Starting phenix.real_space_refine on Thu Dec 14 16:49:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lnc_0930/12_2023/6lnc_0930.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 59 5.49 5 S 151 5.16 5 C 18194 2.51 5 N 4991 2.21 5 O 5542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 178": "NH1" <-> "NH2" Residue "G ARG 210": "NH1" <-> "NH2" Residue "G TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 37": "NH1" <-> "NH2" Residue "F ARG 178": "NH1" <-> "NH2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "F PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 37": "NH1" <-> "NH2" Residue "E ARG 178": "NH1" <-> "NH2" Residue "E ARG 210": "NH1" <-> "NH2" Residue "D PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 178": "NH1" <-> "NH2" Residue "D ARG 210": "NH1" <-> "NH2" Residue "D PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C ARG 178": "NH1" <-> "NH2" Residue "C ARG 210": "NH1" <-> "NH2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 172": "NH1" <-> "NH2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 21": "NH1" <-> "NH2" Residue "H ARG 24": "NH1" <-> "NH2" Residue "H ARG 67": "NH1" <-> "NH2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 93": "NH1" <-> "NH2" Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 228": "NH1" <-> "NH2" Residue "H ARG 234": "NH1" <-> "NH2" Residue "H ARG 243": "NH1" <-> "NH2" Residue "H ARG 259": "NH1" <-> "NH2" Residue "H ARG 274": "NH1" <-> "NH2" Residue "H ARG 503": "NH1" <-> "NH2" Residue "H ARG 584": "NH1" <-> "NH2" Residue "H PHE 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 622": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 121": "NH1" <-> "NH2" Residue "A ARG 125": "NH1" <-> "NH2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "J ARG 5": "NH1" <-> "NH2" Residue "J ARG 20": "NH1" <-> "NH2" Residue "J ARG 58": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 117": "NH1" <-> "NH2" Residue "J TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 274": "NH1" <-> "NH2" Residue "I ARG 5": "NH1" <-> "NH2" Residue "I ARG 20": "NH1" <-> "NH2" Residue "I ARG 58": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 117": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 249": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 28937 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1276 Classifications: {'RNA': 60} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 22, 'rna3p_pyr': 17} Link IDs: {'rna2p': 21, 'rna3p': 38} Chain: "G" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 2 Chain: "F" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2688 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Chain: "E" Number of atoms: 2689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2689 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2697 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2682 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 319} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2500 Classifications: {'peptide': 309} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 292} Chain breaks: 2 Chain: "H" Number of atoms: 3957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3957 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 479} Chain breaks: 3 Chain: "A" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1611 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "J" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Chain: "I" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3070 Classifications: {'peptide': 376} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 357} Chain breaks: 2 Time building chain proxies: 15.80, per 1000 atoms: 0.55 Number of scatterers: 28937 At special positions: 0 Unit cell: (149.04, 170.64, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 151 16.00 P 59 15.00 O 5542 8.00 N 4991 7.00 C 18194 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.85 Conformation dependent library (CDL) restraints added in 5.5 seconds 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6562 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 37 sheets defined 29.3% alpha, 13.8% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 9.62 Creating SS restraints... Processing helix chain 'G' and resid 106 through 123 Processing helix chain 'G' and resid 125 through 134 removed outlier: 3.782A pdb=" N MET G 134 " --> pdb=" O THR G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 183 Processing helix chain 'G' and resid 186 through 200 removed outlier: 3.960A pdb=" N ILE G 190 " --> pdb=" O ASN G 186 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE G 194 " --> pdb=" O ILE G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 269 removed outlier: 3.549A pdb=" N ALA G 266 " --> pdb=" O PHE G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.641A pdb=" N ILE G 309 " --> pdb=" O ASP G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 312 through 320 removed outlier: 3.804A pdb=" N GLU G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU G 320 " --> pdb=" O TYR G 316 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 344 Processing helix chain 'F' and resid 105 through 123 removed outlier: 3.900A pdb=" N LYS F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N THR F 111 " --> pdb=" O LYS F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 137 removed outlier: 4.051A pdb=" N ASN F 135 " --> pdb=" O ARG F 131 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE F 136 " --> pdb=" O TYR F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 3.799A pdb=" N LYS F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 200 removed outlier: 3.794A pdb=" N ILE F 194 " --> pdb=" O ILE