Classifications: {'undetermined': 166} Link IDs: {None: 165} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "5" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "7" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "8" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1223, 1223 Classifications: {'water': 1223} Link IDs: {None: 1222} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "M" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "P" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "T" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "U" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "V" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} 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 2093 SG CYS 5 30 84.838 205.898 129.956 1.00155.73 S ATOM 2113 SG CYS 5 33 83.449 205.802 126.167 1.00177.81 S ATOM 2196 SG CYS 5 43 86.907 205.643 126.474 1.00171.85 S ATOM 2218 SG CYS 5 46 83.787 207.798 126.281 1.00184.57 S ATOM 3633 SG CYS 9 11 141.456 120.656 178.955 1.00 76.98 S ATOM 3657 SG CYS 9 14 137.944 121.916 177.294 1.00 71.84 S ATOM 3761 SG CYS 9 27 140.427 124.176 179.155 1.00 65.02 S Time building chain proxies: 37.44, per 1000 atoms: 0.42 Number of scatterers: 89799 At special positions: 0 Unit cell: (187.718, 233.295, 224.025, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 K 1 19.00 S 68 16.00 P 3022 15.00 Mg 165 11.99 O 26519 8.00 N 16413 7.00 C 43609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS 6 9 " - pdb=" SG CYS 6 12 " distance=2.03 Simple disulfide: pdb=" SG CYS 6 12 " - pdb=" SG CYS 6 36 " distance=2.04 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: 41.51 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 33 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 30 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 43 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 46 " pdb=" ZN 9 101 " pdb="ZN ZN 9 101 " - pdb=" ND1 HIS 9 32 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 14 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 11 " pdb="ZN ZN 9 101 " - pdb=" SG CYS 9 27 " Number of angles added : 9 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5414 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 86 helices and 46 sheets defined 25.5% alpha, 18.9% beta 989 base pairs and 1606 stacking pairs defined. Time for finding SS restraints: 42.41 Creating SS restraints... Processing helix chain '1' and resid 51 through 54 No H-bonds generated for 'chain '1' and resid 51 through 54' Processing helix chain '2' and resid 4 through 7 No H-bonds generated for 'chain '2' and resid 4 through 7' Processing helix chain '2' and resid 11 through 33 Processing helix chain '2' and resid 40 through 60 removed outlier: 3.737A pdb=" N VAL 2 57 " --> pdb=" O LYS 2 54 " (cutoff:3.500A) Processing helix chain '3' and resid 17 through 26 Processing helix chain '3' and resid 41 through 50 Processing helix chain '5' and resid 10 through 19 removed outlier: 4.910A pdb=" N HIS 5 19 " --> pdb=" O LYS 5 15 " (cutoff:3.500A) Processing helix chain '7' and resid 9 through 16 Processing helix chain '7' and resid 18 through 23 Processing helix chain '7' and resid 25 through 37 Processing helix chain '8' and resid 8 through 11 No H-bonds generated for 'chain '8' and resid 8 through 11' Processing helix chain '8' and resid 33 through 35 No H-bonds generated for 'chain '8' and resid 33 through 35' Processing helix chain '8' and resid 38 through 44 Processing helix chain '8' and resid 52 through 62 removed outlier: 5.642A pdb=" N GLN 8 60 " --> pdb=" O LYS 8 56 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N MET 8 61 " --> pdb=" O ARG 8 57 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL 8 62 " --> pdb=" O ILE 8 58 " (cutoff:3.500A) Processing helix chain '9' and resid 30 through 32 No H-bonds generated for 'chain '9' and resid 30 through 32' Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 132 through 134 No H-bonds generated for 'chain 'G' and resid 132 through 134' Processing helix chain 'G' and resid 198 through 202 removed outlier: 4.289A pdb=" N GLU G 201 " --> pdb=" O GLU G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 214 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 265 through 269 removed outlier: 3.817A pdb=" N LYS G 268 " --> pdb=" O ASN G 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 60 No H-bonds generated for 'chain 'H' and resid 58 through 60' Processing helix chain 'H' and resid 63 through 72 removed outlier: 4.003A pdb=" N LYS H 71 " --> pdb=" O GLY H 67 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA H 72 " --> pdb=" O HIS H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 122 through 126 Processing helix chain 'I' and resid 21 through 24 No H-bonds generated for 'chain 'I' and resid 21 through 24' Processing helix chain 'I' and resid 30 through 44 Processing helix chain 'I' and resid 103 through 119 Processing helix chain 'I' and resid 136 through 146 Processing helix chain 'I' and resid 161 through 167 removed outlier: 3.550A pdb=" N LEU I 165 " --> pdb=" O GLU I 161 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 