Starting phenix.real_space_refine on Wed Mar 20 05:14:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/03_2024/7t9n_25763_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/03_2024/7t9n_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_25763/03_2024/7t9n_25763.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/03_2024/7t9n_25763.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/03_2024/7t9n_25763_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t9n_25763/03_2024/7t9n_25763_trim_updated.pdb" } resolution = 2.9 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 ------------------------------------------------------------------------------- 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-dev-5265/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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.74, per 1000 atoms: 0.48 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: 21.59 Conformation dependent library (CDL) restraints added in 2.9 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: 4.35 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: 10.34 Time building geometry restraints manager: 22.44 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 - 22.01: 12025 22.01 - 44.02: 600 44.02 - 66.03: 129 66.03 - 88.05: 24 88.05 - 110.06: 19 Dihedral angle restraints: 12797 sinusoidal: 6842 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 12794 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: 8.740 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: 0.000 Extract box with map and model: 14.450 Check model and map are aligned: 0.460 Set scattering table: 0.260 Process input model: 90.370 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.910 ------------------------------------------------------------------------------- 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 : 13.941 110.058 4940 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 % Allowed : 0.55 % Favored : 99.24 % 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: 0.67 (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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 234 HIS 0.013 0.001 HIS X 357 PHE 0.016 0.001 PHE Y 234 TYR 0.014 0.001 TYR Y 105 ARG 0.002 0.000 ARG N 67 *********************** 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 : 1.734 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: L 30 ASN cc_start: 0.7536 (m-40) cc_final: 0.7236 (m-40) REVERT: L 78 LEU cc_start: 0.6997 (mp) cc_final: 0.6491 (mp) REVERT: L 82 ASP cc_start: 0.6855 (m-30) cc_final: 0.6625 (m-30) REVERT: H 72 ASP cc_start: 0.7187 (t0) cc_final: 0.6821 (t0) REVERT: N 3 GLN cc_start: 0.7157 (tt0) cc_final: 0.6713 (tm-30) REVERT: N 5 GLN cc_start: 0.6786 (tp40) cc_final: 0.6400 (tm-30) REVERT: R 48 PRO cc_start: 0.7621 (Cg_endo) cc_final: 0.7141 (Cg_exo) REVERT: R 61 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6704 (tt0) REVERT: R 102 LYS cc_start: 0.7164 (mttt) cc_final: 0.6903 (mtpp) REVERT: R 160 ASP cc_start: 0.6992 (m-30) cc_final: 0.6563 (t70) REVERT: R 219 ASP cc_start: 0.7521 (m-30) cc_final: 0.7303 (m-30) REVERT: R 251 GLU cc_start: 0.7514 (tt0) cc_final: 0.7269 (tt0) REVERT: R 274 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7436 (ttt90) REVERT: R 461 PHE cc_start: 0.7382 (t80) cc_final: 0.7163 (t80) REVERT: R 535 LEU cc_start: 0.7674 (tp) cc_final: 0.7056 (tm) REVERT: R 536 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6541 (mmt180) REVERT: R 539 CYS cc_start: 0.7333 (t) cc_final: 0.6501 (m) REVERT: X 211 LYS cc_start: 0.7133 (mttp) cc_final: 0.6904 (mtpp) REVERT: X 392 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7006 (mm-30) REVERT: Y 59 TYR cc_start: 0.7793 (m-80) cc_final: 0.7570 (m-80) REVERT: Y 226 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7474 (mt-10) REVERT: Y 336 LEU cc_start: 0.8455 (mp) cc_final: 0.8229 (mt) REVERT: Z 46 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7835 (mppt) outliers start: 3 outliers final: 2 residues processed: 241 average time/residue: 2.6057 time to fit residues: 688.4045 Evaluate side-chains 169 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 167 time to evaluate : 2.