F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 269 removed outlier: 3.572A pdb=" N GLY F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 311 removed outlier: 3.600A pdb=" N ILE F 309 " --> pdb=" O ASP F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 320 Processing helix chain 'F' and resid 329 through 342 Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.703A pdb=" N LEU E 48 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 45 through 49' Processing helix chain 'E' and resid 61 through 66 removed outlier: 3.651A pdb=" N ALA E 66 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 123 removed outlier: 4.429A pdb=" N GLN E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N THR E 111 " --> pdb=" O LYS E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 170 through 175 Processing helix chain 'E' and resid 177 through 183 removed outlier: 3.611A pdb=" N PHE E 181 " --> pdb=" O SER E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 200 removed outlier: 3.899A pdb=" N ALA E 197 " --> pdb=" O MET E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 299 through 303 Processing helix chain 'E' and resid 305 through 311 removed outlier: 3.748A pdb=" N SER E 308 " --> pdb=" O ASP E 305 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU E 310 " --> pdb=" O PHE E 307 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLN E 311 " --> pdb=" O SER E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 320 removed outlier: 3.813A pdb=" N TYR E 316 " --> pdb=" O GLN E 312 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 342 removed outlier: 3.761A pdb=" N ILE E 331 " --> pdb=" O ALA E 327 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN E 332 " --> pdb=" O GLN E 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.922A pdb=" N LEU D 48 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 45 through 49' Processing helix chain 'D' and resid 106 through 123 removed outlier: 3.875A pdb=" N GLN D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 137 removed outlier: 4.181A pdb=" N ASN D 135 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 183 removed outlier: 3.522A pdb=" N ASN D 183 " --> pdb=" O GLN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 299 through 303 Processing helix chain 'D' and resid 305 through 311 removed outlier: 3.517A pdb=" N ILE D 309 " --> pdb=" O ASP D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 320 Processing helix chain 'D' and resid 333 through 344 removed outlier: 3.698A pdb=" N GLY D 344 " --> pdb=" O ASN D 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.870A pdb=" N LYS C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLN C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 138 removed outlier: 4.348A pdb=" N ASN C 135 " --> pdb=" O ARG C 131 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE C 136 " --> pdb=" O TYR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 4.059A pdb=" N LEU C 142 " --> pdb=" O GLY C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 183 removed outlier: 3.796A pdb=" N PHE C 181 " --> pdb=" O SER C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 196 Processing helix chain 'C' and resid 299 through 303 removed outlier: 3.600A pdb=" N GLY C 303 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.539A pdb=" N ILE C 309 " --> pdb=" O ASP C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 320 Processing helix chain 'C' and resid 330 through 344 removed outlier: 3.774A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 123 removed outlier: 4.006A pdb=" N THR B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 138 removed outlier: 4.093A pdb=" N ASN B 135 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 175 removed outlier: 3.788A pdb=" N TYR B 175 " --> pdb=" O ILE B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 183 removed outlier: 3.634A pdb=" N ASN B 183 " --> pdb=" O GLN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 200 Processing helix chain 'B' and resid 305 through 311 Processing helix chain 'B' and resid 312 through 320 Processing helix chain 'B' and resid 330 through 343 removed outlier: 4.103A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 342 " --> pdb=" O MET B 338 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 10 removed outlier: 3.883A pdb=" N SER H 10 " --> pdb=" O LEU H 7 " (cutoff:3.500A) Processing helix chain 'H' and resid 16 through 24 removed outlier: 4.162A pdb=" N LYS H 20 " --> pdb=" O THR H 16 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 44 removed outlier: 3.589A pdb=" N THR H 41 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE H 42 " --> pdb=" O ASP H 38 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 47 No H-bonds generated for 'chain 'H' and resid 45 through 47' Processing helix chain 'H' and resid 62 through 66 removed outlier: 4.439A pdb=" N LYS H 65 " --> pdb=" O CYS H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 80 removed outlier: 3.782A pdb=" N VAL H 79 " --> pdb=" O ILE H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 133 removed outlier: 3.635A pdb=" N SER H 133 " --> pdb=" O VAL H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 153 removed outlier: 4.227A pdb=" N LEU H 152 " --> pdb=" O CYS H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 166 Processing helix chain 'H' and resid 174 through 182 removed outlier: 3.969A pdb=" N ALA H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 228 removed outlier: 4.244A pdb=" N ARG H 228 " --> pdb=" O HIS H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 231 No H-bonds generated for 'chain 'H' and resid 229 through 231' Processing helix chain 'H' and resid 232 through 236 Processing helix