187 Processing helix chain 'I' and resid 196 through 203 Processing helix chain 'J' and resid 5 through 10 Processing helix chain 'J' and resid 13 through 20 Processing helix chain 'J' and resid 25 through 27 No H-bonds generated for 'chain 'J' and resid 25 through 27' Processing helix chain 'J' and resid 42 through 44 No H-bonds generated for 'chain 'J' and resid 42 through 44' Processing helix chain 'J' and resid 48 through 61 removed outlier: 3.533A pdb=" N SER J 52 " --> pdb=" O LYS J 48 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 105 removed outlier: 3.621A pdb=" N PHE J 99 " --> pdb=" O ARG J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 163 through 173 Processing helix chain 'K' and resid 59 through 80 removed outlier: 3.726A pdb=" N GLY K 66 " --> pdb=" O ARG K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 138 through 152 removed outlier: 3.753A pdb=" N VAL K 151 " --> pdb=" O ASN K 147 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 removed outlier: 5.805A pdb=" N SER M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 62 No H-bonds generated for 'chain 'M' and resid 60 through 62' Processing helix chain 'M' and resid 69 through 72 No H-bonds generated for 'chain 'M' and resid 69 through 72' Processing helix chain 'M' and resid 90 through 96 Processing helix chain 'M' and resid 98 through 109 removed outlier: 3.905A pdb=" N MET M 109 " --> pdb=" O SER M 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 114 through 122 removed outlier: 3.658A pdb=" N LYS M 121 " --> pdb=" O ARG M 117 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS M 122 " --> pdb=" O GLN M 118 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 136 No H-bonds generated for 'chain 'M' and resid 134 through 136' Processing helix chain 'N' and resid 104 through 109 Processing helix chain 'N' and resid 112 through 117 Processing helix chain 'O' and resid 23 through 25 No H-bonds generated for 'chain 'O' and resid 23 through 25' Processing helix chain 'O' and resid 38 through 40 No H-bonds generated for 'chain 'O' and resid 38 through 40' Processing helix chain 'O' and resid 57 through 60 No H-bonds generated for 'chain 'O' and resid 57 through 60' Processing helix chain 'O' and resid 79 through 84 Processing helix chain 'O' and resid 93 through 98 Processing helix chain 'O' and resid 130 through 139 Processing helix chain 'P' and resid 44 through 58 Processing helix chain 'P' and resid 111 through 124 removed outlier: 4.110A pdb=" N LYS P 124 " --> pdb=" O LEU P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 27 Processing helix chain 'Q' and resid 34 through 53 removed outlier: 4.507A pdb=" N LYS Q 42 " --> pdb=" O LYS Q 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL Q 43 " --> pdb=" O GLU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 56 through 63 Processing helix chain 'Q' and resid 94 through 100 Processing helix chain 'Q' and resid 103 through 106 Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 69 through 87 Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'S' and resid 3 through 12 removed outlier: 4.783A pdb=" N SER S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLN S 12 " --> pdb=" O ILE S 8 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 56 No H-bonds generated for 'chain 'S' and resid 54 through 56' Processing helix chain 'S' and resid 98 through 102 Processing helix chain 'T' and resid 9 through 21 removed outlier: 3.522A pdb=" N ILE T 17 " --> pdb=" O ARG T 13 " (cutoff:3.500A) Processing helix chain 'T' and resid 26 through 29 Processing helix chain 'T' and resid 32 through 72 removed outlier: 3.943A pdb=" N ARG T 51 " --> pdb=" O TYR T 47 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS T 54 " --> pdb=" O ARG T 50 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG T 55 " --> pdb=" O ARG T 51 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN T 72 " --> pdb=" O ALA T 68 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 86 Processing helix chain 'T' and resid 92 through 101 Processing helix chain 'T' and resid 103 through 116 Processing helix chain 'V' and resid 19 through 29 removed outlier: 4.108A pdb=" N VAL V 25 " --> pdb=" O LYS V 21 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N LEU V 28 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE V 29 " --> pdb=" O VAL V 25 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 42 Processing helix chain 'V' and resid 47 through 65 removed outlier: 4.411A pdb=" N ILE V 51 " --> pdb=" O SER V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 71 through 73 No H-bonds generated for 'chain 'V' and resid 71 through 73' Processing helix chain 'W' and resid 3 through 6 No H-bonds generated for 'chain 'W' and resid 3 through 6' Processing helix chain 'W' and resid 14 through 19 removed outlier: 3.605A pdb=" N ILE W 19 " --> pdb=" O GLU W 15 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 46 Processing helix chain 'X' and resid 65 through 67 No H-bonds generated for 'chain 'X' and resid 65 through 67' Processing sheet with id= A, first strand: chain '1' and