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 113 SER 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: 0.8980 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 153 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: 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: 0.7182 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13686 Z= 0.351 Angle : 0.605 11.147 18598 Z= 0.317 Chirality : 0.057 1.655 2141 Planarity : 0.004 0.045 2349 Dihedral : 6.861 58.723 1964 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.38 % Allowed : 8.08 % Favored : 90.54 % 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: 0.43 (0.21), residues: 1699 helix: 1.84 (0.25), residues: 416 sheet: 0.03 (0.25), residues: 458 loop : -0.30 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.008 0.001 HIS X 357 PHE 0.013 0.002 PHE N 108 TYR 0.014 0.002 TYR Y 105 ARG 0.004 0.000 ARG H 50 *********************** 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 194 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 174 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7527 (m-40) cc_final: 0.7306 (m-40) REVERT: L 82 ASP cc_start: 0.7042 (m-30) cc_final: 0.6832 (m-30) REVERT: H 17 SER cc_start: 0.8667 (p) cc_final: 0.8213 (t) REVERT: N 3 GLN cc_start: 0.7268 (tt0) cc_final: 0.6741 (tm-30) REVERT: N 5 GLN cc_start: 0.6990 (tp40) cc_final: 0.6580 (tm-30) REVERT: R 48 PRO cc_start: 0.7664 (Cg_endo) cc_final: 0.7222 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6975 (mt-10) cc_final: 0.6648 (tt0) REVERT: R 102 LYS cc_start: 0.7229 (mttt) cc_final: 0.6961 (mtpp) REVERT: R 140 MET cc_start: 0.6422 (tmt) cc_final: 0.6031 (tmt) REVERT: R 160 ASP cc_start: 0.6901 (m-30) cc_final: 0.6467 (t70) REVERT: R 219 ASP cc_start: 0.7575 (m-30) cc_final: 0.7361 (m-30) REVERT: R 251 GLU cc_start: 0.7489 (tt0) cc_final: 0.7263 (tt0) REVERT: R 274 ARG cc_start: 0.7851 (mtp-110) cc_final: 0.7406 (ttt90) REVERT: R 523 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7639 (mt) REVERT: R 535 LEU cc_start: 0.7760 (tp) cc_final: 0.7094 (tm) REVERT: R 536 ARG cc_start: 0.6911 (mtt180) cc_final: 0.6581 (mmt180) REVERT: R 539 CYS cc_start: 0.7342 (t) cc_final: 0.6544 (m) REVERT: R 624 LYS cc_start: 0.7031 (mmpt) cc_final: 0.6121 (mmmt) REVERT: X 211 LYS cc_start: 0.7253 (mttp) cc_final: 0.7010 (mtpp) REVERT: X 392 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7137 (mm-30) REVERT: Y 197 ARG cc_start: 0.7256 (tpp80) cc_final: 0.6887 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8645 (mp) cc_final: 0.8342 (mt) outliers start: 20 outliers final: 7 residues processed: 184 average time/residue: 2.5792 time to fit residues: 522.7478 Evaluate side-chains 166 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 158 time to evaluate : 2.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 523 ILE Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 635 ILE Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 146 LEU 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: 0.0570 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- 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: 0.7182 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13686 Z= 0.246 Angle : 0.538 10.960 18598 Z= 0.280 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.059 2349 Dihedral : 5.679 54.639 1962 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.24 % Allowed : 9.81 % Favored : 88.95 % 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: 0.39 (0.21), residues: 1699 helix: 1.76 (0.26), residues: 416 sheet: -0.07 (0.24), residues: 461 loop : -0.24 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 82 HIS 0.005 0.001 HIS X 357 PHE 0.013 0.001 PHE X 212 TYR 0.012 0.001 TYR Y 105 ARG 0.007 0.000 ARG L 18 *********************** 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 185 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 2.