chain 'H' and resid 248 through 254 removed outlier: 4.148A pdb=" N CYS H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 427 removed outlier: 4.115A pdb=" N PHE H 415 " --> pdb=" O SER H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.538A pdb=" N LEU H 500 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing helix chain 'H' and resid 515 through 519 removed outlier: 3.903A pdb=" N HIS H 518 " --> pdb=" O ASP H 515 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE H 519 " --> pdb=" O PHE H 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 515 through 519' Processing helix chain 'H' and resid 528 through 532 removed outlier: 3.603A pdb=" N SER H 531 " --> pdb=" O ALA H 528 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU H 532 " --> pdb=" O ILE H 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 528 through 532' Processing helix chain 'H' and resid 550 through 555 Processing helix chain 'A' and resid 17 through 31 removed outlier: 4.060A pdb=" N LYS A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'J' and resid 14 through 26 Processing helix chain 'J' and resid 30 through 43 Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.906A pdb=" N THR J 82 " --> pdb=" O LEU J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 129 through 134 Processing helix chain 'J' and resid 139 through 144 removed outlier: 3.896A pdb=" N TRP J 142 " --> pdb=" O SER J 139 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N HIS J 143 " --> pdb=" O TYR J 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 Processing helix chain 'J' and resid 216 through 231 removed outlier: 3.954A pdb=" N ARG J 220 " --> pdb=" O PRO J 216 " (cutoff:3.500A) Processing helix chain 'J' and resid 236 through 243 removed outlier: 3.597A pdb=" N PHE J 240 " --> pdb=" O ASP J 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 265 Processing helix chain 'J' and resid 274 through 280 removed outlier: 3.563A pdb=" N LEU J 278 " --> pdb=" O ARG J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 297 through 309 removed outlier: 3.669A pdb=" N GLY J 301 " --> pdb=" O ASN J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 317 Processing helix chain 'J' and resid 327 through 332 Processing helix chain 'J' and resid 335 through 344 Processing helix chain 'J' and resid 369 through 379 Processing helix chain 'I' and resid 13 through 24 removed outlier: 3.717A pdb=" N PHE I 17 " --> pdb=" O SER I 13 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE I 18 " --> pdb=" O LEU I 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS I 24 " --> pdb=" O ARG I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 44 removed outlier: 4.165A pdb=" N PHE I 33 " --> pdb=" O ASP I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 59 removed outlier: 3.714A pdb=" N ARG I 58 " --> pdb=" O ASP I 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE I 59 " --> pdb=" O ILE I 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 55 through 59' Processing helix chain 'I' and resid 60 through 64 removed outlier: 3.689A pdb=" N ALA I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 79 Processing helix chain 'I' and resid 128 through 135 removed outlier: 3.619A pdb=" N LEU I 132 " --> pdb=" O CYS I 128 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 removed outlier: 4.275A pdb=" N HIS I 143 " --> pdb=" O TYR I 140 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE I 144 " --> pdb=" O LEU I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 144' Processing helix chain 'I' and resid 196 through 202 Processing helix chain 'I' and resid 219 through 232 removed outlier: 3.541A pdb=" N LYS I 231 " --> pdb=" O TRP I 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 244 Processing helix chain 'I' and resid 251 through 265 removed outlier: 4.173A pdb=" N LEU I 263 " --> pdb=" O VAL I 259 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS I 265 " --> pdb=" O PHE I 261 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 285 removed outlier: 3.523A pdb=" N GLY I 285 " --> pdb=" O ARG I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 297 through 310 removed outlier: 3.783A pdb=" N LEU I 303 " --> pdb=" O ILE I 299 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 332 Processing helix chain 'I' and resid 335 through 344 Processing helix chain 'I' and resid 368 through 375 Processing helix chain 'I' and resid 375 through 380 removed outlier: 3.579A pdb=" N PHE I 380 " --> pdb=" O TRP I 376 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 390 removed outlier: 3.876A pdb=" N PHE I 389 " --> pdb=" O ASN I 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 7 through 8 removed outlier: 3.541A pdb=" N LYS G 102 " --> pdb=" O ALA G 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 29 through 31 removed outlier: 3.871A pdb=" N HIS G 84 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N CYS G 151 " --> pdb=" O HIS G 214 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 35 through 41 Processing sheet with id=AA4, first strand: chain 'G' and resid 248 through 251 Processing sheet with id=AA5, first strand: chain 'F' and resid 7 through 8 Processing sheet with id=AA6, first strand: chain 'F' and resid 29 through 31 removed outlier: 3.704A pdb=" N HIS F 84 " --> pdb=" O VAL F 23 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 35 through 41 Processing sheet with id=AA8, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.699A pdb=" N SER F 256 " --> pdb=" O THR F 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 270 through 272 Processing sheet with id=AB1, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.559A pdb=" N LYS E 102 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY E 345 " --> pdb=" O TYR E 9 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 13 through 15 Processing sheet with id=AB3, first strand: chain 'E' and resid 13 through 15 removed outlier: 3.931A pdb=" N CYS E 151 " --> pdb=" O HIS E 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 35 through 42 Processing sheet with id=AB5, first strand: chain 'E' and resid 289 through 290 removed outlier: 3.909A pdb=" N THR E 295 " --> pdb=" O HIS E 290 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.606A pdb=" N HIS D 84 " --> pdb=" O VAL D 23 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.686A pdb=" N CYS D 151 " --> pdb=" O HIS D 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 35 through 42 Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 251 Processing sheet with id=AC1, first strand: chain 'C' and resid 102 through 103 removed outlier: 3.627A pdb=" N LYS C 102 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY C 345 " --> pdb=" O TYR C 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.501A pdb=" N CYS C 87 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS C 151 " --> pdb=" O HIS C 214 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 35 through 40 removed outlier: 3.721A pdb=" N ASN C 35 " --> pdb=" O PHE C 75 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 102 through 103 Processing sheet with id=AC5, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.747A pdb=" N HIS B 84 " --> pdb=" O VAL B 23 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 72 through 75 removed outlier: 7.420A pdb=" N ILE A 146 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR B 38 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 248 through 251 Processing sheet with id=AC8, first strand: chain 'H' and resid 82 through 83 removed outlier: 3.565A pdb=" N SER H 122 " --> pdb=" O GLN H 83 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 203 through 204 Processing sheet with id=AD1, first strand: chain 'H' and resid 438 through 449 removed outlier: 6.373A pdb=" N PHE H 438 " --> pdb=" O ASN H 484 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN H 484 " --> pdb=" O PHE H 438 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE H 440 " --> pdb=" O ILE H 482 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE H 482 " --> pdb=" O ILE H 440 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL H 442 " --> pdb=" O SER H 480 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER H 480 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS H 446 " --> pdb=" O ASP H 476 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS H 475 " --> pdb=" O CYS H 396 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N CYS H 396 " --> pdb=" O CYS H 475 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 477 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG H 394 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 479 " --> pdb=" O ASN H 392 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 392 " --> pdb=" O PHE H 479 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU H 504 " --> pdb=" O GLY H 507 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 438 through 449 removed outlier: 6.373A pdb=" N PHE H 438 " --> pdb=" O ASN H 484 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N ASN H 484 " --> pdb=" O PHE H 438 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE H 440 " --> pdb=" O ILE H 482 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE H 482 " --> pdb=" O ILE H 440 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N VAL H 442 " --> pdb=" O SER H 480 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N SER H 480 " --> pdb=" O VAL H 442 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS H 446 " --> pdb=" O ASP H 476 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N CYS H 475 " --> pdb=" O CYS H 396 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N CYS H 396 " --> pdb=" O CYS H 475 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL H 477 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ARG H 394 " --> pdb=" O VAL H 477 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N PHE H 479 " --> pdb=" O ASN H 392 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN H 392 " --> pdb=" O PHE H 479 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN H 520 " --> pdb=" O VAL H 389 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 539 through 542 removed outlier: 3.592A pdb=" N TRP H 539 " --> pdb=" O ILE H 601 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 591 through 594 removed outlier: 4.014A pdb=" N GLY H 569 " --> pdb=" O ILE H 594 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AD6, first strand: chain 'A' and resid 150 through 152 removed outlier: 3.804A pdb=" N HIS A 150 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 107 through 110 Processing sheet with id=AD8, first strand: chain 'J' and resid 322 through 323 removed outlier: 3.573A pdb=" N MET J 323 " --> pdb=" O PHE J 367 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE J 367 " --> pdb=" O MET J 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'I' and resid 94 through 100 removed outlier: 4.290A pdb=" N THR I 97 " --> pdb=" O ALA I 107 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ALA I 107 " --> pdb=" O THR I 97 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 149 through 150 814 hydrogen bonds defined for protein. 2283 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 15 hydrogen bonds 22 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 9.30 Time building geometry restraints manager: 12.