resid 13 through 18 Processing sheet with id= B, first strand: chain '1' and resid 33 through 38 Processing sheet with id= C, first strand: chain '3' and resid 34 through 37 Processing sheet with id= D, first strand: chain '4' and resid 44 through 48 Processing sheet with id= E, first strand: chain '5' and resid 27 through 29 Processing sheet with id= F, first strand: chain '6' and resid 17 through 21 removed outlier: 4.039A pdb=" N TYR 6 17 " --> pdb=" O LEU 6 7 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '8' and resid 14 through 16 Processing sheet with id= H, first strand: chain '9' and resid 15 through 19 Processing sheet with id= I, first strand: chain 'G' and resid 3 through 5 Processing sheet with id= J, first strand: chain 'G' and resid 34 through 36 Processing sheet with id= K, first strand: chain 'G' and resid 101 through 105 removed outlier: 3.547A pdb=" N THR G 80 " --> pdb=" O LEU G 93 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ASN G 95 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL G 78 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 129 through 131 Processing sheet with id= M, first strand: chain 'G' and resid 181 through 185 removed outlier: 3.584A pdb=" N TYR G 171 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ARG G 175 " --> pdb=" O VAL G 164 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N VAL G 164 " --> pdb=" O ARG G 175 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'H' and resid 168 through 171 removed outlier: 4.663A pdb=" N VAL H 113 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU H 199 " --> pdb=" O VAL H 113 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL H 27 " --> pdb=" O VAL H 10 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET H 12 " --> pdb=" O VAL H 25 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 25 " --> pdb=" O MET H 12 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN H 14 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE H 23 " --> pdb=" O GLN H 14 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LYS H 189 " --> pdb=" O ILE H 176 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE H 176 " --> pdb=" O LYS H 189 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 80 through 84 removed outlier: 6.260A pdb=" N GLY H 52 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL H 35 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'I' and resid 123 through 126 removed outlier: 6.420A pdb=" N LEU I 192 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N LEU I 126 " --> pdb=" O LEU I 192 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE I 194 " --> pdb=" O LEU I 126 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 88 through 91 removed outlier: 7.093A pdb=" N VAL J 157 " --> pdb=" O ASP J 32 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE J 34 " --> pdb=" O VAL J 155 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL J 155 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE J 36 " --> pdb=" O ASP J 153 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ASP J 153 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL J 132 " --> pdb=" O MET J 152 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'K' and resid 16 through 20 removed outlier: 3.778A pdb=" N LYS K 27 " --> pdb=" O THR K 16 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 42 through 44 removed outlier: 3.593A pdb=" N ASN K 51 " --> pdb=" O LYS K 44 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'K' and resid 130 through 135 Processing sheet with id= U, first strand: chain 'K' and resid 95 through 99 removed outlier: 3.688A pdb=" N LYS K 102 " --> pdb=" O GLN K 99 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 16 through 20 removed outlier: 6.405A pdb=" N PHE M 54 " --> pdb=" O TYR M 17 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE M 19 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE M 56 " --> pdb=" O ILE M 19 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 74 through 78 Processing sheet with id= X, first strand: chain 'N' and resid 7 through 9 removed outlier: 6.673A pdb=" N VAL N 40 " --> pdb=" O ILE N 22 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL N 24 " --> pdb=" O VAL N 38 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N VAL N 38 " --> pdb=" O VAL N 24 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS N 59 " --> pdb=" O ILE N 87 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA N 83 " --> pdb=" O VAL N 63 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 75 through 78 Processing sheet with id= Z, first strand: chain 'O' and resid 122 through 125 removed outlier: 6.357A pdb=" N LYS O 142 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N ALA O 125 " --> pdb=" O LYS O 142 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N GLU O 144 " --> pdb=" O ALA O 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'P' and resid 129 through 133 removed outlier: 3.732A pdb=" N PHE P 104 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA P 36 " --> pdb=" O ILE P 102 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE P 102 " --> pdb=" O ALA P 36 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'P' and resid 40 through 43 removed outlier: 3.573A pdb=" N ALA P 89 " --> pdb=" O SER P 76 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N TYR P 74 " --> pdb=" O GLU P 91 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TRP P 93 " --> pdb=" O LYS P 72 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS P 72 " --> pdb=" O TRP P 93 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'Q' and resid 29 through 33 removed outlier: 5.879A pdb=" N ILE Q 131 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N LYS Q 118 " --> pdb=" O ILE Q 131 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU Q 133 " --> pdb=" O ILE Q 116 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ILE Q 116 " --> pdb=" O GLU Q 133 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'Q' and resid 70 through 73 removed outlier: 6.818A pdb=" N VAL Q 92 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'R' and resid 93 through 95 Processing sheet with id= AF, first strand: chain 'S' and resid 83 through 88 removed outlier: 3.588A pdb=" N LYS S 83 " --> pdb=" O HIS S 29 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR S 25 " --> pdb=" O ILE S 87 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG S 37 " --> pdb=" O GLU S 34 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N GLU S 44 " --> pdb=" O ILE S 64 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ILE S 64 " --> pdb=" O GLU S 44 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR S 60 " --> pdb=" O ILE S 48 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG S 50 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR S 58 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'U' and resid 10 through 15 removed outlier: 3.627A pdb=" N PHE U 40 " --> pdb=" O ILE U 4 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU U 6 " --> pdb=" O VAL U 38 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL U 38 " --> pdb=" O GLU U 6 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 19 through 23 Processing sheet with id= AI, first strand: chain 'U' and resid 32 through 35 removed outlier: 6.142A pdb=" N LYS U 61 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ILE U 97 " --> pdb=" O LYS U 61 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'U' and resid 71 through 77 removed outlier: 4.151A pdb=" N TYR U 82 " --> pdb=" O LYS U 77 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'V' and resid 7 through 12 removed outlier: 6.624A pdb=" N SER V 113 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL V 76 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 87 through 92 Processing sheet with id= AM, first strand: chain 'W' and resid 7 through 10 removed outlier: 6.889A pdb=" N GLU W 28 " --> pdb=" O LYS W 8 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR W 26 " --> pdb=" O PRO W 10 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ARG W 76 " --> pdb=" O VAL W 29 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'W' and resid 62 through 64 Processing sheet with id= AO, first strand: chain 'X' and resid 20 through 22 Processing sheet with id= AP, first strand: chain 'X' and resid 40 through 45 Processing sheet with id= AQ, first strand: chain 'X' and resid 81 through 85 Processing sheet with id= AR, first strand: chain 'X' and resid 23 through 27 removed outlier: 6.640A pdb=" N LEU X 34 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA X 26 " --> pdb=" O ARG X 32 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ARG X 32 " --> pdb=" O ALA X 26 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Z' and resid 59 through 61 Processing sheet with id= AT, first strand: chain 'Z' and resid 74 through 79 722 hydrogen bonds defined for protein. 1980 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2463 hydrogen bonds 3872 hydrogen bond angles 0 basepair planarities 989 basepair parallelities 1606 stacking parallelities Total time for adding SS restraints: 237.62 Time building geometry restraints manager: 44.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 10091 1.33 - 1.45: 45679 1.45 - 1.58: 34437 1.58 - 1.71: 6040 1.71 - 1.84: 122 Bond restraints: 96369 Sorted by residual: bond pdb=" CE1 HIS G 15 " pdb=" NE2 HIS G 15 " ideal model delta sigma weight residual 1.321 1.378 -0.057 1.00e-02 1.00e+04 3.23e+01 bond pdb=" CE1 HIS O 35 " pdb=" NE2 HIS O 35 " ideal model delta sigma weight residual 1.321 1.375 -0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" CE1 HIS U 83 " pdb=" NE2 HIS U 83 " ideal model delta sigma weight residual 1.321 1.373 -0.052 1.00e-02 1.00e+04 2.71e+01 bond pdb=" CE1 HIS T 29 " pdb=" NE2 HIS T 29 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.65e+01 bond pdb=" CE1 HIS G 142 " pdb=" NE2 HIS G 142 " ideal model delta sigma weight residual 1.321 1.372 -0.051 1.00e-02 1.00e+04 2.56e+01 ... (remaining 96364 not shown) Histogram of bond angle deviations from ideal: 85.25 - 95.50: 26 95.50 - 105.75: 15659 105.75 - 116.00: 70434 116.00 - 126.25: 49104 126.25 - 136.50: 9876 Bond angle restraints: 145099 Sorted by residual: angle pdb=" O3' A