Starting phenix.real_space_refine (version: dev) on Mon May 16 00:24:56 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxf_11519/05_2022/6zxf_11519_updated.pdb" } resolution = 3.7 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= -0.000 sd= 0.009 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 "C PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 80133 Number of models: 1 Model: "" Number of chains: 41 Chain: "2" Number of atoms: 35367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1656, 35367 Classifications: {'RNA': 1656} Modifications used: {'rna3p_pyr': 660, 'rna2p_pur': 140, 'rna3p_pur': 743, 'rna2p_pyr': 113} Link IDs: {'rna3p': 1403, 'rna2p': 252} Chain breaks: 12 Chain: "A" Number of atoms: 1705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1705 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "B" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1715 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 5, 'TRANS': 205} Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1674 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain: "E" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2031 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 14, 'TRANS': 240} Chain: "D" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1745 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "G" Number of atoms: 1802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1802 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain: "H" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1446 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 9, 'TRANS': 169} Chain breaks: 3 Chain: "I" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 7, 'TRANS': 191} Chain breaks: 1 Chain: "J" Number of atoms: 1465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1465 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 6, 'TRANS': 169} Chain breaks: 1 Chain: "F" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1461 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 1 Chain: "L" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1127 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "K" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 799 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 7, 'TRANS': 87} Chain: "N" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "O" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 947 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain breaks: 2 Chain: "P" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1072 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "R" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 983 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 1116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1116 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "S" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1162 Classifications: {'peptide': 141} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 137} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "T" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1094 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "W" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 125, 'PCIS': 2} Chain: "X" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1080 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 987 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "U" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 557 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "b" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 611 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 5, 'TRANS': 71} Chain breaks: 1 Chain: "c" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 479 Classifications: {'peptide': 61} Link IDs: {'PTRANS': 1, 'TRANS': 59} Chain: "d" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 458 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "e" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 398 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain breaks: 1 Chain: "f" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 465 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain breaks: 1 Chain: "g" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2306 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 10, 'TRANS': 284} Chain breaks: 3 Chain: "j" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 928 Classifications: {'peptide': 115} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "z" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3041 Classifications: {'peptide': 373} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "y" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1838 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 12, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "k" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 2117 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 362} Link IDs: {'PTRANS': 36, 'TRANS': 393} Chain breaks: 5 Unresolved chain link angles: 36 Unresolved non-hydrogen bonds: 1241 Unresolved non-hydrogen angles: 1570 Unresolved non-hydrogen dihedrals: 1001 Unresolved non-hydrogen chiralities: 127 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 17, 'TYR:plan': 6, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 32, 'ARG:plan': 34} Unresolved non-hydrogen planarities: 590 Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 68712 SG CYS d 21 158.618 155.825 68.676 1.00 40.12 S ATOM 68736 SG CYS d 24 155.586 154.064 68.057 1.00 42.19 S ATOM 68857 SG CYS d 39 154.312 156.763 70.001 1.00 42.74 S ATOM 68883 SG CYS d 42 156.187 154.228 71.552 1.00 39.64 S ATOM 69809 SG CYS f 141 179.219 144.025 27.354 1.00107.22 S ATOM 69828 SG CYS f 144 180.243 147.205 28.541 1.00106.78 S ATOM 77303 SG CYS y 270 107.647 167.507 147.397 1.00 57.24 S ATOM 77323 SG CYS y 273 110.255 167.278 149.812 1.00 63.12 S ATOM 77420 SG CYS y 285 111.093 168.541 146.341 1.00 59.69 S ATOM 77442 SG CYS y 288 109.922 165.005 145.908 1.00 65.00 S Time building chain proxies: 34.16, per 1000 atoms: 0.43 Number of scatterers: 80133 At special positions: 0 Unit cell: (214.632, 247.152, 194.036, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 201 16.00 P 1659 15.00 Mg 2 11.99 O 19484 8.00 N 14752 7.00 C 44032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS g 240 " - pdb=" SG CYS g 249 " distance=2.06 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: 30.29 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN d 101 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 21 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 39 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 24 " pdb="ZN ZN d 101 " - pdb=" SG CYS d 42 " pdb=" ZN f 500 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 144 " pdb="ZN ZN f 500 " - pdb=" SG CYS f 141 " pdb=" ZN y 500 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 270 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 285 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 273 " pdb="ZN ZN y 500 " - pdb=" SG CYS y 288 " Number of angles added : 12 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10718 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 189 helices and 68 sheets defined 29.3% alpha, 14.8% beta 490 base pairs and 852 stacking pairs defined. Time for finding SS restraints: 25.32 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 32 through 35 removed outlier: 3.585A pdb=" N GLU A 35 " --> pdb=" O PHE A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 32 through 35' Processing helix chain 'A' and resid 51 through 66 Processing helix chain 'A' and resid 81 through 93 removed outlier: 5.421A pdb=" N ARG A 85 