Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 27 22:45:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/04_2023/7t9n_25763_trim_updated.pdb" } resolution = 2.9 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= 0.009 sd= 0.032 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 S 78 5.16 5 C 8538 2.51 5 N 2266 2.21 5 O 2507 1.98 5 H 13037 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "R GLU 178": "OE1" <-> "OE2" Residue "X GLU 309": "OE1" <-> "OE2" Residue "Y TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 172": "OE1" <-> "OE2" Residue "Y TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 26426 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3122 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "H" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3230 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1889 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 8866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 8866 Classifications: {'peptide': 555} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 529} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3257 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 102 Chain: "Y" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {'NAG': 3, 'Z41': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 11.42, per 1000 atoms: 0.43 Number of scatterers: 26426 At special positions: 0 Unit cell: (186.524, 124.068, 91.152, 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 78 16.00 O 2507 8.00 N 2266 7.00 C 8538 6.00 H 13037 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 283 " - pdb=" SG CYS R 398 " distance=2.03 Simple disulfide: pdb=" SG CYS R 284 " - pdb=" SG CYS R 408 " distance=2.03 Simple disulfide: pdb=" SG CYS R 494 " - pdb=" SG CYS R 569 " distance=2.02 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 Links applied NAG-ASN " NAG R 802 " - " ASN R 198 " " NAG R 803 " - " ASN R 177 " " NAG R 804 " - " ASN R 77 " Time building additional restraints: 23.06 Conformation dependent library (CDL) restraints added in 2.1 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 21 sheets defined 26.1% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'L' and resid 27B through 29 No H-bonds generated for 'chain 'L' and resid 27B through 29' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 183 through 187 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 155 through 157 No H-bonds generated for 'chain 'H' and resid 155 through 157' Processing helix chain 'H' and resid 187 through 190 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 74 through 76 No H-bonds generated for 'chain 'N' and resid 74 through 76' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 218 through 220 No H-bonds generated for 'chain 'R' and resid 218 through 220' Processing helix chain 'R' and resid 246 through 248 No H-bonds generated for 'chain 'R' and resid 246 through 248' Processing helix chain 'R' and resid 280 through 286 Processing helix chain 'R' and resid 415 through 441 removed outlier: 3.884A pdb=" N ILE R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 477 Processing helix chain 'R' and resid 481 through 490 removed outlier: 5.088A pdb=" N ILE R 486 " --> pdb=" O TYR R 482 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP R 487 " --> pdb=" O ASN R 483 " (cutoff:3.500A) Processing helix chain 'R' and resid 492 through 524 Processing helix chain 'R' and resid 529 through 531 No H-bonds generated for 'chain 'R' and resid 529 through 531' Processing helix chain 'R' and resid 535 through 558 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 577 through 608 Processing helix chain 'R' and resid 620 through 648 Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 656 through 665 removed outlier: 4.279A pdb=" N ILE R 661 " --> pdb=" O SER R 657 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU R 662 " --> pdb=" O ASN R 658 " (cutoff:3.500A) Processing helix chain 'R' and resid 669 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 683 through 696 removed outlier: 3.544A pdb=" N PHE R 696 " --> pdb=" O LEU R 692 " (cutoff:3.500A) Processing helix chain 'X' and resid 15 through 39 Processing helix chain 'X' and resid 53 through 60 removed outlier: 3.531A pdb=" N MET X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 234 through 238 Processing helix chain 'X' and resid 266 through 278 Processing helix chain 'X' and resid 294 through 303 Processing helix chain 'X' and resid 313 through 317 Processing helix chain 'X' and resid 332 through 351 Processing helix chain 'X' and resid 369 through 391 removed outlier: 4.023A pdb=" N ALA X 372 " --> pdb=" O THR X 369 " (cutoff:3.500A) Processing helix chain 'Y' and resid 4 through 25 Processing helix chain 'Y' and resid 30 through 33 No H-bonds generated for 'chain 'Y' and resid 30 through 33' Processing helix chain 'Z' and resid 8 through 23 Processing helix chain 'Z' and resid 30 through 47 removed outlier: 4.816A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLU Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'L' and resid 9 through 13 removed outlier: 5.654A pdb=" N ARG L 103 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY L 13 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N THR L 105 " --> pdb=" O GLY