A 731 " pdb=" P U A 732 " pdb=" O5' U A 732 " ideal model delta sigma weight residual 104.00 85.25 18.75 1.50e+00 4.44e-01 1.56e+02 angle pdb=" O3' C A1849 " pdb=" C3' C A1849 " pdb=" C2' C A1849 " ideal model delta sigma weight residual 113.70 96.27 17.43 1.50e+00 4.44e-01 1.35e+02 angle pdb=" C3' A A2809 " pdb=" O3' A A2809 " pdb=" P G A2810 " ideal model delta sigma weight residual 120.20 136.50 -16.30 1.50e+00 4.44e-01 1.18e+02 angle pdb=" O3' A A2908 " pdb=" C3' A A2908 " pdb=" C2' A A2908 " ideal model delta sigma weight residual 109.50 125.73 -16.23 1.50e+00 4.44e-01 1.17e+02 angle pdb=" C3' A A2458 " pdb=" O3' A A2458 " pdb=" P A A2459 " ideal model delta sigma weight residual 120.20 136.32 -16.12 1.50e+00 4.44e-01 1.16e+02 ... (remaining 145094 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 49120 35.96 - 71.92: 1672 71.92 - 107.88: 144 107.88 - 143.85: 13 143.85 - 179.81: 39 Dihedral angle restraints: 50988 sinusoidal: 42553 harmonic: 8435 Sorted by residual: dihedral pdb=" C5' A A 548 " pdb=" C4' A A 548 " pdb=" C3' A A 548 " pdb=" O3' A A 548 " ideal model delta sinusoidal sigma weight residual 147.00 77.90 69.10 1 8.00e+00 1.56e-02 9.65e+01 dihedral pdb=" C5' C A1148 " pdb=" C4' C A1148 " pdb=" C3' C A1148 " pdb=" O3' C A1148 " ideal model delta sinusoidal sigma weight residual 147.00 80.80 66.20 1 8.00e+00 1.56e-02 8.95e+01 dihedral pdb=" O4' C A1118 " pdb=" C1' C A1118 " pdb=" N1 C A1118 " pdb=" C2 C A1118 " ideal model delta sinusoidal sigma weight residual -160.00 17.93 -177.93 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 50985 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.139: 13960 0.139 - 0.278: 4334 0.278 - 0.417: 300 0.417 - 0.556: 50 0.556 - 0.695: 9 Chirality restraints: 18653 Sorted by residual: chirality pdb=" C3' C A 251 " pdb=" C4' C A 251 " pdb=" O3' C A 251 " pdb=" C2' C A 251 " both_signs ideal model delta sigma weight residual False -2.74 -2.05 -0.69 2.00e-01 2.50e+01 1.21e+01 chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.06 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" C3' A A2809 " pdb=" C4' A A2809 " pdb=" O3' A A2809 " pdb=" C2' A A2809 " both_signs ideal model delta sigma weight residual False -2.74 -2.07 -0.67 2.00e-01 2.50e+01 1.13e+01 ... (remaining 18650 not shown) Planarity restraints: 7087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 43 " -0.850 9.50e-02 1.11e+02 3.81e-01 8.97e+01 pdb=" NE ARG G 43 " 0.058 2.00e-02 2.50e+03 pdb=" CZ ARG G 43 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG G 43 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 43 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Q 122 " -0.805 9.50e-02 1.11e+02 3.61e-01 7.92e+01 pdb=" NE ARG Q 122 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG Q 122 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG Q 122 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG Q 122 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 1 18 " -0.749 9.50e-02 1.11e+02 3.36e-01 6.90e+01 pdb=" NE ARG 1 18 " 0.048 2.00e-02 2.50e+03 pdb=" CZ ARG 1 18 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 1 18 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG 1 18 " -0.018 2.00e-02 2.50e+03 ... (remaining 7084 not shown) Histogram of nonbonded interaction distances: 1.23 - 2.01: 174 2.01 - 2.80: 21700 2.80 - 3.58: 163102 3.58 - 4.36: 362902 4.36 - 5.14: 485532 Nonbonded interactions: 1033410 Sorted by model distance: nonbonded pdb="MG MG A3035 " pdb=" O HOH A3274 " model vdw 1.234 2.170 nonbonded pdb=" OD1 ASN 5 32 " pdb=" SG CYS 5 46 " model vdw 1.641 3.400 nonbonded pdb="MG MG A3038 " pdb=" O HOH A4403 " model vdw 1.755 2.170 nonbonded pdb="MG MG A3024 " pdb=" O HOH A3616 " model vdw 1.811 2.170 nonbonded pdb="MG MG A3072 " pdb=" O HOH A4423 " model vdw 1.812 2.170 ... (remaining 1033405 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 Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians K 1 8.98 5 Zn 2 6.06 5 P 3022 5.49 5 Mg 165 5.21 5 S 68 5.16 5 C 43609 2.51 5 N 16413 2.21 5 O 26519 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 6.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 19.370 Check model and map are aligned: 0.980 Convert atoms to be neutral: 0.580 Process input model: 431.610 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 469.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.066 96369 Z= 0.642 Angle : 1.725 18.752 145099 Z= 1.132 Chirality : 0.122 0.695 18653 Planarity : 0.022 0.381 7087 Dihedral : 15.566 179.808 45568 Min Nonbonded Distance : 1.234 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 1.37 % Allowed : 5.42 % Favored : 93.21 % Rotamer Outliers : 2.48 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.88 % 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: -2.45 (0.13), residues: 2917 helix: -2.07 (0.15), residues: 757 sheet: -1.19 (0.19), residues: 624 loop : -1.50 (0.14), residues: 1536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 580 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 10 residues processed: 620 average time/residue: 2.1087 time to fit residues: 1690.8012 