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 139 removed outlier: 4.037A pdb=" N TYR A 139 " --> pdb=" O THR A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 199 through 201 No H-bonds generated for 'chain 'A' and resid 199 through 201' Processing helix chain 'A' and resid 207 through 215 removed outlier: 4.653A pdb=" N GLU A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 61 No H-bonds generated for 'chain 'B' and resid 58 through 61' Processing helix chain 'B' and resid 107 through 113 Processing helix chain 'B' and resid 158 through 176 Processing helix chain 'B' and resid 181 through 189 Processing helix chain 'B' and resid 192 through 200 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'C' and resid 65 through 71 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 147 through 160 Processing helix chain 'C' and resid 208 through 217 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 265 through 268 No H-bonds generated for 'chain 'C' and resid 265 through 268' Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'E' and resid 16 through 18 No H-bonds generated for 'chain 'E' and resid 16 through 18' Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 58 through 66 Processing helix chain 'E' and resid 72 through 74 No H-bonds generated for 'chain 'E' and resid 72 through 74' Processing helix chain 'E' and resid 222 through 224 No H-bonds generated for 'chain 'E' and resid 222 through 224' Processing helix chain 'E' and resid 248 through 253 Processing helix chain 'D' and resid 7 through 28 Processing helix chain 'D' and resid 55 through 58 No H-bonds generated for 'chain 'D' and resid 55 through 58' Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 98 through 109 Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'G' and resid 138 through 145 Processing helix chain 'G' and resid 182 through 220 Processing helix chain 'H' and resid 18 through 32 removed outlier: 3.649A pdb=" N MET H 32 " --> pdb=" O LEU H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 42 No H-bonds generated for 'chain 'H' and resid 40 through 42' Processing helix chain 'H' and resid 66 through 72 removed outlier: 4.873A pdb=" N LYS H 70 " --> pdb=" O PRO H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 118 through 120 No H-bonds generated for 'chain 'H' and resid 118 through 120' Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 163 through 166 No H-bonds generated for 'chain 'H' and resid 163 through 166' Processing helix chain 'H' and resid 169 through 180 Processing helix chain 'I' and resid 26 through 28 No H-bonds generated for 'chain 'I' and resid 26 through 28' Processing helix chain 'I' and resid 89 through 92 No H-bonds generated for 'chain 'I' and resid 89 through 92' Processing helix chain 'I' and resid 107 through 114 Processing helix chain 'I' and resid 131 through 137 Processing helix chain 'I' and resid 143 through 155 removed outlier: 4.469A pdb=" N ASN I 155 " --> pdb=" O GLU I 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 168 Processing helix chain 'I' and resid 179 through 182 No H-bonds generated for 'chain 'I' and resid 179 through 182' Processing helix chain 'I' and resid 192 through 205 Processing helix chain 'J' and resid 22 through 35 Processing helix chain 'J' and resid 40 through 60 Processing helix chain 'J' and resid 68 through 84 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 94 through 97 removed outlier: 3.893A pdb=" N ILE J 97 " --> pdb=" O LEU J 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 94 through 97' Processing helix chain 'J' and resid 102 through 105 No H-bonds generated for 'chain 'J' and resid 102 through 105' Processing helix chain 'J' and resid 110 through 115 Processing helix chain 'J' and resid 123 through 130 Processing helix chain 'J' and resid 153 through 156 Processing helix chain 'J' and resid 172 through 177 removed outlier: 3.567A pdb=" N ASN J 177 " --> pdb=" O VAL J 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 21 No H-bonds generated for 'chain 'F' and resid 19 through 21' Processing helix chain 'F' and resid 34 through 37 removed outlier: 4.025A pdb=" N ASP F 37 " --> pdb=" O SER F 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 34 through 37' Processing helix chain 'F' and resid 68 through 74 Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.514A pdb=" N ARG F 91 " --> pdb=" O LEU F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 117 Processing helix chain 'F' and resid 143 through 158 removed outlier: 4.804A pdb=" N GLY F 157 " --> pdb=" O LEU F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 181 removed outlier: 3.547A pdb=" N ALA F 181 " --> pdb=" O LEU F 177 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 203 removed outlier: 4.209A pdb=" N GLU F 195 " --> pdb=" O LYS F 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 18 removed outlier: 4.048A pdb=" N GLU K 18 " --> pdb=" O LEU K 14 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 35 No H-bonds generated for 'chain 'K' and resid 33 through 35' Processing helix chain 'K' and resid 42 through 54 Processing helix chain 'K' and resid 73 through 83 removed outlier: 3.595A pdb=" N GLN K 77 " --> pdb=" O ASN K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 94 No H-bonds generated for 'chain 'K' and resid 92 through 94' Processing helix chain 'N' and resid 30 through 43 removed outlier: 3.808A pdb=" N LYS N 43 " --> pdb=" O LYS N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 47 through 56 Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 71 through 77 Processing helix chain 'N' and resid 86 through 104 Processing helix chain 'N' and resid 109 through 131 Processing helix chain 'N' and resid 146 through 149 No H-bonds generated for 'chain 'N' and resid 146 through 149' Processing helix chain 'O' and resid 58 through 60 No H-bonds generated for 'chain 'O' and resid 58 through 60' Processing helix chain 'O' and resid 65 through 67 No H-bonds generated for 'chain 'O' and resid 65 through 67' Processing helix chain 'O' and resid 71 through 87 Processing helix chain 'O' and resid 113 through 122 removed outlier: 3.797A pdb=" N ARG O 121 " --> pdb=" O ARG O 117 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 19 through 27 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 59 through 71 removed outlier: 4.319A pdb=" N LYS M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU M 64 " --> pdb=" O MET M 60 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU M 66 " --> pdb=" O VAL M 62 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 120 through 128 removed outlier: 4.499A pdb=" N TYR M 127 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE M 128 " --> pdb=" O ILE M 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 26 Processing helix chain 'P' and resid 30 through 34 Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 51 through 65 Processing helix chain 'P' and resid 87 through 89 No H-bonds generated for 'chain 'P' and resid 87 through 89' Processing helix chain 'P' and resid 109 through 111 No H-bonds generated for 'chain 'P' and resid 109 through 111' Processing helix chain 'P' and resid 116 through 118 No H-bonds generated for 'chain 'P' and resid 116 through 118' Processing helix chain 'R' and resid 7 through 17 Processing helix chain 'R' and resid 28 through 38 removed outlier: 3.568A pdb=" N ARG R 33 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 Processing helix chain 'R' and resid 72 through 82 Processing helix chain 'R' and resid 100 through 108 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 45 through 58 removed outlier: 4.537A pdb=" N TYR Q 49 " --> pdb=" O THR Q 46 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU Q 53 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) Proline residue: Q 54 - end of helix Processing helix chain 'Q' and resid 60 through 63 No H-bonds generated for 'chain 'Q' and resid 60 through 63' Processing helix chain 'Q' and resid 79 through 99 Processing helix chain 'Q' and resid 106 through 115 Processing helix chain 'Q' and resid 117 through 119 No H-bonds generated for 'chain 'Q' and resid 117 through 119' Processing helix chain 'S' and resid 26 through 28 No H-bonds generated for 'chain 'S' and resid 26 through 28' Processing helix chain 'S' and resid 30 through 32 No H-bonds generated for 'chain 'S' and resid 30 through 32' Processing helix chain 'S' and resid 38 through 47 Processing helix chain 'S' and resid 56 through 58 No H-bonds generated for 'chain 'S' and resid 56 through 58' Processing helix chain 'S' and resid 61 through 72 Processing helix chain 'S' and resid 75 through 77 No H-bonds generated for 'chain 'S' and resid 75 through 77' Processing helix chain 'S' and resid 102 through 116 Processing helix chain 'S' and resid 120 through 126 Processing helix chain 'T' and resid 11 through 25 Processing helix chain 'T' and resid 32 through 35 removed outlier: 4.165A pdb=" N ASP T 35 " --> pdb=" O GLU T 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 32 through 35' Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 72 through 78 removed outlier: 3.894A pdb=" N LYS T 77 " --> pdb=" O GLY T 73 " (cutoff:3.500A) Processing helix chain 'T' and resid 97 through 109 Processing helix chain 'T' and resid 125 through 141 removed outlier: 3.659A pdb=" N ALA T 141 " --> pdb=" O GLN T 137 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 61 Processing helix chain 'V' and resid 65 through 74 Processing helix chain 'W' and resid 6 through 19 Processing helix chain 'W' and resid 32 through 44 removed outlier: 3.885A pdb=" N HIS W 44 " --> pdb=" O VAL W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 113 through 118 Processing helix chain 'X' and resid 10 through 23 removed outlier: 4.160A pdb=" N TRP X 22 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS X 23 " --> pdb=" O ASP X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 31 Processing helix chain 'X' and resid 34 through 38 Processing helix chain 'X' and resid 91 through 93 No H-bonds generated for 'chain 'X' and resid 91 through 93' Processing helix chain 'X' and resid 130 through 134 Processing helix chain 'Y' and resid 37 through 48 Processing helix chain 'Y' and resid 52 through 54 No H-bonds generated for 'chain 'Y' and resid 52 through 54' Processing helix chain 'Y' and resid 79 through 84 Processing helix chain 'Y' and resid 88 through 94 Processing helix chain 'Y' and resid 104 through 116 removed outlier: 3.502A pdb=" N LYS Y 108 " --> pdb=" O ARG Y 104 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS Y 116 " --> pdb=" O ASN Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 119 through 122 removed outlier: 3.604A pdb=" N LYS Y 122 " --> pdb=" O GLY Y 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 119 through 122' Processing helix chain 'U' and resid 29 through 45 Processing helix chain 'U' and resid 95 through 104 Processing helix chain 'Z' and resid 52 through 60 removed outlier: 3.762A pdb=" N ASP Z 56 " --> pdb=" O LYS Z 52 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N LYS Z 57 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 64 No H-bonds generated for 'chain 'Z' and resid 62 through 64' Processing helix chain 'Z' and resid 70 through 77 Processing helix chain 'Z' and resid 81 through 93 removed outlier: 3.888A pdb=" N SER Z 93 " --> pdb=" O GLN Z 89 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 16 Processing helix chain 'd' and resid 33 through 35 No H-bonds generated for 'chain 'd' and resid 33 through 35' Processing helix chain 'd' and resid 40 through 50 removed outlier: 6.006A pdb=" N LYS d 48 " --> pdb=" O ARG d 44 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP d 49 " --> pdb=" O GLN d 45 " (cutoff:3.500A) Processing helix chain 'e' and resid 11 through 14 No H-bonds generated for 'chain 'e' and resid 11 through 14' Processing helix chain 'e' and resid 31 through 42 Processing helix chain 'j' and resid 4 through 14 Processing helix chain 'j' and resid 90 through 97 Processing helix chain 'j' and resid 104 through 106 No H-bonds generated for 'chain 'j' and resid 104 through 106' Processing helix chain 'z' and resid 131 through 145 removed outlier: 4.323A pdb=" N ASP z 145 " --> pdb=" O GLN z 141 " (cutoff:3.500A) Processing helix chain 'z' and resid 164 through 176 Processing helix chain 'z' and resid 220 through 222 No H-bonds generated for 'chain 'z' and resid 220 through 222' Processing helix chain 'z' and resid 228 through 231 No H-bonds generated for 'chain 'z' and resid 228 through 231' Processing helix chain 'z' and resid 239 through 259 Processing helix chain 'z' and resid 298 through 316 Processing helix chain 'z' and resid 353 through 371 removed outlier: 3.745A pdb=" N LEU z 357 " --> pdb=" O ALA z 353 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N HIS z 371 " --> pdb=" O PHE z 367 " (cutoff:3.500A) Processing helix chain 'z' and resid 378 through 386 Processing helix chain 'z' and resid 396 through 406 Processing helix chain 'z' and resid 421 through 424 No H-bonds generated for 'chain 'z' and resid 421 through 424' Processing helix chain 'z' and resid 441 through 445 Processing helix chain 'z' and resid 447 through 449 No H-bonds generated for 'chain 'z' and resid 447 through 449' Processing helix chain 'z' and resid 533 through 547 removed outlier: 3.636A pdb=" N LYS z 547 " --> pdb=" O ARG z 543 " (cutoff:3.500A) Processing helix chain 'z' and resid 552 through 557 Processing helix chain 'y' and resid 31 through 33 No H-bonds generated for 'chain 'y' and resid 31 through 33' Processing helix chain 'y' and resid 40 through 43 No H-bonds generated for 'chain 'y' and resid 40 through 43' Processing helix chain 'y' and resid 45 through 47 No H-bonds generated for 'chain 'y' and resid 45 through 47' Processing helix chain 'y' and resid 60 through 73 removed outlier: 3.587A pdb=" N PHE y 69 " --> pdb=" O LEU y 65 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS y 71 " --> pdb=" O THR y 67 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS y 72 " --> pdb=" O GLU y 68 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR y 73 " --> pdb=" O PHE y 69 " (cutoff:3.500A) Processing helix chain 'y' and resid 81 through 97 Processing helix chain 'y' and resid 239 through 247 Processing helix chain 'k' and resid 12 through 18 removed outlier: 3.729A pdb=" N ALA k 16 " --> pdb=" O GLU k 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 29 through 36 Processing helix chain 'k' and resid 46 through 48 No H-bonds generated for 'chain 'k' and resid 46 through 48' Processing helix chain 'k' and resid 146 through 151 removed outlier: 4.190A pdb=" N CYS k 151 " --> pdb=" O LEU k 148 " (cutoff:3.500A) Processing helix chain 'k' and resid 196 through 200 Processing helix chain 'k' and resid 219 through 223 Processing helix chain 'k' and resid 242 through 248 removed outlier: 3.832A pdb=" N SER k 247 " --> pdb=" O GLU k 243 " (cutoff:3.500A) Processing helix chain 'k' and resid 251 through 260 removed outlier: 4.279A pdb=" N VAL k 260 " --> pdb=" O GLU k 256 " (cutoff:3.500A) Processing helix chain 'k' and resid 352 through 366 Processing helix chain 'k' and resid 411 through 424 removed outlier: 3.855A pdb=" N GLU k 421 " --> pdb=" O GLN k 417 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ARG k 424 " --> pdb=" O LEU k 418 " (cutoff:3.500A) Processing helix chain 'k' and resid 