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7859 1.33 - 1.45: 6773 1.45 - 1.58: 14838 1.58 - 1.70: 118 1.70 - 1.82: 216 Bond restraints: 29804 Sorted by residual: bond pdb=" CB VAL D 23 " pdb=" CG2 VAL D 23 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.19e+00 bond pdb=" CG1 ILE G 171 " pdb=" CD1 ILE G 171 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.99e+00 bond pdb=" C LYS H 579 " pdb=" N PRO H 580 " ideal model delta sigma weight residual 1.334 1.395 -0.061 2.34e-02 1.83e+03 6.72e+00 bond pdb=" CB VAL F 23 " pdb=" CG2 VAL F 23 " ideal model delta sigma weight residual 1.521 1.441 0.080 3.30e-02 9.18e+02 5.87e+00 bond pdb=" CG1 ILE B 13 " pdb=" CD1 ILE B 13 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.72e+00 ... (remaining 29799 not shown) Histogram of bond angle deviations from ideal: 94.59 - 103.30: 409 103.30 - 112.02: 14012 112.02 - 120.74: 15902 120.74 - 129.46: 10082 129.46 - 138.18: 332 Bond angle restraints: 40737 Sorted by residual: angle pdb=" C PHE A 193 " pdb=" N GLN A 194 " pdb=" CA GLN A 194 " ideal model delta sigma weight residual 120.94 134.27 -13.33 1.90e+00 2.77e-01 4.92e+01 angle pdb=" N VAL H 79 " pdb=" CA VAL H 79 " pdb=" C VAL H 79 " ideal model delta sigma weight residual 112.96 106.02 6.94 1.00e+00 1.00e+00 4.81e+01 angle pdb=" CA TRP J 203 " pdb=" CB TRP J 203 " pdb=" CG TRP J 203 " ideal model delta sigma weight residual 113.60 126.06 -12.46 1.90e+00 2.77e-01 4.30e+01 angle pdb=" O3' G M 15 " pdb=" C3' G M 15 " pdb=" C2' G M 15 " ideal model delta sigma weight residual 109.50 101.27 8.23 1.50e+00 4.44e-01 3.01e+01 angle pdb=" C LYS I 276 " pdb=" N ASP I 277 " pdb=" CA ASP I 277 " ideal model delta sigma weight residual 123.47 131.66 -8.19 1.53e+00 4.27e-01 2.87e+01 ... (remaining 40732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.29: 17372 34.29 - 68.59: 328 68.59 - 102.88: 33 102.88 - 137.17: 1 137.17 - 171.46: 5 Dihedral angle restraints: 17739 sinusoidal: 7637 harmonic: 10102 Sorted by residual: dihedral pdb=" CA VAL D 52 " pdb=" C VAL D 52 " pdb=" N SER D 53 " pdb=" CA SER D 53 " ideal model delta harmonic sigma weight residual -180.00 -116.38 -63.62 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" CA SER H 242 " pdb=" C SER H 242 " pdb=" N ARG H 243 " pdb=" CA ARG H 243 " ideal model delta harmonic sigma weight residual 180.00 135.12 44.88 0 5.00e+00 4.00e-02 8.06e+01 dihedral pdb=" O4' C M 38 " pdb=" C1' C M 38 " pdb=" N1 C M 38 " pdb=" C2 C M 38 " ideal model delta sinusoidal sigma weight residual 232.00 60.54 171.46 1 1.70e+01 3.46e-03 6.61e+01 ... (remaining 17736 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 3671 0.083 - 0.167: 727 0.167 - 0.250: 79 0.250 - 0.334: 18 0.334 - 0.417: 3 Chirality restraints: 4498 Sorted by residual: chirality pdb=" CB ILE J 94 " pdb=" CA ILE J 94 " pdb=" CG1 ILE J 94 " pdb=" CG2 ILE J 94 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" C3' U M 2 " pdb=" C4' U M 2 " pdb=" O3' U M 2 " pdb=" C2' U M 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" CA SER D 53 " pdb=" N SER D 53 " pdb=" C SER D 53 " pdb=" CB SER D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 ... (remaining 4495 not shown) Planarity restraints: 4998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP J 203 " 0.047 2.00e-02 2.50e+03 3.16e-02 2.50e+01 pdb=" CG TRP J 203 " -0.085 2.00e-02 2.50e+03 pdb=" CD1 TRP J 203 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP J 203 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 203 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP J 203 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP J 203 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 203 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 203 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 203 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 181 " 0.040 2.00e-02 2.50e+03 2.59e-02 1.17e+01 pdb=" CG PHE A 181 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 181 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 181 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 PHE A 181 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 PHE A 181 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE A 181 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 9 " 0.022 2.00e-02 2.50e+03 2.40e-02 1.15e+01 pdb=" CG TYR E 9 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR E 9 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR E 9 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR E 9 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR E 9 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR E 9 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 9 " 0.002 2.00e-02 2.50e+03 ... (remaining 4995 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 3 2.22 - 2.89: 10681 2.89 - 3.56: 36734 3.56 - 4.23: 64729 4.23 - 4.90: 110587 Nonbonded interactions: 222734 Sorted by model distance: nonbonded pdb=" O2' A M 7 " pdb=" O THR H 453 " model vdw 1.550 2.440 nonbonded pdb=" N7 G M 41 " pdb=" NH2 ARG B 244 " model vdw 2.033 2.600 nonbonded pdb=" OP1 C M 29 " pdb=" NH2 ARG D 222 " model vdw 2.100 2.520 nonbonded pdb=" OG SER C 12 " pdb=" O SER C 94 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 19 " pdb=" O VAL I 268 " model vdw 2.254 2.440 ... (remaining 222729 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and (resid 2 through 322 or resid 325 through 349)) selection = (chain 'C' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'D' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'E' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) selection = (chain 'F' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 349)) selection = (chain 'G' and (resid 2 through 43 or resid 70 through 229 or resid 