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7577 (m-40) cc_final: 0.7333 (m-40) REVERT: H 17 SER cc_start: 0.8691 (p) cc_final: 0.8244 (t) REVERT: H 79 TYR cc_start: 0.7844 (m-80) cc_final: 0.7606 (m-80) REVERT: N 3 GLN cc_start: 0.7346 (tt0) cc_final: 0.6812 (tm-30) REVERT: N 5 GLN cc_start: 0.7031 (tp40) cc_final: 0.6642 (tm-30) REVERT: R 48 PRO cc_start: 0.7724 (Cg_endo) cc_final: 0.7276 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6639 (tt0) REVERT: R 102 LYS cc_start: 0.7226 (mttt) cc_final: 0.6969 (mtpp) REVERT: R 140 MET cc_start: 0.6535 (tmt) cc_final: 0.6119 (tmt) REVERT: R 160 ASP cc_start: 0.7006 (m-30) cc_final: 0.6559 (t70) REVERT: R 219 ASP cc_start: 0.7583 (m-30) cc_final: 0.7338 (m-30) REVERT: R 274 ARG cc_start: 0.7830 (mtp-110) cc_final: 0.7376 (ttt90) REVERT: R 474 ASP cc_start: 0.5604 (t70) cc_final: 0.5014 (t0) REVERT: R 523 ILE cc_start: 0.7916 (OUTLIER) cc_final: 0.7671 (mt) REVERT: R 535 LEU cc_start: 0.7761 (tp) cc_final: 0.7466 (tp) REVERT: R 539 CYS cc_start: 0.7311 (t) cc_final: 0.6590 (m) REVERT: R 624 LYS cc_start: 0.7025 (mmpt) cc_final: 0.6149 (mmmt) REVERT: Y 59 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7593 (m-80) REVERT: Y 197 ARG cc_start: 0.7281 (tpp80) cc_final: 0.6923 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8628 (mp) cc_final: 0.8271 (mt) outliers start: 18 outliers final: 7 residues processed: 175 average time/residue: 2.4134 time to fit residues: 468.2086 Evaluate side-chains 165 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 2.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 439 LEU Chi-restraints excluded: chain R residue 523 ILE Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU 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: 20.0000 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.2582 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= 0.346 Angle : 0.574 10.824 18598 Z= 0.300 Chirality : 0.057 1.658 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.734 58.931 1962 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.24 % Allowed : 11.19 % Favored : 87.57 % 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 (0.20), residues: 1699 helix: 1.65 (0.26), residues: 408 sheet: -0.16 (0.24), residues: 472 loop : -0.37 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.006 0.001 HIS Y 142 PHE 0.015 0.002 PHE N 108 TYR 0.014 0.002 TYR L 49 ARG 0.004 0.000 ARG H 50 *********************** 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: 18 poor density : 152 time to evaluate : 2.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7654 (m-40) cc_final: 0.7414 (m-40) REVERT: H 17 SER cc_start: 0.8692 (p) cc_final: 0.8240 (t) REVERT: N 3 GLN cc_start: 0.7385 (tt0) cc_final: 0.6824 (tm-30) REVERT: N 5 GLN cc_start: 0.7149 (tp40) cc_final: 0.6754 (tm-30) REVERT: R 48 PRO cc_start: 0.7749 (Cg_endo) cc_final: 0.7333 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6679 (tt0) REVERT: R 102 LYS cc_start: 0.7192 (mttt) cc_final: 0.6982 (mtpp) REVERT: R 160 ASP cc_start: 0.6974 (m-30) cc_final: 0.6568 (t70) REVERT: R 274 ARG cc_start: 0.7853 (mtp-110) cc_final: 0.7329 (ttt90) REVERT: R 474 ASP cc_start: 0.5589 (t70) cc_final: 0.5356 (t0) REVERT: R 523 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7736 (mt) REVERT: R 535 LEU cc_start: 0.7769 (tp) cc_final: 0.7478 (tp) REVERT: R 539 CYS cc_start: 0.7307 (t) cc_final: 0.6599 (m) REVERT: R 635 ILE cc_start: 0.8191 (mm) cc_final: 0.7986 (mm) REVERT: Y 59 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: Y 161 SER cc_start: 0.8588 (m) cc_final: 0.8357 (m) REVERT: Y 197 ARG cc_start: 0.7331 (tpp80) cc_final: 0.6950 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 161 average time/residue: 2.5698 time to fit residues: 456.4840 Evaluate side-chains 163 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 149 time to evaluate : 2.