437 through 440 Processing helix chain 'k' and resid 468 through 470 No H-bonds generated for 'chain 'k' and resid 468 through 470' Processing helix chain 'k' and resid 492 through 502 Processing sheet with id= A, first strand: chain 'A' and resid 97 through 100 Processing sheet with id= B, first strand: chain 'A' and resid 38 through 41 removed outlier: 7.181A pdb=" N ILE A 48 " --> pdb=" O TYR A 39 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 28 through 32 Processing sheet with id= D, first strand: chain 'B' and resid 66 through 70 removed outlier: 4.579A pdb=" N ILE B 87 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N PHE B 100 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.724A pdb=" N ASP B 90 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 121 through 128 removed outlier: 3.637A pdb=" N LEU B 134 " --> pdb=" O LYS B 219 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS B 219 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ARG B 136 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N MET B 217 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N PHE B 138 " --> pdb=" O VAL B 215 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL B 215 " --> pdb=" O PHE B 138 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 139 through 144 removed outlier: 3.697A pdb=" N GLY C 119 " --> pdb=" O THR C 116 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS C 108 " --> pdb=" O PHE C 127 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA C 129 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL C 106 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY C 131 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ASP C 104 " --> pdb=" O GLY C 131 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 184 through 188 Processing sheet with id= I, first strand: chain 'E' and resid 41 through 43 removed outlier: 3.825A pdb=" N ALA E 84 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 70 through 72 Processing sheet with id= K, first strand: chain 'E' and resid 121 through 125 removed outlier: 6.549A pdb=" N ASP E 163 " --> pdb=" O ILE E 169 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ILE E 169 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 128 through 132 removed outlier: 3.755A pdb=" N LYS E 128 " --> pdb=" O VAL E 140 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 217 through 221 removed outlier: 3.882A pdb=" N ASN E 197 " --> pdb=" O HIS E 209 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS E 211 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE E 195 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 180 through 183 removed outlier: 3.614A pdb=" N LEU E 180 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 229 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N MET E 182 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL E 227 " --> pdb=" O MET E 182 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 84 through 86 removed outlier: 7.317A pdb=" N THR D 46 " --> pdb=" O GLU D 85 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 148 through 155 removed outlier: 3.620A pdb=" N GLY D 133 " --> pdb=" O MET D 189 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 12 through 17 removed outlier: 7.221A pdb=" N VAL G 49 " --> pdb=" O VAL G 114 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 72 through 77 Processing sheet with id= S, first strand: chain 'H' and resid 91 through 95 removed outlier: 3.736A pdb=" N HIS H 91 " --> pdb=" O LYS H 58 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 141 through 146 Processing sheet with id= U, first strand: chain 'I' and resid 62 through 67 Processing sheet with id= V, first strand: chain 'I' and resid 170 through 174 removed outlier: 3.623A pdb=" N ASP I 80 " --> pdb=" O LEU I 103 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ASP I 105 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE I 78 " --> pdb=" O ASP I 105 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 42 through 47 removed outlier: 7.111A pdb=" N HIS I 44 " --> pdb=" O ALA I 57 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ALA I 57 " --> pdb=" O HIS I 44 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL I 46 " --> pdb=" O TYR I 55 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR I 55 " --> pdb=" O VAL I 46 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 135 through 137 Processing sheet with id= Y, first strand: chain 'F' and resid 123 through 127 Processing sheet with id= Z, first strand: chain 'L' and resid 101 through 112 removed outlier: 5.989A pdb=" N ARG L 89 " --> pdb=" O VAL L 77 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL L 77 " --> pdb=" O ARG L 89 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N ASP L 91 " --> pdb=" O GLY L 75 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N GLY L 75 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 15.298A pdb=" N LEU L 93 " --> pdb=" O LEU L 73 " (cutoff:3.500A) removed outlier: 16.775A pdb=" N LEU L 73 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLY L 129 " --> pdb=" O VAL L 142 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL L 142 " --> pdb=" O GLY L 129 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 20 through 23 removed outlier: 3.529A pdb=" N ALA K 23 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'O' and resid 129 through 131 removed outlier: 6.357A pdb=" N ILE O 95 " --> pdb=" O GLU O 130 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'M' and resid 108 through 111 removed outlier: 6.235A pdb=" N ILE M 77 " --> pdb=" O LEU M 52 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'P' and resid 76 through 78 Processing sheet with id= AE, first strand: chain 'R' and resid 96 through 98 Processing sheet with id= AF, first strand: chain 'Q' and resid 9 through 15 Processing sheet with id= AG, first strand: chain 'S' and resid 12 through 14 Processing sheet with id= AH, first strand: chain 'T' and resid 81 through 83 Processing sheet with id= AI, first strand: chain 'T' and resid 113 through 115 Processing sheet with id= AJ, first strand: chain 'V' and resid 32 through 37 Processing sheet with id= AK, first strand: chain 'W' and resid 24 through 27 Processing sheet with id= AL, first strand: chain 'W' and resid 72 through 74 removed outlier: 6.732A pdb=" N VAL W 103 " --> pdb=" O LEU W 126 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE W 128 " --> pdb=" O PHE W 101 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N PHE W 101 " --> pdb=" O PHE W 128 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 120 through 122 removed outlier: 6.906A pdb=" N ARG X 71 " --> pdb=" O LEU X 52 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS X 54 " --> pdb=" O CYS X 69 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N CYS X 69 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY X 56 " --> pdb=" O ARG X 67 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ARG X 67 " --> pdb=" O GLY X 56 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'Y' and resid 6 through 10 Processing sheet with id= AO, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id= AP, first strand: chain 'U' and resid 111 through 115 removed outlier: 4.008A pdb=" N LYS U 49 " --> pdb=" O HIS U 92 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 54 through 56 removed outlier: 4.511A pdb=" N LYS U 86 " --> pdb=" O MET U 56 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'U' and resid 59 through 66 Processing sheet with id= AS, first strand: chain 'Z' and resid 97 through 102 removed outlier: 7.015A pdb=" N ILE Z 108 " --> pdb=" O VAL Z 100 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'b' and resid 