L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'L' and resid 19 through 24 Processing sheet with id= C, first strand: chain 'L' and resid 95B through 98 removed outlier: 5.786A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.083A pdb=" N TYR L 173 " --> pdb=" O ASP L 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 145 through 149 Processing sheet with id= F, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.573A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'H' and resid 107 through 109 removed outlier: 5.744A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 120 through 124 Processing sheet with id= I, first strand: chain 'H' and resid 151 through 154 Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.528A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.204A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'R' and resid 30 through 32 removed outlier: 6.212A pdb=" N THR R 56 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N CYS R 41 " --> pdb=" O THR R 56 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS R 58 " --> pdb=" O CYS R 41 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ARG R 80 " --> pdb=" O LEU R 57 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU R 59 " --> pdb=" O ARG R 80 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N TYR R 82 " --> pdb=" O LEU R 59 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N HIS R 105 " --> pdb=" O ILE R 81 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL R 83 " --> pdb=" O HIS R 105 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU R 107 " --> pdb=" O VAL R 83 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N PHE R 130 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ILE R 108 " --> pdb=" O PHE R 130 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLY R 132 " --> pdb=" O ILE R 108 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N LEU R 131 " --> pdb=" O PHE R 153 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE R 155 " --> pdb=" O LEU R 131 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N ILE R 133 " --> pdb=" O ILE R 155 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU R 157 " --> pdb=" O ILE R 133 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR R 179 " --> pdb=" O PHE R 154 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU R 156 " --> pdb=" O THR R 179 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR R 181 " --> pdb=" O LEU R 156 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ILE R 158 " --> pdb=" O THR R 181 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS R 183 " --> pdb=" O ILE R 158 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'R' and resid 204 through 206 removed outlier: 6.512A pdb=" N LEU R 230 " --> pdb=" O VAL R 205 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLU R 251 " --> pdb=" O LEU R 231 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG R 274 " --> pdb=" O LEU R 252 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'X' and resid 359 through 362 removed outlier: 7.172A pdb=" N VAL X 287 " --> pdb=" O TYR X 360 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N HIS X 362 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU X 289 " --> pdb=" O HIS X 362 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ILE X 244 " --> pdb=" O ILE X 288 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N PHE X 290 " --> pdb=" O ILE X 244 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N PHE X 246 " --> pdb=" O PHE X 290 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ASN X 292 " --> pdb=" O PHE X 246 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL X 248 " --> pdb=" O ASN X 292 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA X 243 " --> pdb=" O ARG X 42 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'Y' and resid 58 through 63 removed outlier: 6.971A pdb=" N ALA Y 73 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N MET Y 61 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL Y 71 " --> pdb=" O MET Y 61 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N TRP Y 63 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N LEU Y 69 " --> pdb=" O TRP Y 63 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS Y 78 " --> pdb=" O SER Y 74 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LYS Y 89 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.696A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'Y' and resid 146 through 151 removed outlier: 6.699A pdb=" N SER Y 160 " --> pdb=" O SER Y 147 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS Y 149 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL Y 158 " --> pdb=" O CYS Y 149 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE Y 151 " --> pdb=" O GLN Y 156 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N GLN Y 156 " --> pdb=" O PHE Y 151 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'Y' and resid 187 through 192 removed outlier: 6.769A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN Y 220 " --> pdb=" O LEU Y 210 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'Y' and resid 229 through 234 removed outlier: 6.539A pdb=" N GLY Y 244 " --> pdb=" O ASN Y 230 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE Y 232 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA Y 242 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE Y 234 " --> pdb=" O ALA Y 240 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA Y 240 " --> pdb=" O PHE Y 234 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET Y 262 " --> pdb=" O LEU Y 252 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N ASP Y 254 " --> pdb=" O GLU Y 260 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU Y 260 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'Y' and resid 273 through 278 removed outlier: 6.345A pdb=" N GLY Y 288 " --> pdb=" O THR Y 274 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL Y 276 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU Y 286 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N PHE Y 278 " --> pdb=" O LEU Y 284 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU Y 284 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'Y' and resid 327 through 330 removed outlier: 3.592A pdb=" N LYS Y 337 " --> pdb=" O THR Y 329 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1371 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.96 Time building geometry restraints manager: 23.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 13002 1.02 - 1.22: 45 1.22 - 1.42: 5653 1.42 - 1.61: 7918 1.61 - 1.81: 105 Bond restraints: 26723 Sorted by residual: bond pdb=" N GLY L 108 " pdb=" H GLY L 108 " ideal model delta sigma weight residual 0.860 1.134 -0.274 2.00e-02 2.50e+03 1.87e+02 bond pdb=" N ALA H 114 " pdb=" H ALA H 114 " ideal model delta sigma weight residual 0.860 1.127 -0.267 2.00e-02 2.50e+03 1.78e+02 bond pdb=" C ALA X 303 " pdb=" O ALA X 303 " ideal model delta sigma weight residual 1.237 1.098 0.139 1.19e-02 7.06e+03 1.36e+02 bond pdb=" C SER X 352 " pdb=" O SER X 352 " ideal model delta sigma weight residual 1.236 1.107 0.129 1.14e-02 7.69e+03 1.29e+02 bond pdb=" C SER H 113 " pdb=" N ALA H 114 " ideal model delta sigma weight residual 1.332 1.470 -0.137 1.40e-02 5.10e+03 9.60e+01 ... (remaining 26718 not shown) Histogram of bond angle deviations from ideal: 74.14 - 89.83: 6 89.83 - 105.53: 257 105.53 - 121.23: 42223 121.23 - 136.93: 5600 136.93 - 152.63: 2 Bond angle restraints: 48088 Sorted by residual: angle pdb=" O ALA X 303 " pdb=" C ALA X 303 " pdb=" N GLY X 304 " ideal model delta sigma weight residual 122.15 103.36 18.79 1.14e+00 7.69e-01 2.72e+02 angle pdb=" O SER X 352 " pdb=" C SER X 352 " pdb=" N GLY X 353 " ideal model delta sigma weight residual 123.12 103.61 19.51 1.32e+00 5.74e-01 2.18e+02 angle pdb=" C ALA R 285 " pdb=" CA ALA R 285 " pdb=" HA ALA R 285 " ideal model delta sigma weight residual 109.00 74.14 34.86 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N ALA R 285 " pdb=" CA ALA R 285 " pdb=" HA ALA R 285 " ideal model delta sigma weight residual 110.00 75.47 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" CB ALA R 285 " pdb=" CA ALA R 285 " pdb=" HA ALA R 285 " ideal model delta sigma weight residual 109.00 75.25 33.75 3.00e+00 1.11e-01 1.27e+02 ... (remaining 48083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 10027 17.95 - 35.90: 671 35.90 - 53.86: 104 53.86 - 71.81: 26 71.81 - 89.76: 17 Dihedral angle restraints: 10845 sinusoidal: 4890 harmonic: 5955 Sorted by residual: dihedral pdb=" CB CYS R 494 " pdb=" SG CYS R 494 " pdb=" SG CYS R 569 " pdb=" CB CYS R 569 " ideal model delta sinusoidal sigma weight residual -86.00 -130.47 44.47 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 57.20 35.80 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CA ALA R 679 " pdb=" C ALA R 679 " pdb=" N ILE R 680 " pdb=" CA ILE R 680 " ideal model delta harmonic sigma weight residual -180.00 -160.35 -19.65 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 10842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 2137 0.329 - 0.658: 2 0.658 - 0.987: 0 0.987 - 1.317: 1 1.317 - 1.646: 1 Chirality restraints: 2141 Sorted by residual: chirality pdb=" CG LEU R 267 " pdb=" CB LEU R 267 " pdb=" CD1 LEU R 267 " pdb=" CD2 LEU R 267 " both_signs ideal model delta sigma weight residual False -2.59 -0.94 -1.65 2.00e-01 2.50e+01 6.77e+01 chirality pdb=" C1 NAG R 804 " pdb=" ND2 ASN R 77 " pdb=" C2 NAG R 804 " pdb=" O5 NAG R 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.38 -1.02 2.00e-01 2.50e+01 2.58e+01 chirality pdb=" CA LEU L 107 " pdb=" N LEU L 107 " pdb=" C LEU L 107 " pdb=" CB LEU L 107 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 2138 not shown) Planarity restraints: 3985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 802 " -0.292 2.00e-02 2.50e+03 2.44e-01 7.44e+02 pdb=" C7 NAG R 802 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG R 802 " -0.190 2.00e-02 2.50e+03 pdb=" N2 NAG R 802 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG R 802 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 804 " 0.279 2.00e-02 2.50e+03 2.38e-01 7.06e+02 pdb=" C7 NAG R 804 " -0.063 2.00e-02 2.50e+03 pdb=" C8 NAG R 804 " -0.027 2.00e-02 2.50e+03 pdb=" N2 NAG R 804 " -0.396 2.00e-02 2.50e+03 pdb=" O7 NAG R 804 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN L 109 " 0.130 2.00e-02 2.50e+03 1.47e-01 3.22e+02 pdb=" CD GLN L 109 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN L 109 " -0.132 2.00e-02 2.50e+03 pdb=" NE2 GLN L 109 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN L 109 " -0.217 2.00e-02 2.50e+03 pdb="HE22 GLN L 109 " 0.218 2.00e-02 2.50e+03 ... (remaining 3982 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.12: 746 2.12 - 2.74: 48210 2.74 - 3.36: 77412 3.36 - 3.98: 101953 3.98 - 4.60: 158824 Nonbonded interactions: 387145 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" H VAL H 69 " model vdw 1.495 1.850 nonbonded pdb=" H TYR R 195 " pdb=" O ASP R 219 " model vdw 1.498 1.850 nonbonded pdb=" OD2 ASP R 410 " pdb="HH22 ARG R 418 " model vdw 1.527 1.850 nonbonded pdb=" H ARG H 38 " pdb=" O GLU H 46 " model vdw 1.531 1.850 nonbonded pdb=" O ILE Y 58 " pdb=" HG SER Y 316 " model vdw 1.586 1.850 ... (remaining 387140 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.440 Extract box with map and model: 17.280 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 82.340 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.139 13686 Z= 0.413 Angle : 0.722 19.506 18598 Z= 0.422 Chirality : 0.062 1.646 2141 Planarity : 0.009 0.244 2349 Dihedral : 12.670 89.762 4869 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 0.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.67 (0.21), residues: 1699 helix: 2.02 (0.26), residues: 425 sheet: 0.14 (0.25), residues: 474 loop : -0.14 (0.23), residues: 800 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.963 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 241 average time/residue: 2.6211 time to fit residues: 693.0736 Evaluate side-chains 160 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 158 time to evaluate : 2.080 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 2.6699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 17 GLN L 26 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 39 GLN R 173 GLN X 278 ASN Y 32 GLN Y 266 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 13686 Z= 0.395 Angle : 0.619 11.154 18598 Z= 0.325 Chirality : 0.059 1.654 2141 Planarity : 0.005 0.060 2349 Dihedral : 5.473 53.653 1891 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.34 (0.21), residues: 1699 helix: 1.75 (0.25), residues: 415 sheet: -0.07 (0.25), residues: 461 loop : -0.31 (0.22), residues: 823 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 190 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 2.148 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 9 residues processed: 178 average time/residue: 2.5654 time to fit residues: 503.3634 Evaluate side-chains 161 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 7 residues processed: 3 average time/residue: 0.3326 time to fit residues: 4.3627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 13686 Z= 0.221 Angle : 0.537 10.995 18598 Z= 0.279 Chirality : 0.056 1.660 2141 Planarity : 0.004 0.051 2349 Dihedral : 5.194 54.757 1891 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.41 (0.21), residues: 1699 helix: 1.77 (0.26), residues: 416 sheet: -0.11 (0.24), residues: 456 loop : -0.20 (0.22), residues: 827 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 2.136 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 170 average time/residue: 2.5795 time to fit residues: 484.4057 Evaluate side-chains 160 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 2.208 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 6 average time/residue: 0.9115 time to fit residues: 9.6013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 163 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN X 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13686 Z= 0.285 Angle : 0.553 10.857 18598 Z= 0.287 Chirality : 0.057 1.663 2141 Planarity : 0.004 0.035 2349 Dihedral : 5.229 56.763 1891 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.20), residues: 1699 helix: 1.69 (0.26), residues: 415 sheet: -0.15 (0.24), residues: 458 loop : -0.30 (0.22), residues: 826 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 170 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 151 time to evaluate : 2.035 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. 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: 19 outliers final: 14 residues processed: 161 average time/residue: 2.6534 time to fit residues: 471.5551 Evaluate side-chains 163 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 2.089 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 1.1009 time to fit residues: 10.7426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 173 GLN X 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 13686 Z= 0.301 Angle : 0.560 10.771 18598 Z= 0.290 Chirality : 0.057 1.656 2141 Planarity : 0.004 0.037 2349 Dihedral : 5.278 51.637 1891 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 1.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.24 (0.20), residues: 1699 helix: 1.65 (0.26), residues: 409 sheet: -0.14 (0.23), residues: 470 loop : -0.33 (0.22), residues: 820 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 166 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 2.537 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 157 average time/residue: 2.6822 time to fit residues: 467.3912 Evaluate side-chains 150 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 2.337 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 7 residues processed: 4 average time/residue: 1.2187 time to fit residues: 8.7928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 13 optimal weight: 9.9990 chunk 85 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 13686 Z= 0.338 Angle : 0.572 10.704 18598 Z= 0.297 Chirality : 0.057 1.657 2141 Planarity : 0.004 0.038 2349 Dihedral : 5.365 41.683 1891 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.13 (0.20), residues: 1699 helix: 1.55 (0.26), residues: 410 sheet: -0.21 (0.23), residues: 476 loop : -0.40 (0.22), residues: 813 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 173 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.998 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. 