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 523 ILE Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Z residue 52 THR 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: 0.4980 chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN X 271 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13686 Z= 0.243 Angle : 0.530 10.752 18598 Z= 0.276 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.037 2349 Dihedral : 5.472 56.999 1962 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.24 % Allowed : 11.74 % Favored : 87.02 % 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: 0.26 (0.20), residues: 1699 helix: 1.68 (0.26), residues: 410 sheet: -0.15 (0.24), residues: 456 loop : -0.33 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 82 HIS 0.004 0.001 HIS Y 142 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR R 482 ARG 0.002 0.000 ARG L 18 *********************** 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 175 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 2.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7626 (m-40) cc_final: 0.7393 (m-40) REVERT: H 17 SER cc_start: 0.8678 (p) cc_final: 0.8226 (t) REVERT: H 79 TYR cc_start: 0.7831 (m-80) cc_final: 0.7590 (m-80) REVERT: N 3 GLN cc_start: 0.7389 (tt0) cc_final: 0.6832 (tm-30) REVERT: N 5 GLN cc_start: 0.7137 (tp40) cc_final: 0.6833 (tm-30) REVERT: R 48 PRO cc_start: 0.7751 (Cg_endo) cc_final: 0.7344 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6642 (tt0) REVERT: R 102 LYS cc_start: 0.7175 (mttt) cc_final: 0.6966 (mtpp) REVERT: R 160 ASP cc_start: 0.6978 (m-30) cc_final: 0.6556 (t70) REVERT: R 274 ARG cc_start: 0.7844 (mtp-110) cc_final: 0.7403 (ttt90) REVERT: R 416 PHE cc_start: 0.6610 (p90) cc_final: 0.6404 (p90) REVERT: R 474 ASP cc_start: 0.5577 (t70) cc_final: 0.5338 (t0) REVERT: R 523 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7696 (mt) REVERT: R 535 LEU cc_start: 0.7788 (tp) cc_final: 0.7497 (tp) REVERT: R 539 CYS cc_start: 0.7292 (t) cc_final: 0.6592 (m) REVERT: R 624 LYS cc_start: 0.7094 (mmpt) cc_final: 0.6234 (mmmt) REVERT: R 635 ILE cc_start: 0.8190 (mm) cc_final: 0.7975 (mm) REVERT: Y 59 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7364 (m-10) REVERT: Y 197 ARG cc_start: 0.7338 (tpp80) cc_final: 0.6965 (tpp-160) outliers start: 18 outliers final: 11 residues processed: 168 average time/residue: 2.5558 time to fit residues: 474.9158 Evaluate side-chains 166 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 523 ILE Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 691 ILE Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 365 CYS Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 0.9980 chunk 157 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.2886 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= 0.388 Angle : 0.578 10.683 18598 Z= 0.302 Chirality : 0.057 1.657 2141 Planarity : 0.004 0.040 2349 Dihedral : 5.682 48.225 1962 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.38 % Allowed : 11.95 % Favored : 86.67 % 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: 0.06 (0.20), residues: 1699 helix: 1.43 (0.26), residues: 411 sheet: -0.22 (0.23), residues: 476 loop : -0.44 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.005 0.001 HIS Y 142 PHE 0.014 0.002 PHE N 108 TYR 0.014 0.002 TYR L 49 ARG 0.004 0.000 ARG H 50 *********************** 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 174 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 2.