32 through 36 Processing sheet with id= AU, first strand: chain 'c' and resid 55 through 58 removed outlier: 6.856A pdb=" N ARG c 31 " --> pdb=" O THR c 15 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL c 17 " --> pdb=" O GLN c 29 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLN c 29 " --> pdb=" O VAL c 17 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'c' and resid 19 through 21 Processing sheet with id= AW, first strand: chain 'f' and resid 133 through 135 Processing sheet with id= AX, first strand: chain 'g' and resid 58 through 60 removed outlier: 3.805A pdb=" N THR g 39 " --> pdb=" O SER g 35 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'g' and resid 43 through 45 Processing sheet with id= AZ, first strand: chain 'g' and resid 66 through 69 removed outlier: 6.907A pdb=" N GLY g 81 " --> pdb=" O SER g 67 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N VAL g 69 " --> pdb=" O LEU g 79 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU g 79 " --> pdb=" O VAL g 69 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP g 91 " --> pdb=" O THR g 97 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N THR g 97 " --> pdb=" O ASP g 91 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'g' and resid 108 through 113 removed outlier: 7.040A pdb=" N GLY g 123 " --> pdb=" O LEU g 109 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL g 111 " --> pdb=" O VAL g 121 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N VAL g 121 " --> pdb=" O VAL g 111 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE g 129 " --> pdb=" O VAL g 142 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'g' and resid 151 through 156 removed outlier: 6.830A pdb=" N CYS g 168 " --> pdb=" O SER g 152 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL g 154 " --> pdb=" O VAL g 166 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL g 166 " --> pdb=" O VAL g 154 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE g 156 " --> pdb=" O ILE g 164 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE g 164 " --> pdb=" O PHE g 156 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ASN g 178 " --> pdb=" O LEU g 184 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N LEU g 184 " --> pdb=" O ASN g 178 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'g' and resid 195 through 200 removed outlier: 7.053A pdb=" N GLY g 210 " --> pdb=" O ASN g 196 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL g 198 " --> pdb=" O ALA g 208 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA g 208 " --> pdb=" O VAL g 198 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL g 200 " --> pdb=" O LEU g 206 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU g 206 " --> pdb=" O VAL g 200 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY g 211 " --> pdb=" O GLN g 215 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N GLN g 215 " --> pdb=" O GLY g 211 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ASP g 220 " --> pdb=" O HIS g 226 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N HIS g 226 " --> pdb=" O ASP g 220 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'g' and resid 239 through 241 removed outlier: 4.317A pdb=" N CYS g 240 " --> pdb=" O CYS g 249 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'g' and resid 307 through 311 Processing sheet with id= BF, first strand: chain 'g' and resid 256 through 259 removed outlier: 3.831A pdb=" N ASP g 268 " --> pdb=" O ILE g 258 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'j' and resid 68 through 71 removed outlier: 6.669A pdb=" N GLU j 40 " --> pdb=" O LEU j 31 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N SER j 52 " --> pdb=" O LYS j 81 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU j 83 " --> pdb=" O SER j 52 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE j 70 " --> pdb=" O SER j 85 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL j 87 " --> pdb=" O PHE j 68 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N PHE j 68 " --> pdb=" O VAL j 87 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'z' and resid 267 through 271 removed outlier: 7.141A pdb=" N VAL z 276 " --> pdb=" O ILE z 268 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU z 270 " --> pdb=" O VAL z 274 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL z 274 " --> pdb=" O LEU z 270 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'z' and resid 330 through 333 Processing sheet with id= BJ, first strand: chain 'z' and resid 185 through 188 removed outlier: 6.802A pdb=" N VAL z 194 " --> pdb=" O ILE z 186 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'y' and resid 26 through 28 Processing sheet with id= BL, first strand: chain 'y' and resid 275 through 277 removed outlier: 3.705A pdb=" N LYS y 275 " --> pdb=" O CYS y 270 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N SER y 265 " --> pdb=" O VAL y 298 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER y 297 " --> pdb=" O HIS y 309 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'k' and resid 79 through 81 removed outlier: 7.179A pdb=" N VAL k 103 " --> pdb=" O LEU k 80 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER k 133 " --> pdb=" O LEU k 104 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'k' and resid 157 through 159 removed outlier: 6.570A pdb=" N GLU k 183 " --> pdb=" O LEU k 158 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR k 206 " --> pdb=" O LEU k 184 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU k 229 " --> pdb=" O LEU k 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'k' and resid 336 through 339 Processing sheet with id= BP, first strand: chain 'k' and resid 388 through 392 1419 hydrogen bonds defined for protein. 4011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1227 hydrogen bonds 1948 hydrogen bond angles 0 basepair planarities 490 basepair parallelities 852 stacking parallelities Total time for adding SS restraints: 53.70 Time building geometry restraints manager: 32.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 10413 1.32 - 1.44: 31798 1.44 - 1.57: 39204 1.57 - 1.70: 3303 1.70 - 1.82: 314 Bond restraints: 85032 Sorted by residual: bond pdb=" C4 ATP z 603 " pdb=" C5 ATP z 603 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.22e+01 bond pdb=" C5 ATP z 603 " pdb=" C6 ATP z 603 " ideal model delta sigma weight residual 1.409 1.466 -0.057 1.00e-02 1.00e+04 3.19e+01 bond pdb=" C4 ATP z 603 " pdb=" N9 ATP z 603 " ideal model delta sigma weight residual 1.374 1.320 0.054 1.00e-02 1.00e+04 2.92e+01 bond pdb=" C5 ATP z 603 " pdb=" N7 ATP z 603 " ideal model delta sigma weight residual 1.387 1.335 0.052 1.00e-02 1.00e+04 2.71e+01 bond pdb=" C8 ATP z 603 " pdb=" N7 ATP z 603 " ideal model delta sigma weight residual 1.310 1.353 -0.043 1.00e-02 1.00e+04 1.82e+01 ... (remaining 85027 not shown) Histogram of bond angle deviations from ideal: 97.86 - 105.47: 8958 105.47 - 113.09: 49745 113.09 - 120.71: 37931 120.71 - 128.33: 23510 128.33 - 135.95: 2621 Bond angle restraints: 122765 Sorted by residual: angle pdb=" PA ATP z 603 " pdb=" O3A ATP z 603 " pdb=" PB ATP z 603 " ideal model delta sigma weight residual 136.83 115.12 21.71 1.00e+00 1.00e+00 4.71e+02 angle pdb=" PB ATP z 603 " pdb=" O3B ATP z 603 " pdb=" PG ATP z 603 " ideal model delta sigma weight residual 139.87 123.14 16.73 1.00e+00 1.00e+00 2.80e+02 angle pdb=" C5 ATP z 603 " pdb=" C4 ATP z 603 " pdb=" N3 ATP z 603 " ideal model delta sigma weight residual 126.80 119.08 7.72 1.00e+00 1.00e+00 5.97e+01 angle pdb=" N3 ATP z 603 " pdb=" C4 ATP z 603 " pdb=" N9 ATP z 603 " ideal model delta sigma weight residual 127.04 134.54 -7.50 1.15e+00 7.59e-01 4.27e+01 angle