Evaluate side-chains 433 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 423 time to evaluate : 3.673 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 2 average time/residue: 0.6220 time to fit residues: 6.2491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 495 optimal weight: 6.9990 chunk 444 optimal weight: 5.9990 chunk 246 optimal weight: 10.0000 chunk 151 optimal weight: 30.0000 chunk 300 optimal weight: 8.9990 chunk 237 optimal weight: 10.0000 chunk 460 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 279 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 chunk 533 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 41 ASN 2 17 GLN 2 31 GLN 3 17 GLN 4 6 HIS 5 32 ASN 6 4 ASN 6 22 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 38 GLN 9 29 ASN G 194 GLN G 199 GLN G 226 ASN H 66 GLN I 171 GLN J 46 ASN K 99 GLN K 130 GLN K 137 ASN O 35 HIS R 32 ASN S 12 GLN T 52 GLN V 33 GLN V 95 GLN W 37 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.069 96369 Z= 0.355 Angle : 0.900 12.373 145099 Z= 0.455 Chirality : 0.047 0.471 18653 Planarity : 0.009 0.171 7087 Dihedral : 15.042 178.955 39553 Min Nonbonded Distance : 1.538 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.41 % Allowed : 3.26 % Favored : 96.33 % Rotamer Outliers : 3.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.84 (0.14), residues: 2917 helix: 0.11 (0.18), residues: 759 sheet: -0.50 (0.20), residues: 624 loop : -0.86 (0.15), residues: 1534 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 467 time to evaluate : 3.865 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 32 residues processed: 507 average time/residue: 2.1170 time to fit residues: 1386.2033 Evaluate side-chains 454 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 422 time to evaluate : 3.668 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 19 residues processed: 13 average time/residue: 1.0953 time to fit residues: 25.9985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 296 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 443 optimal weight: 0.1980 chunk 362 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 576 optimal weight: 0.4980 chunk 475 optimal weight: 0.6980 chunk 529 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 428 optimal weight: 0.0030 overall best weight: 1.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN 9 29 ASN G 194 GLN G 199 GLN H 201 GLN I 119 ASN J 172 GLN K 137 ASN R 58 ASN T 52 GLN T 101 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 96369 Z= 0.148 Angle : 0.601 9.495 145099 Z= 0.321 Chirality : 0.037 0.296 18653 Planarity : 0.005 0.091 7087 Dihedral : 14.628 177.052 39553 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.46 % Favored : 96.37 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.26 (0.15), residues: 2917 helix: 0.79 (0.19), residues: 771 sheet: -0.20 (0.20), residues: 648 loop : -0.61 (0.15), residues: 1498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 435 time to evaluate : 3.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 31 residues processed: 470 average time/residue: 2.0625 time to fit residues: 1260.5865 Evaluate side-chains 450 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 419 time to evaluate : 3.723 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 21 residues processed: 10 average time/residue: 0.7924 time to fit residues: 17.7529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 527 optimal weight: 9.9990 chunk 401 optimal weight: 0.0770 chunk 277 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 254 optimal weight: 40.0000 chunk 358 optimal weight: 20.0000 chunk 535 optimal weight: 5.9990 chunk 567 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 chunk 507 optimal weight: 9.9990 chunk 152 optimal weight: 320.0000 overall best weight: 7.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 5 41 HIS 6 4 ASN 6 22 ASN 6 26 ASN 9 29 ASN G 194 GLN G 199 GLN H 66 GLN H 191 ASN I 119 ASN K 106 ASN ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 137 ASN N 110 ASN O 70 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN T 52 GLN V 33 GLN V 73 ASN ** X 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.075 96369 Z= 0.357 Angle : 0.878 10.090 145099 Z= 0.445 Chirality : 0.047 0.380 18653 Planarity : 0.008 0.137 7087 Dihedral : 14.920 179.799 39553 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.63 % Favored : 96.13 % Rotamer Outliers : 3.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.40 (0.15), residues: 2917 helix: 0.60 (0.19), residues: 743 sheet: -0.12 (0.20), residues: 637 loop : -0.71 (0.15), residues: 1537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 425 time to evaluate : 3.