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7661 (m-40) cc_final: 0.7425 (m-40) REVERT: H 17 SER cc_start: 0.8676 (p) cc_final: 0.8213 (t) REVERT: N 3 GLN cc_start: 0.7420 (tt0) cc_final: 0.6844 (tm-30) REVERT: N 5 GLN cc_start: 0.7161 (tp40) cc_final: 0.6851 (tm-30) REVERT: R 48 PRO cc_start: 0.7733 (Cg_endo) cc_final: 0.7322 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6613 (tt0) REVERT: R 160 ASP cc_start: 0.6977 (m-30) cc_final: 0.6574 (t70) REVERT: R 274 ARG cc_start: 0.7842 (mtp-110) cc_final: 0.7413 (ttt90) REVERT: R 535 LEU cc_start: 0.7821 (tp) cc_final: 0.7532 (tp) REVERT: R 539 CYS cc_start: 0.7236 (t) cc_final: 0.6537 (m) REVERT: R 624 LYS cc_start: 0.7108 (mmpt) cc_final: 0.6235 (mmmt) REVERT: Y 59 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: Y 197 ARG cc_start: 0.7380 (tpp80) cc_final: 0.7006 (tpp-160) outliers start: 20 outliers final: 13 residues processed: 164 average time/residue: 2.6482 time to fit residues: 478.9706 Evaluate side-chains 161 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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** N 35 ASN R 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13686 Z= 0.248 Angle : 0.534 10.663 18598 Z= 0.278 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.036 2349 Dihedral : 5.520 44.744 1962 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.38 % Allowed : 12.57 % Favored : 86.05 % 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: 0.18 (0.20), residues: 1699 helix: 1.55 (0.26), residues: 412 sheet: -0.16 (0.23), residues: 472 loop : -0.37 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Y 82 HIS 0.004 0.001 HIS Y 142 PHE 0.011 0.001 PHE N 108 TYR 0.010 0.001 TYR Y 59 ARG 0.003 0.000 ARG Z 62 *********************** 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 178 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7670 (m-40) cc_final: 0.7440 (m-40) REVERT: L 95 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6359 (mp) REVERT: H 17 SER cc_start: 0.8683 (p) cc_final: 0.8225 (t) REVERT: N 3 GLN cc_start: 0.7411 (tt0) cc_final: 0.6833 (tm-30) REVERT: N 5 GLN cc_start: 0.7142 (tp40) cc_final: 0.6846 (tm-30) REVERT: R 48 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7363 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6590 (tt0) REVERT: R 160 ASP cc_start: 0.6978 (m-30) cc_final: 0.6560 (t70) REVERT: R 271 HIS cc_start: 0.4794 (m-70) cc_final: 0.4535 (m90) REVERT: R 274 ARG cc_start: 0.7792 (mtp-110) cc_final: 0.7377 (ttt90) REVERT: R 535 LEU cc_start: 0.7823 (tp) cc_final: 0.7555 (tp) REVERT: R 539 CYS cc_start: 0.7247 (t) cc_final: 0.6564 (m) REVERT: R 554 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6294 (tt) REVERT: R 624 LYS cc_start: 0.7027 (mmpt) cc_final: 0.6176 (mmmt) REVERT: Y 59 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7435 (m-10) REVERT: Y 82 TRP cc_start: 0.8473 (OUTLIER) cc_final: 0.6370 (m-90) REVERT: Y 197 ARG cc_start: 0.7364 (tpp80) cc_final: 0.6996 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8362 (mt) outliers start: 20 outliers final: 13 residues processed: 169 average time/residue: 2.4775 time to fit residues: 461.9739 Evaluate side-chains 169 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 95 LEU Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 635 ILE Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 336 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 2.9990 chunk 148 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** N 35 ASN R 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13686 Z= 0.341 Angle : 0.564 10.630 18598 Z= 0.294 Chirality : 0.057 1.655 2141 Planarity : 0.004 0.038 2349 Dihedral : 5.675 50.889 1962 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.80 % Allowed : 12.71 % Favored : 85.50 % 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: 0.07 (0.20), residues: 1699 helix: 1.45 (0.26), residues: 411 sheet: -0.22 (0.23), residues: 476 loop : -0.45 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 82 HIS 0.005 0.001 HIS X 357 PHE 0.013 0.002 PHE N 108 TYR 0.013 0.001 TYR L 49 ARG 0.004 0.000 ARG Z 62 *********************** 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 176 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7672 (m-40) cc_final: 0.7436 (m-40) REVERT: H 17 SER cc_start: 0.8683 (p) cc_final: 0.8217 (t) REVERT: N 3 GLN cc_start: 0.7421 (tt0) cc_final: 0.6841 (tm-30) REVERT: N 5 GLN cc_start: 0.7151 (tp40) cc_final: 0.6845 (tm-30) REVERT: R 48 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7370 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6916 (mt-10) cc_final: 0.6593 (tt0) REVERT: R 160 ASP cc_start: 0.6978 (m-30) cc_final: 0.6547 (t70) REVERT: R 271 HIS cc_start: 0.4890 (m-70) cc_final: 0.4643 (m90) REVERT: R 274 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7356 (ttt90) REVERT: R 535 LEU cc_start: 0.7803 (tp) cc_final: 0.7553 (tp) REVERT: R 539 CYS cc_start: 0.7193 (t) cc_final: 0.6527 (m) REVERT: R 624 LYS cc_start: 0.7040 (mmpt) cc_final: 0.6222 (mmmt) REVERT: Y 59 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: Y 82 TRP cc_start: 0.8500 (OUTLIER) cc_final: 0.6004 (m-90) REVERT: Y 197 ARG cc_start: 0.7379 (tpp80) cc_final: 0.7013 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8416 (mt) outliers start: 26 outliers final: 16 residues processed: 164 average time/residue: 2.5919 time to fit residues: 469.6174 Evaluate side-chains 166 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 2.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain R residue 682 THR Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 336 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** N 35 ASN R 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13686 Z= 0.216 Angle : 0.526 10.637 18598 Z= 0.275 Chirality : 0.055 1.660 2141 Planarity : 0.004 0.033 2349 Dihedral : 5.531 54.870 1962 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 12.98 % Favored : 85.57 % 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: 0.20 (0.20), residues: 1699 helix: 1.57 (0.26), residues: 412 sheet: -0.09 (0.24), residues: 465 loop : -0.39 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 82 HIS 0.003 0.001 HIS R 271 PHE 0.010 0.001 PHE N 108 TYR 0.012 0.001 TYR H 79 ARG 0.004 0.000 ARG Z 62 *********************** 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 178 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 157 time to evaluate : 2.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7666 (m-40) cc_final: 0.7444 (m-40) REVERT: H 17 SER cc_start: 0.8682 (p) cc_final: 0.8230 (t) REVERT: N 3 GLN cc_start: 0.7406 (tt0) cc_final: 0.6866 (tm-30) REVERT: N 5 GLN cc_start: 0.7144 (tp40) cc_final: 0.6848 (tm-30) REVERT: R 48 PRO cc_start: 0.7801 (Cg_endo) cc_final: 0.7405 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6915 (mt-10) cc_final: 0.6590 (tt0) REVERT: R 160 ASP cc_start: 0.6990 (m-30) cc_final: 0.6579 (t70) REVERT: R 271 HIS cc_start: 0.4831 (m-70) cc_final: 0.4604 (m90) REVERT: R 274 ARG cc_start: 0.7800 (mtp-110) cc_final: 0.7383 (ttt90) REVERT: R 535 LEU cc_start: 0.7792 (tp) cc_final: 0.7513 (tp) REVERT: R 536 ARG cc_start: 0.7074 (mtt180) cc_final: 0.6738 (mmt180) REVERT: R 539 CYS cc_start: 0.7227 (t) cc_final: 0.6539 (m) REVERT: R 554 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6374 (tt) REVERT: R 624 LYS cc_start: 0.7033 (mmpt) cc_final: 0.6220 (mmmt) REVERT: X 20 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6853 (mtm110) REVERT: Y 59 TYR cc_start: 0.8723 (OUTLIER) cc_final: 0.7500 (m-80) REVERT: Y 82 TRP cc_start: 0.8454 (OUTLIER) cc_final: 0.6408 (m-90) REVERT: Y 197 ARG cc_start: 0.7369 (tpp80) cc_final: 0.7010 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8346 (mt) outliers start: 21 outliers final: 12 residues processed: 169 average time/residue: 2.5959 time to fit residues: 483.1216 Evaluate side-chains 168 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 151 time to evaluate : 2.