pdb=" C3' A 21060 " pdb=" O3' A 21060 " pdb=" P U 21061 " ideal model delta sigma weight residual 120.20 128.12 -7.92 1.50e+00 4.44e-01 2.79e+01 ... (remaining 122760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 45975 35.84 - 71.68: 1674 71.68 - 107.51: 156 107.51 - 143.35: 13 143.35 - 179.19: 32 Dihedral angle restraints: 47850 sinusoidal: 31283 harmonic: 16567 Sorted by residual: dihedral pdb=" CB CYS g 240 " pdb=" SG CYS g 240 " pdb=" SG CYS g 249 " pdb=" CB CYS g 249 " ideal model delta sinusoidal sigma weight residual -86.00 -1.67 -84.33 1 1.00e+01 1.00e-02 8.65e+01 dihedral pdb=" O4' C 21139 " pdb=" C1' C 21139 " pdb=" N1 C 21139 " pdb=" C2 C 21139 " ideal model delta sinusoidal sigma weight residual -160.00 19.19 -179.19 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 21485 " pdb=" C1' U 21485 " pdb=" N1 U 21485 " pdb=" C2 U 21485 " ideal model delta sinusoidal sigma weight residual -160.00 17.89 -177.89 1 1.50e+01 4.44e-03 8.53e+01 ... (remaining 47847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 13139 0.078 - 0.156: 1843 0.156 - 0.233: 139 0.233 - 0.311: 14 0.311 - 0.389: 10 Chirality restraints: 15145 Sorted by residual: chirality pdb=" C1' A 2 25 " pdb=" O4' A 2 25 " pdb=" C2' A 2 25 " pdb=" N9 A 2 25 " both_signs ideal model delta sigma weight residual False 2.46 2.07 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C3' U 21367 " pdb=" C4' U 21367 " pdb=" O3' U 21367 " pdb=" C2' U 21367 " both_signs ideal model delta sigma weight residual False -2.48 -2.09 -0.39 2.00e-01 2.50e+01 3.76e+00 chirality pdb=" C3' G 2 509 " pdb=" C4' G 2 509 " pdb=" O3' G 2 509 " pdb=" C2' G 2 509 " both_signs ideal model delta sigma weight residual False -2.48 -2.10 -0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 15142 not shown) Planarity restraints: 9458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U 2 918 " -0.055 2.00e-02 2.50e+03 2.76e-02 1.71e+01 pdb=" N1 U 2 918 " 0.054 2.00e-02 2.50e+03 pdb=" C2 U 2 918 " 0.012 2.00e-02 2.50e+03 pdb=" O2 U 2 918 " 0.005 2.00e-02 2.50e+03 pdb=" N3 U 2 918 " -0.005 2.00e-02 2.50e+03 pdb=" C4 U 2 918 " -0.013 2.00e-02 2.50e+03 pdb=" O4 U 2 918 " -0.010 2.00e-02 2.50e+03 pdb=" C5 U 2 918 " -0.009 2.00e-02 2.50e+03 pdb=" C6 U 2 918 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 2 961 " 0.054 2.00e-02 2.50e+03 2.31e-02 1.60e+01 pdb=" N9 G 2 961 " -0.050 2.00e-02 2.50e+03 pdb=" C8 G 2 961 " -0.008 2.00e-02 2.50e+03 pdb=" N7 G 2 961 " -0.002 2.00e-02 2.50e+03 pdb=" C5 G 2 961 " -0.003 2.00e-02 2.50e+03 pdb=" C6 G 2 961 " 0.024 2.00e-02 2.50e+03 pdb=" O6 G 2 961 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G 2 961 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G 2 961 " -0.008 2.00e-02 2.50e+03 pdb=" N2 G 2 961 " -0.007 2.00e-02 2.50e+03 pdb=" N3 G 2 961 " -0.006 2.00e-02 2.50e+03 pdb=" C4 G 2 961 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE J 105 " 0.021 2.00e-02 2.50e+03 2.99e-02 1.57e+01 pdb=" CG PHE J 105 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 PHE J 105 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE J 105 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE J 105 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE J 105 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE J 105 " -0.001 2.00e-02 2.50e+03 ... (remaining 9455 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 779 2.53 - 3.12: 57400 3.12 - 3.71: 144933 3.71 - 4.31: 197216 4.31 - 4.90: 292651 Nonbonded interactions: 692979 Sorted by model distance: nonbonded pdb="MG MG z 602 " pdb=" O2G ATP z 603 " model vdw 1.937 2.170 nonbonded pdb="MG MG z 601 " pdb=" O2B ATP z 603 " model vdw 1.956 2.170 nonbonded pdb="MG MG z 602 " pdb=" O2A ATP z 603 " model vdw 1.962 2.170 nonbonded pdb="MG MG z 602 " pdb=" O3B ATP z 603 " model vdw 1.991 2.170 nonbonded pdb="MG MG z 601 " pdb=" O2G ATP z 603 " model vdw 2.086 2.170 ... (remaining 692974 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1659 5.49 5 Mg 2 5.21 5 S 201 5.16 5 C 44032 2.51 5 N 14752 2.21 5 O 19484 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 group one per residue 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: 3.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.420 Construct map_model_manager: 0.100 Extract box with map and model: 14.960 Check model and map are aligned: 0.900 Convert atoms to be neutral: 0.540 Process input model: 215.680 Find NCS groups from input model: 2.040 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 241.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 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 : 0.010 0.121 85032 Z= 0.590 Angle : 0.981 21.705 122765 Z= 0.507 Chirality : 0.054 0.389 15145 Planarity : 0.006 0.071 9458 Dihedral : 16.798 179.189 37129 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.49 % Favored : 91.48 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.09), residues: 5632 helix: -2.43 (0.09), residues: 1769 sheet: -2.18 (0.15), residues: 921 loop : -2.56 (0.10), residues: 2942 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1267 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1237 time to evaluate : 5.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 11 residues processed: 1256 average time/residue: 0.7557 time to fit residues: 1595.1731 Evaluate side-chains 885 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 874 time to evaluate : 5.155 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6330 time to fit residues: 18.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 612 optimal weight: 6.9990 chunk 549 optimal weight: 2.9990 chunk 304 optimal weight: 0.7980 chunk 187 optimal weight: 2.9990 chunk 370 optimal weight: 0.4980 chunk 293 optimal weight: 6.9990 chunk 568 optimal weight: 4.9990 chunk 219 optimal weight: 0.8980 chunk 345 optimal weight: 0.1980 chunk 422 optimal weight: 10.0000 chunk 658 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 141 ASN ** B 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 ASN C 136 HIS C 235 ASN E 8 HIS E 50 ASN E 98 ASN E 112 HIS ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN G 56 ASN G 65 GLN G 155 GLN ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN H 114 GLN H 165 ASN H 193 GLN ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 116 HIS I 168 GLN J 113 GLN ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 GLN J 154 GLN F 29 GLN F 83 ASN F 114 ASN L 121 GLN K 61 GLN N 58 HIS ** O 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN P 104 GLN Q 86 GLN S 72 GLN ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 35 ASN W 16 ASN W 113 HIS X 46 HIS ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 97 ASN U 28 ASN Z 46 ASN Z 106 GLN d 4 GLN d 5 GLN d 45 GLN e 56 ASN e 58 ASN g 4 GLN g 14 HIS g 56 GLN g 143 GLN ** g 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 305 ASN g 311 GLN j 25 GLN z 160 GLN z 316 GLN z 363 ASN z 463 ASN z 553 HIS y 6 HIS y 85 GLN y 318 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 85032 Z= 0.165 Angle : 0.617 13.480 122765 Z= 0.319 Chirality : 0.039 0.327 15145 Planarity : 0.004 0.079 9458 Dihedral : 15.804 179.895 26145 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.55 (0.10), residues: 5632 helix: -1.10 (0.11), residues: 1774 sheet: -1.77 (0.16), residues: 919 loop : -2.03 (0.11), residues: 2939 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1057 time to evaluate : 5.