243 through \ 322 or resid 325 through 349)) } ncs_group { reference = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.090 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 82.810 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 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 : 0.009 0.103 29804 Z= 0.560 Angle : 1.168 15.706 40737 Z= 0.650 Chirality : 0.068 0.417 4498 Planarity : 0.009 0.080 4998 Dihedral : 14.196 171.465 11177 Min Nonbonded Distance : 1.550 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.31 % Favored : 89.69 % Rotamer: Outliers : 0.20 % Allowed : 4.43 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.31 % 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: -4.69 (0.11), residues: 3395 helix: -3.57 (0.10), residues: 955 sheet: -1.39 (0.23), residues: 500 loop : -3.49 (0.11), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.004 TRP J 203 HIS 0.019 0.003 HIS C 335 PHE 0.055 0.004 PHE C 89 TYR 0.057 0.004 TYR E 9 ARG 0.017 0.002 ARG E 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 336 time to evaluate : 3.045 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 342 average time/residue: 0.4338 time to fit residues: 234.1770 Evaluate side-chains 233 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 3.100 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2452 time to fit residues: 5.0169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 290 optimal weight: 0.9990 chunk 260 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 175 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 104 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 312 optimal weight: 30.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 179 GLN ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 145 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 214 HIS F 311 GLN E 6 ASN E 153 ASN E 214 HIS E 241 GLN D 174 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN C 335 HIS B 77 HIS B 84 HIS B 183 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS H 45 ASN H 77 ASN H 80 ASN H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS H 131 ASN H 162 ASN H 420 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 HIS H 520 ASN H 548 ASN H 581 ASN A 32 ASN A 34 GLN A 39 ASN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN J 42 GLN J 46 HIS J 50 GLN ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 HIS J 214 ASN J 324 ASN J 381 GLN I 23 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 29804 Z= 0.280 Angle : 0.693 10.409 40737 Z= 0.364 Chirality : 0.046 0.240 4498 Planarity : 0.006 0.062 4998 Dihedral : 14.022 177.750 4604 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 1.64 % Allowed : 7.82 % Favored : 90.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -3.74 (0.12), residues: 3395 helix: -2.34 (0.14), residues: 993 sheet: -1.08 (0.23), residues: 508 loop : -3.09 (0.12), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP J 203 HIS 0.010 0.001 HIS C 335 PHE 0.027 0.002 PHE C 89 TYR 0.020 0.002 TYR J 219 ARG 0.007 0.001 ARG E 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 262 time to evaluate : 3.627 Fit side-chains outliers start: 50 outliers final: 29 residues processed: 299 average time/residue: 0.4199 time to fit residues: 201.8793 Evaluate side-chains 254 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 225 time to evaluate : 3.017 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2481 time to fit residues: 18.0218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 173 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 259 optimal weight: 0.2980 chunk 212 optimal weight: 10.0000 chunk 86 optimal weight: 0.1980 chunk 312 optimal weight: 50.0000 chunk 338 optimal weight: 20.0000 chunk 278 optimal weight: 0.0870 chunk 310 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 251 optimal weight: 4.9990 overall best weight: 0.4760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 135 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN E 69 ASN E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN B 179 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 ASN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29804 Z= 0.134 Angle : 0.556 9.597 40737 Z= 0.293 Chirality : 0.041 0.214 4498 Planarity : 0.005 0.056 4998 Dihedral : 13.270 178.212 4604 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 1.64 % Allowed : 9.36 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.13), residues: 3395 helix: -1.42 (0.16), residues: 981 sheet: -0.85 (0.23), residues: 501 loop : -2.77 (0.12), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP J 203 HIS 0.009 0.001 HIS H 125 PHE 0.023 0.001 PHE J 240 TYR 0.020 0.001 TYR C 275 ARG 0.004 0.000 ARG J 110 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 290 time to evaluate : 3.779 Fit side-chains outliers start: 50 outliers final: 19 residues processed: 322 average time/residue: 0.4104 time to fit residues: 212.1111 Evaluate side-chains 263 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 244 time to evaluate : 3.257 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2619 time to fit residues: 13.9353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 309 optimal weight: 50.0000 chunk 235 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 210 optimal weight: 0.0980 chunk 314 optimal weight: 50.0000 chunk 332 optimal weight: 9.9990 chunk 164 optimal weight: 4.9990 chunk 297 optimal weight: 20.0000 chunk 89 optimal weight: 0.1980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 349 HIS E 69 ASN E 162 ASN E 241 GLN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 349 HIS H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 