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 336 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 154 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 13 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13686 Z= 0.244 Angle : 0.532 10.644 18598 Z= 0.278 Chirality : 0.055 1.657 2141 Planarity : 0.004 0.031 2349 Dihedral : 5.527 59.337 1962 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.59 % Allowed : 12.98 % Favored : 85.43 % 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: -0.09 (0.24), residues: 468 loop : -0.37 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP Y 82 HIS 0.004 0.001 HIS X 357 PHE 0.027 0.001 PHE R 631 TYR 0.010 0.001 TYR Y 59 ARG 0.003 0.000 ARG Z 62 ********************** 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 172 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 149 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7669 (m-40) cc_final: 0.7446 (m-40) REVERT: H 17 SER cc_start: 0.8681 (p) cc_final: 0.8147 (t) REVERT: H 79 TYR cc_start: 0.7827 (m-80) cc_final: 0.7620 (m-10) REVERT: N 3 GLN cc_start: 0.7408 (tt0) cc_final: 0.6860 (tm-30) REVERT: N 5 GLN cc_start: 0.7148 (tp40) cc_final: 0.6847 (tm-30) REVERT: R 48 PRO cc_start: 0.7805 (Cg_endo) cc_final: 0.7406 (Cg_exo) REVERT: R 61 GLU cc_start: 0.6926 (mt-10) cc_final: 0.6534 (tt0) REVERT: R 160 ASP cc_start: 0.6988 (m-30) cc_final: 0.6559 (t70) REVERT: R 271 HIS cc_start: 0.4883 (m-70) cc_final: 0.4664 (m90) REVERT: R 274 ARG cc_start: 0.7802 (mtp-110) cc_final: 0.7363 (ttt90) REVERT: R 535 LEU cc_start: 0.7812 (tp) cc_final: 0.7570 (tp) REVERT: R 539 CYS cc_start: 0.7222 (t) cc_final: 0.6538 (m) REVERT: R 554 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6393 (tt) REVERT: R 624 LYS cc_start: 0.7019 (mmpt) cc_final: 0.6216 (mmmt) REVERT: X 20 ARG cc_start: 0.7346 (OUTLIER) cc_final: 0.6861 (mtm110) REVERT: Y 59 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: Y 82 TRP cc_start: 0.8467 (OUTLIER) cc_final: 0.6344 (m-90) REVERT: Y 197 ARG cc_start: 0.7374 (tpp80) cc_final: 0.7010 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8369 (mt) outliers start: 23 outliers final: 15 residues processed: 163 average time/residue: 2.5431 time to fit residues: 457.7163 Evaluate side-chains 165 residues out of total 1495 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 145 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain N residue 57 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 554 LEU Chi-restraints excluded: chain R residue 562 SER Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 207 ILE Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 82 TRP Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Y residue 275 SER Chi-restraints excluded: chain Y residue 336 LEU Chi-restraints excluded: chain Z residue 52 THR Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 62 ARG 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: 20.0000 chunk 37 optimal weight: 20.0000 chunk 134 optimal weight: 1.9990 chunk 56 optimal weight: 0.0980 chunk 137 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** N 35 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.130820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.105089 restraints weight = 68257.514| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.62 r_work: 0.3360 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13686 Z= 0.310 Angle : 0.557 10.648 18598 Z= 0.291 Chirality : 0.056 1.654 2141 Planarity : 0.004 0.035 2349 Dihedral : 5.630 57.925 1962 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.52 % Allowed : 13.26 % Favored : 85.22 % 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: 0.12 (0.20), residues: 1699 helix: 1.50 (0.26), residues: 412 sheet: -0.08 (0.24), residues: 468 loop : -0.49 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 82 HIS 0.005 0.001 HIS Z 44 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR Y 59 ARG 0.004 0.000 ARG Z 62 =============================================================================== Job complete usr+sys time: 9456.27 seconds wall clock time: 165 minutes 44.42 seconds (9944.42 seconds total)