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 62 residues processed: 1117 average time/residue: 0.7697 time to fit residues: 1481.5807 Evaluate side-chains 956 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 894 time to evaluate : 5.122 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5645 time to fit residues: 73.5166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 365 optimal weight: 6.9990 chunk 204 optimal weight: 6.9990 chunk 547 optimal weight: 2.9990 chunk 448 optimal weight: 4.9990 chunk 181 optimal weight: 0.5980 chunk 659 optimal weight: 0.0770 chunk 712 optimal weight: 20.0000 chunk 587 optimal weight: 20.0000 chunk 654 optimal weight: 9.9990 chunk 224 optimal weight: 2.9990 chunk 529 optimal weight: 2.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 95 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN E 50 ASN E 98 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 ASN O 79 GLN ** O 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN Q 24 HIS ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 GLN X 20 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN U 81 GLN Z 46 ASN Z 103 HIS e 44 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN ** y 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 318 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 85032 Z= 0.185 Angle : 0.590 10.621 122765 Z= 0.304 Chirality : 0.038 0.353 15145 Planarity : 0.004 0.069 9458 Dihedral : 15.595 179.801 26145 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 2.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.00 (0.11), residues: 5632 helix: -0.50 (0.12), residues: 1774 sheet: -1.48 (0.16), residues: 924 loop : -1.79 (0.11), residues: 2934 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1088 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 968 time to evaluate : 5.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 120 outliers final: 60 residues processed: 1038 average time/residue: 0.7375 time to fit residues: 1318.2343 Evaluate side-chains 938 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 878 time to evaluate : 5.326 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 0 residues processed: 60 average time/residue: 0.5874 time to fit residues: 72.8247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 651 optimal weight: 7.9990 chunk 495 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 314 optimal weight: 3.9990 chunk 442 optimal weight: 1.9990 chunk 661 optimal weight: 10.0000 chunk 700 optimal weight: 0.0870 chunk 345 optimal weight: 0.1980 chunk 627 optimal weight: 3.9990 chunk 188 optimal weight: 20.0000 overall best weight: 2.0564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN O 113 GLN ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN ** X 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 89 HIS g 64 HIS j 3 GLN j 25 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.095 85032 Z= 0.185 Angle : 0.576 12.748 122765 Z= 0.297 Chirality : 0.038 0.367 15145 Planarity : 0.004 0.096 9458 Dihedral : 15.463 179.462 26145 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.11), residues: 5632 helix: -0.15 (0.12), residues: 1775 sheet: -1.39 (0.16), residues: 932 loop : -1.58 (0.11), residues: 2925 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 971 time to evaluate : 5.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 104 outliers final: 58 residues processed: 1026 average time/residue: 0.7341 time to fit residues: 1298.9805 Evaluate side-chains 938 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 880 time to evaluate : 5.203 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 0 residues processed: 58 average time/residue: 0.6057 time to fit residues: 72.1611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 583 optimal weight: 10.0000 chunk 397 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 521 optimal weight: 0.0470 chunk 289 optimal weight: 6.9990 chunk 598 optimal weight: 5.9990 chunk 484 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 357 optimal weight: 7.9990 chunk 629 optimal weight: 10.0000 chunk 176 optimal weight: 1.9990 overall best weight: 3.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN C 272 HIS ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN G 187 HIS ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN J 132 GLN J 143 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 91 HIS V 49 GLN X 73 GLN X 127 ASN g 64 HIS g 226 HIS ** j 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 292 ASN ** y 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.083 85032 Z= 0.242 Angle : 0.603 10.509 122765 Z= 0.309 Chirality : 0.039 0.374 15145 Planarity : 0.004 0.069 9458 Dihedral : 15.452 179.776 26145 Min Nonbonded Distance : 1.533 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5632 helix: -0.00 (0.12), residues: 1775 sheet: -1.38 (0.16), residues: 952 loop : -1.47 (0.12), residues: 2905 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1029 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 931 time to evaluate : 5.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 59 residues processed: 980 average time/residue: 0.7510 time to fit residues: 1280.6224 Evaluate side-chains 929 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 870 time to evaluate : 5.277 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.5967 time to fit residues: 73.3373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 235 optimal weight: 0.3980 chunk 631 optimal weight: 3.9990 chunk 138 optimal weight: 10.0000 chunk 411 optimal weight: 6.9990 chunk 172 optimal weight: 6.9990 chunk 701 optimal weight: 40.0000 chunk 582 optimal weight: 0.4980 chunk 324 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 232 optimal weight: 4.9990 chunk 368 optimal weight: 0.0770 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN C 115 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 HIS ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN I 168 GLN ** J 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 143 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN ** z 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.072 85032 Z= 0.149 Angle : 0.571 12.136 122765 Z= 0.291 Chirality : 0.036 0.357 15145 Planarity : 0.004 0.072 9458 Dihedral : 15.324 179.838 26145 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 1.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.11), residues: 5632 helix: 0.16 (0.13), residues: 1765 sheet: -1.24 (0.16), residues: 936 loop : -1.34 (0.12), residues: 2931 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 985 time to evaluate : 6.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 1014 average time/residue: 0.7464 time to fit residues: 1308.9350 Evaluate side-chains 941 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 908 time to evaluate : 5.243 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5918 time to fit residues: 43.4601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 676 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 512 optimal weight: 0.7980 chunk 396 optimal weight: 3.9990 chunk 590 optimal weight: 10.0000 chunk 391 optimal weight: 5.9990 chunk 698 optimal weight: 0.0570 chunk 437 optimal weight: 0.0270 chunk 426 optimal weight: 4.9990 chunk 322 optimal weight: 0.8980 overall best weight: 1.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 174 HIS ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN J 143 ASN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 55 ASN ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 31 ASN ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 21 ASN X 127 ASN z 363 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.088 85032 Z= 0.152 Angle : 0.578 15.373 122765 Z= 0.294 Chirality : 0.036 0.372 15145 Planarity : 0.005 0.306 9458 Dihedral : 15.232 179.629 26145 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 1.