571 HIS ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 GLN ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 ASN J 237 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 29804 Z= 0.242 Angle : 0.611 9.302 40737 Z= 0.318 Chirality : 0.044 0.375 4498 Planarity : 0.005 0.055 4998 Dihedral : 13.150 177.416 4604 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.81 % Allowed : 11.14 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.13), residues: 3395 helix: -1.20 (0.16), residues: 985 sheet: -0.77 (0.23), residues: 511 loop : -2.66 (0.13), residues: 1899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP J 203 HIS 0.007 0.001 HIS H 125 PHE 0.024 0.002 PHE C 89 TYR 0.015 0.002 TYR B 316 ARG 0.006 0.000 ARG E 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 251 time to evaluate : 3.180 Fit side-chains outliers start: 55 outliers final: 24 residues processed: 293 average time/residue: 0.4115 time to fit residues: 193.1592 Evaluate side-chains 258 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 3.416 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2718 time to fit residues: 16.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 247 optimal weight: 9.9990 chunk 137 optimal weight: 0.7980 chunk 283 optimal weight: 30.0000 chunk 229 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 298 optimal weight: 50.0000 chunk 83 optimal weight: 3.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 311 GLN G 315 HIS E 162 ASN D 214 HIS ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 HIS ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 493 GLN ** A 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 95 ASN J 202 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 29804 Z= 0.567 Angle : 0.826 10.847 40737 Z= 0.425 Chirality : 0.053 0.396 4498 Planarity : 0.007 0.073 4998 Dihedral : 13.533 172.870 4604 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.60 % Favored : 89.40 % Rotamer: Outliers : 2.40 % Allowed : 12.09 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.13), residues: 3395 helix: -1.46 (0.16), residues: 979 sheet: -0.83 (0.24), residues: 492 loop : -2.80 (0.12), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 143 HIS 0.010 0.002 HIS D 77 PHE 0.036 0.003 PHE C 89 TYR 0.023 0.003 TYR H 622 ARG 0.015 0.001 ARG E 283 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 230 time to evaluate : 2.946 Fit side-chains outliers start: 73 outliers final: 45 residues processed: 284 average time/residue: 0.4049 time to fit residues: 185.1748 Evaluate side-chains 263 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 218 time to evaluate : 3.172 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.2847 time to fit residues: 27.6296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 2.9990 chunk 299 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 chunk 195 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 332 optimal weight: 9.9990 chunk 276 optimal weight: 0.0170 chunk 154 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 174 optimal weight: 4.9990 overall best weight: 1.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS F 99 GLN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN I 338 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 29804 Z= 0.206 Angle : 0.604 9.136 40737 Z= 0.314 Chirality : 0.044 0.577 4498 Planarity : 0.005 0.074 4998 Dihedral : 13.054 179.624 4604 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 1.25 % Allowed : 13.11 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.13), residues: 3395 helix: -1.09 (0.16), residues: 993 sheet: -0.71 (0.24), residues: 504 loop : -2.59 (0.13), residues: 1898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 PHE 0.023 0.001 PHE J 240 TYR 0.015 0.001 TYR C 275 ARG 0.008 0.000 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 243 time to evaluate : 3.417 Fit side-chains outliers start: 38 outliers final: 15 residues processed: 275 average time/residue: 0.4275 time to fit residues: 189.5403 Evaluate side-chains 242 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 3.349 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.2793 time to fit residues: 12.4296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 320 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 243 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 331 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 202 optimal weight: 40.0000 chunk 153 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS E 162 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN I 320 ASN I 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 29804 Z= 0.421 Angle : 0.728 9.458 40737 Z= 0.376 Chirality : 0.049 0.535 4498 Planarity : 0.006 0.068 4998 Dihedral : 13.216 175.751 4604 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Rotamer: Outliers : 1.51 % Allowed : 13.67 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.13), residues: 3395 helix: -1.22 (0.16), residues: 993 sheet: -0.71 (0.24), residues: 508 loop : -2.63 (0.13), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 152 HIS 0.007 0.002 HIS C 290 PHE 0.034 0.002 PHE C 89 TYR 0.018 0.002 TYR F 175 ARG 0.010 0.001 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 225 time to evaluate : 3.177 Fit side-chains outliers start: 46 outliers final: 25 residues processed: 250 average time/residue: 0.4351 time to fit residues: 175.4946 Evaluate side-chains 239 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 214 time to evaluate : 3.279 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3113 time to fit residues: 18.2488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 205 optimal weight: 20.0000 chunk 