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: 22 outliers final: 18 residues processed: 163 average time/residue: 2.5648 time to fit residues: 462.1415 Evaluate side-chains 164 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 8 average time/residue: 0.9079 time to fit residues: 11.7269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 6.9990 chunk 93 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 13686 Z= 0.331 Angle : 0.571 10.660 18598 Z= 0.296 Chirality : 0.057 1.657 2141 Planarity : 0.004 0.037 2349 Dihedral : 5.394 45.059 1891 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.11 (0.20), residues: 1699 helix: 1.46 (0.26), residues: 412 sheet: -0.19 (0.24), residues: 471 loop : -0.39 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 175 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 2.039 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 166 average time/residue: 2.6476 time to fit residues: 485.1325 Evaluate side-chains 158 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 142 time to evaluate : 2.103 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.0013 time to fit residues: 9.0839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13686 Z= 0.245 Angle : 0.549 10.631 18598 Z= 0.284 Chirality : 0.056 1.662 2141 Planarity : 0.003 0.032 2349 Dihedral : 5.261 45.690 1891 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer Outliers : 1.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.21 (0.21), residues: 1699 helix: 1.54 (0.26), residues: 412 sheet: -0.15 (0.24), residues: 471 loop : -0.32 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 168 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 2.010 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 12 residues processed: 162 average time/residue: 2.6786 time to fit residues: 482.3451 Evaluate side-chains 156 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.3580 time to fit residues: 3.9906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 143 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13686 Z= 0.250 Angle : 0.544 10.625 18598 Z= 0.281 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.225 47.837 1891 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.22 (0.21), residues: 1699 helix: 1.58 (0.26), residues: 412 sheet: -0.16 (0.24), residues: 471 loop : -0.32 (0.22), residues: 816 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 162 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 2.192 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 159 average time/residue: 2.6422 time to fit residues: 463.4710 Evaluate side-chains 156 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.3642 time to fit residues: 3.3018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 168 optimal weight: 0.0770 chunk 154 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 13 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13686 Z= 0.226 Angle : 0.538 10.629 18598 Z= 0.278 Chirality : 0.056 1.662 2141 Planarity : 0.003 0.048 2349 Dihedral : 5.167 48.757 1891 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 0.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.27 (0.21), residues: 1699 helix: 1.59 (0.26), residues: 413 sheet: -0.12 (0.23), residues: 469 loop : -0.28 (0.22), residues: 817 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.083 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 12 residues processed: 159 average time/residue: 2.6352 time to fit residues: 462.2398 Evaluate side-chains 155 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 2.058 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.3637 time to fit residues: 3.2712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 19 optimal weight: 30.0000 chunk 37 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 137 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.130630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105039 restraints weight = 68215.776| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.60 r_work: 0.3359 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 13686 Z= 0.350 Angle : 0.585 10.605 18598 Z= 0.303 Chirality : 0.057 1.652 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.418 54.498 1891 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % 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: 0.09 (0.20), residues: 1699 helix: 1.45 (0.26), residues: 412 sheet: -0.21 (0.24), residues: 473 loop : -0.42 (0.22), residues: 814 =============================================================================== Job complete usr+sys time: 9065.44 seconds wall clock time: 159 minutes 34.24 seconds (9574.24 seconds total)