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.11), residues: 5632 helix: 0.18 (0.13), residues: 1773 sheet: -1.17 (0.16), residues: 948 loop : -1.27 (0.12), residues: 2911 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 979 time to evaluate : 5.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 40 residues processed: 1016 average time/residue: 0.7356 time to fit residues: 1286.8564 Evaluate side-chains 948 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 908 time to evaluate : 5.170 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.6062 time to fit residues: 51.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 432 optimal weight: 0.2980 chunk 279 optimal weight: 0.6980 chunk 417 optimal weight: 0.0470 chunk 210 optimal weight: 0.0270 chunk 137 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 444 optimal weight: 4.9990 chunk 476 optimal weight: 6.9990 chunk 345 optimal weight: 0.9990 chunk 65 optimal weight: 10.0000 chunk 549 optimal weight: 0.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 GLN ** H 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 GLN ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 ASN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 181 GLN ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 104 GLN ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 GLN X 20 GLN ** Y 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 56 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 311 GLN j 25 GLN z 232 HIS z 363 ASN y 271 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.052 85032 Z= 0.139 Angle : 0.581 15.820 122765 Z= 0.294 Chirality : 0.036 0.370 15145 Planarity : 0.004 0.100 9458 Dihedral : 15.128 178.786 26145 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.11), residues: 5632 helix: 0.29 (0.13), residues: 1776 sheet: -1.11 (0.16), residues: 944 loop : -1.21 (0.12), residues: 2912 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1020 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 975 time to evaluate : 5.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 24 residues processed: 988 average time/residue: 0.7414 time to fit residues: 1267.9090 Evaluate side-chains 924 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 900 time to evaluate : 5.302 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.5904 time to fit residues: 33.3270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 635 optimal weight: 10.0000 chunk 669 optimal weight: 3.9990 chunk 610 optimal weight: 10.0000 chunk 651 optimal weight: 3.9990 chunk 391 optimal weight: 9.9990 chunk 283 optimal weight: 0.0570 chunk 511 optimal weight: 0.9990 chunk 199 optimal weight: 0.0870 chunk 588 optimal weight: 9.9990 chunk 615 optimal weight: 7.9990 chunk 648 optimal weight: 3.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN E 67 GLN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** G 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 141 ASN N 36 GLN O 38 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 GLN X 127 ASN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 3 GLN j 25 GLN ** z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.161 85032 Z= 0.189 Angle : 0.593 14.114 122765 Z= 0.302 Chirality : 0.036 0.376 15145 Planarity : 0.004 0.077 9458 Dihedral : 15.092 179.918 26145 Min Nonbonded Distance : 1.507 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5632 helix: 0.36 (0.13), residues: 1779 sheet: -1.07 (0.16), residues: 950 loop : -1.16 (0.12), residues: 2903 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 958 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 919 time to evaluate : 5.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 23 residues processed: 937 average time/residue: 0.7594 time to fit residues: 1233.9371 Evaluate side-chains 915 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 892 time to evaluate : 5.419 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.6205 time to fit residues: 33.4704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 427 optimal weight: 0.1980 chunk 688 optimal weight: 50.0000 chunk 420 optimal weight: 9.9990 chunk 326 optimal weight: 9.9990 chunk 478 optimal weight: 6.9990 chunk 722 optimal weight: 40.0000 chunk 664 optimal weight: 0.8980 chunk 575 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 444 optimal weight: 10.0000 chunk 352 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 235 ASN ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 157 ASN ** E 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 GLN ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 HIS ** L 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 ASN ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN ** R 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 HIS ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 76 GLN ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN ** Y 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 65 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 285 GLN ** j 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN ** z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 271 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 85032 Z= 0.302 Angle : 0.662 14.449 122765 Z= 0.337 Chirality : 0.039 0.403 15145 Planarity : 0.005 0.124 9458 Dihedral : 15.250 179.825 26145 Min Nonbonded Distance : 1.056 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.11), residues: 5632 helix: 0.27 (0.13), residues: 1775 sheet: -1.07 (0.17), residues: 922 loop : -1.18 (0.12), residues: 2935 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11264 Ramachandran restraints generated. 5632 Oldfield, 0 Emsley, 5632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 894 time to evaluate : 5.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 21 residues processed: 906 average time/residue: 0.7550 time to fit residues: 1181.4606 Evaluate side-chains 880 residues out of total 4990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 859 time to evaluate : 5.265 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.5703 time to fit residues: 29.2534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 725 random chunks: chunk 456 optimal weight: 0.0870 chunk 612 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 530 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 576 optimal weight: 0.2980 chunk 241 optimal weight: 0.4980 chunk 591 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 overall best weight: 2.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 112 HIS ** O 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 93 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 101 ASN ** S 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 127 ASN b 65 GLN ** g 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 25 GLN ** z 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.066399 restraints weight = 273831.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.067947 restraints weight = 129434.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.068151 restraints weight = 94303.222| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 85032 Z= 0.198 Angle : 0.611 13.882 122765 Z= 0.311 Chirality : 0.037 0.375 15145 Planarity : 0.004 0.093 9458 Dihedral : 15.197 178.863 26145 Min Nonbonded Distance : 1.090 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.82 % 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: -0.98 (0.11), residues: 5632 helix: 0.35 (0.13), residues: 1767 sheet: -1.05 (0.17), residues: 925 loop : -1.11 (0.12), residues: 2940 =============================================================================== Job complete usr+sys time: 18672.69 seconds wall clock time: 329 minutes 30.46 seconds (19770.46 seconds total)