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 37 residues processed: 481 average time/residue: 2.1425 time to fit residues: 1339.5920 Evaluate side-chains 448 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 411 time to evaluate : 3.744 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 27 residues processed: 10 average time/residue: 1.0872 time to fit residues: 20.8015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 472 optimal weight: 0.8980 chunk 322 optimal weight: 20.0000 chunk 8 optimal weight: 6.9990 chunk 422 optimal weight: 30.0000 chunk 234 optimal weight: 20.0000 chunk 484 optimal weight: 9.9990 chunk 392 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 289 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 29 ASN G 194 GLN G 199 GLN I 119 ASN I 145 ASN I 171 GLN K 74 ASN K 106 ASN ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 70 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN V 33 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.080 96369 Z= 0.355 Angle : 0.867 10.484 145099 Z= 0.441 Chirality : 0.047 0.366 18653 Planarity : 0.008 0.131 7087 Dihedral : 15.008 179.732 39553 Min Nonbonded Distance : 1.559 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.98 % Favored : 95.75 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: 2917 helix: 0.44 (0.19), residues: 744 sheet: -0.18 (0.20), residues: 631 loop : -0.75 (0.15), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 429 time to evaluate : 3.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 87 outliers final: 48 residues processed: 486 average time/residue: 2.0943 time to fit residues: 1320.4640 Evaluate side-chains 468 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 420 time to evaluate : 3.761 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 36 residues processed: 12 average time/residue: 1.0015 time to fit residues: 23.0916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 190 optimal weight: 10.0000 chunk 510 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 333 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 567 optimal weight: 5.9990 chunk 471 optimal weight: 3.9990 chunk 262 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 187 optimal weight: 20.0000 chunk 298 optimal weight: 10.0000 overall best weight: 6.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN K 65 HIS ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 70 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN V 33 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 96369 Z= 0.324 Angle : 0.828 10.851 145099 Z= 0.423 Chirality : 0.045 0.364 18653 Planarity : 0.007 0.120 7087 Dihedral : 14.944 178.181 39553 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.11 % Favored : 95.61 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.15), residues: 2917 helix: 0.54 (0.19), residues: 742 sheet: -0.24 (0.20), residues: 635 loop : -0.73 (0.15), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 416 time to evaluate : 3.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 89 outliers final: 48 residues processed: 480 average time/residue: 2.0971 time to fit residues: 1306.4119 Evaluate side-chains 456 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 408 time to evaluate : 3.907 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.8312 time to fit residues: 23.1406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 547 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 323 optimal weight: 10.0000 chunk 414 optimal weight: 7.9990 chunk 321 optimal weight: 10.9990 chunk 478 optimal weight: 7.9990 chunk 317 optimal weight: 10.0000 chunk 565 optimal weight: 1.9990 chunk 354 optimal weight: 20.0000 chunk 344 optimal weight: 2.9990 chunk 261 optimal weight: 30.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 70 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 96369 Z= 0.317 Angle : 0.822 10.517 145099 Z= 0.420 Chirality : 0.045 0.366 18653 Planarity : 0.007 0.119 7087 Dihedral : 14.932 179.549 39553 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.11 % Favored : 95.61 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.48 (0.15), residues: 2917 helix: 0.54 (0.19), residues: 747 sheet: -0.23 (0.20), residues: 630 loop : -0.73 (0.15), residues: 1540 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 412 time to evaluate : 3.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 49 residues processed: 465 average time/residue: 2.0918 time to fit residues: 1265.5173 Evaluate side-chains 457 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 408 time to evaluate : 3.679 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 40 residues processed: 10 average time/residue: 1.3140 time to fit residues: 23.3716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 350 optimal weight: 1.9990 chunk 225 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 170 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 109 optimal weight: 10.0000 chunk 359 optimal weight: 9.9990 chunk 385 optimal weight: 0.9990 chunk 279 optimal weight: 10.0000 chunk 52 optimal weight: 20.0000 chunk 444 optimal weight: 9.9990 overall best weight: 6.