132 optimal weight: 0.0980 chunk 198 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 260 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 315 HIS ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 349 HIS H 83 GLN ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 29804 Z= 0.133 Angle : 0.548 8.800 40737 Z= 0.286 Chirality : 0.041 0.375 4498 Planarity : 0.005 0.055 4998 Dihedral : 12.828 177.377 4604 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 0.49 % Allowed : 14.32 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3395 helix: -0.70 (0.17), residues: 987 sheet: -0.49 (0.24), residues: 503 loop : -2.45 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 143 HIS 0.011 0.001 HIS G 315 PHE 0.020 0.001 PHE I 367 TYR 0.020 0.001 TYR C 275 ARG 0.013 0.000 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 3.076 Fit side-chains outliers start: 15 outliers final: 4 residues processed: 252 average time/residue: 0.4623 time to fit residues: 185.0384 Evaluate side-chains 225 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 221 time to evaluate : 3.290 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2620 time to fit residues: 6.4252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 301 optimal weight: 40.0000 chunk 317 optimal weight: 8.9990 chunk 289 optimal weight: 1.9990 chunk 308 optimal weight: 40.0000 chunk 185 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 242 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 279 optimal weight: 0.0270 chunk 292 optimal weight: 6.9990 chunk 307 optimal weight: 40.0000 overall best weight: 2.9644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 183 ASN ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 ASN E 162 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 29804 Z= 0.351 Angle : 0.681 8.797 40737 Z= 0.351 Chirality : 0.047 0.425 4498 Planarity : 0.006 0.061 4998 Dihedral : 12.964 177.423 4604 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.92 % Allowed : 14.29 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.14), residues: 3395 helix: -0.87 (0.17), residues: 988 sheet: -0.61 (0.24), residues: 511 loop : -2.49 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 152 HIS 0.007 0.001 HIS C 290 PHE 0.027 0.002 PHE C 89 TYR 0.026 0.002 TYR G 275 ARG 0.013 0.001 ARG H 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 232 time to evaluate : 3.202 Fit side-chains outliers start: 28 outliers final: 15 residues processed: 246 average time/residue: 0.4542 time to fit residues: 178.3489 Evaluate side-chains 238 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 223 time to evaluate : 3.159 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3330 time to fit residues: 13.2006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 202 optimal weight: 20.0000 chunk 326 optimal weight: 20.0000 chunk 199 optimal weight: 0.0570 chunk 154 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 342 optimal weight: 2.9990 chunk 315 optimal weight: 50.0000 chunk 272 optimal weight: 0.0970 chunk 28 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN ** E 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 320 ASN ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29804 Z= 0.218 Angle : 0.607 8.772 40737 Z= 0.315 Chirality : 0.044 0.386 4498 Planarity : 0.005 0.057 4998 Dihedral : 12.849 179.996 4604 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.33 % Allowed : 14.78 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.14), residues: 3395 helix: -0.75 (0.17), residues: 994 sheet: -0.53 (0.24), residues: 512 loop : -2.42 (0.13), residues: 1889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 203 HIS 0.006 0.001 HIS C 290 PHE 0.047 0.001 PHE A 193 TYR 0.021 0.001 TYR G 275 ARG 0.013 0.000 ARG H 240 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6790 Ramachandran restraints generated. 3395 Oldfield, 0 Emsley, 3395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 223 time to evaluate : 3.493 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 231 average time/residue: 0.4496 time to fit residues: 167.6017 Evaluate side-chains 223 residues out of total 3052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 218 time to evaluate : 3.145 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2828 time to fit residues: 6.8449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 216 optimal weight: 0.8980 chunk 290 optimal weight: 30.0000 chunk 83 optimal weight: 0.9990 chunk 251 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 273 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 280 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 162 ASN C 6 ASN ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 338 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.221108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.161768 restraints weight = 34838.093| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 8.26 r_work: 0.3147 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29804 Z= 0.252 Angle : 0.625 12.496 40737 Z= 0.321 Chirality : 0.044 0.381 4498 Planarity : 0.005 0.056 4998 Dihedral : 12.827 179.219 4604 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.36 % Allowed : 14.98 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.14), residues: 3395 helix: -0.70 (0.17), residues: 982 sheet: -0.55 (0.24), residues: 506 loop : -2.38 (0.13), residues: 1907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 203 HIS 0.006 0.001 HIS C 290 PHE 0.024 0.001 PHE J 240 TYR 0.019 0.002 TYR G 275 ARG 0.013 0.000 ARG H 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5682.15 seconds wall clock time: 105 minutes 1.82 seconds (6301.82 seconds total)