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 70 ASN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 102 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.074 96369 Z= 0.333 Angle : 0.843 11.029 145099 Z= 0.430 Chirality : 0.045 0.371 18653 Planarity : 0.007 0.119 7087 Dihedral : 14.962 178.759 39553 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.29 % Favored : 95.41 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.53 (0.15), residues: 2917 helix: 0.48 (0.18), residues: 743 sheet: -0.24 (0.20), residues: 632 loop : -0.76 (0.15), residues: 1542 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 415 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 52 residues processed: 468 average time/residue: 2.1465 time to fit residues: 1307.4535 Evaluate side-chains 460 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 408 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 41 residues processed: 12 average time/residue: 1.0036 time to fit residues: 23.4522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 514 optimal weight: 0.8980 chunk 542 optimal weight: 6.9990 chunk 494 optimal weight: 0.8980 chunk 527 optimal weight: 9.9990 chunk 541 optimal weight: 6.9990 chunk 317 optimal weight: 10.0000 chunk 229 optimal weight: 20.0000 chunk 414 optimal weight: 0.0970 chunk 161 optimal weight: 9.9990 chunk 476 optimal weight: 9.9990 chunk 498 optimal weight: 10.0000 overall best weight: 3.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 70 ASN R 58 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 96369 Z= 0.193 Angle : 0.652 9.373 145099 Z= 0.344 Chirality : 0.038 0.328 18653 Planarity : 0.006 0.082 7087 Dihedral : 14.693 179.841 39553 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.87 % Favored : 95.92 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.29 (0.15), residues: 2917 helix: 0.81 (0.19), residues: 752 sheet: -0.14 (0.20), residues: 644 loop : -0.68 (0.15), residues: 1521 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 419 time to evaluate : 3.923 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 38 residues processed: 462 average time/residue: 2.0855 time to fit residues: 1255.3622 Evaluate side-chains 450 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 412 time to evaluate : 3.746 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 36 residues processed: 3 average time/residue: 0.9822 time to fit residues: 9.0216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 525 optimal weight: 7.9990 chunk 346 optimal weight: 0.8980 chunk 557 optimal weight: 6.9990 chunk 340 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 387 optimal weight: 9.9990 chunk 584 optimal weight: 20.0000 chunk 538 optimal weight: 5.9990 chunk 465 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 359 optimal weight: 0.0770 overall best weight: 2.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 110 ASN O 70 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 96369 Z= 0.184 Angle : 0.637 8.906 145099 Z= 0.336 Chirality : 0.037 0.325 18653 Planarity : 0.006 0.079 7087 Dihedral : 14.599 179.846 39553 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.91 % Favored : 95.92 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2917 helix: 0.96 (0.19), residues: 747 sheet: -0.10 (0.20), residues: 648 loop : -0.63 (0.15), residues: 1522 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 418 time to evaluate : 4.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 37 residues processed: 456 average time/residue: 2.1015 time to fit residues: 1245.7122 Evaluate side-chains 450 residues out of total 2497 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 413 time to evaluate : 3.737 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 36 residues processed: 1 average time/residue: 2.0359 time to fit residues: 6.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 587 random chunks: chunk 285 optimal weight: 9.9990 chunk 369 optimal weight: 10.0000 chunk 496 optimal weight: 6.9990 chunk 142 optimal weight: 9.9990 chunk 429 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 466 optimal weight: 0.0050 chunk 195 optimal weight: 20.0000 chunk 478 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 5.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 31 GLN 3 17 GLN 6 4 ASN 6 22 ASN 6 26 ASN ** 8 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 29 ASN G 194 GLN G 199 GLN G 265 ASN H 66 GLN I 119 ASN I 145 ASN ** J 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 110 ASN O 70 ASN V 33 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.167302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.120610 restraints weight = 61925.624| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 0.94 r_work: 0.3017 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.2781 rms_B_bonded: 4.59 restraints_weight: 0.1250 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.065 96369 Z= 0.283 Angle : 0.768 10.702 145099 Z= 0.395 Chirality : 0.042 0.355 18653 Planarity : 0.007 0.101 7087 Dihedral : 14.779 178.722 39553 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.88 % 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: -0.31 (0.15), residues: 2917 helix: 0.79 (0.19), residues: 744 sheet: -0.16 (0.20), residues: 637 loop : -0.68 (0.15), residues: 1536 =============================================================================== Job complete usr+sys time: 22327.74 seconds wall clock time: 393 minutes 21.69 seconds (23601.69 seconds total)