Starting phenix.real_space_refine on Fri Mar 6 00:28:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_25763_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_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/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_25763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_25763.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_25763_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9n_25763/03_2026/7t9n_25763_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 8538 2.51 5 N 2266 2.21 5 O 2507 1.98 5 H 13037 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'ASN:plan1': 4, 'GLU:plan': 8, 'GLN:plan1': 2, 'ASP:plan': 10, 'ARG:plan': 4} 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: 4.63, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 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: 2.29 Conformation dependent library (CDL) restraints added in 922.2 milliseconds 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... Secondary structure from input PDB file: 40 helices and 25 sheets defined 29.4% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'L' and resid 27A through 30 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'L' and resid 122 through 127 Processing helix chain 'L' and resid 182 through 188 Processing helix chain 'H' and resid 28 through 32 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 83 through 87 Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 186 through 190 removed outlier: 4.219A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 186 through 190' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 62 through 65 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 87 through 91 Processing helix chain 'R' and resid 218 through 221 removed outlier: 4.308A pdb=" N PHE R 221 " --> pdb=" O LYS R 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 218 through 221' Processing helix chain 'R' and resid 245 through 249 removed outlier: 4.108A pdb=" N HIS R 248 " --> pdb=" O GLY R 245 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 287 Processing helix chain 'R' and resid 414 through 442 removed outlier: 3.564A pdb=" N ARG R 418 " --> pdb=" O TYR R 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE R 419 " --> pdb=" O LYS R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 447 through 477 Processing helix chain 'R' and resid 480 through 491 removed outlier: 3.724A pdb=" N HIS R 484 " --> pdb=" O GLU R 480 " (cutoff:3.500A) 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 491 through 525 Processing helix chain 'R' and resid 528 through 532 Processing helix chain 'R' and resid 534 through 559 Proline residue: R 556 - end of helix Processing helix chain 'R' and resid 576 through 609 Processing helix chain 'R' and resid 620 through 649 Proline residue: R 639 - end of helix Processing helix chain 'R' and resid 655 through 666 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 668 through 679 Proline residue: R 675 - end of helix Processing helix chain 'R' and resid 682 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 40 Processing helix chain 'X' and resid 52 through 61 removed outlier: 3.531A pdb=" N MET X 60 " --> pdb=" O ILE X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.568A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 279 Processing helix chain 'X' and resid 293 through 303 Processing helix chain 'X' and resid 312 through 318 removed outlier: 3.744A pdb=" N TYR X 318 " --> pdb=" O PHE X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 331 through 352 removed outlier: 4.136A pdb=" N THR X 335 " --> pdb=" O ASP X 331 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER X 352 " --> pdb=" O ILE X 348 " (cutoff:3.500A) Processing helix chain 'X' and resid 370 through 391 Processing helix chain 'Y' and resid 4 through 26 Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Z' and resid 8 through 24 Processing helix chain 'Z' and resid 29 through 45 Processing helix chain 'Z' and resid 46 through 48 No H-bonds generated for 'chain 'Z' and resid 46 through 48' Processing sheet with id=AA1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.797A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) 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=AA2, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.797A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AA4, 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=AA5, first strand: chain 'L' and resid 145 through 149 Processing sheet with id=AA6, 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=AA7, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.849A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASN H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 56 through 59 removed outlier: 6.849A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ARG H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.507A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.507A pdb=" N ASP H 144 " --> pdb=" O TYR H 176 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 151 through 154 removed outlier: 4.714A pdb=" N TYR H 194 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AB3, 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=AB4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.343A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 30 through 32 removed outlier: 6.623A pdb=" N ILE R 106 " --> pdb=" O GLY R 132 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N PHE R 134 " --> pdb=" O ILE R 106 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE R 108 " --> pdb=" O PHE R 134 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU R 182 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL R 205 " --> pdb=" O LEU R 182 " (cutoff:3.500A) removed outlier: 9.766A pdb=" N LEU R 230 " --> pdb=" O LYS R 201 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP R 203 " --> pdb=" O LEU R 230 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASP R 232 " --> pdb=" O ASP R 203 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL R 205 " --> pdb=" O ASP R 232 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU R 231 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU R 252 " --> pdb=" O ASP R 276 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'R' and resid 97 through 98 removed outlier: 6.785A pdb=" N PHE R 97 " --> pdb=" O LYS R 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'R' and resid 166 through 167 Processing sheet with id=AB9, first strand: chain 'X' and resid 207 through 214 removed outlier: 4.493A pdb=" N VAL X 224 " --> pdb=" O LEU X 45 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLY X 47 " --> pdb=" O VAL X 224 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA X 243 " --> pdb=" O ARG X 42 " (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) Processing sheet with id=AC1, first strand: chain 'Y' and resid 46 through 51 removed outlier: 5.726A pdb=" N THR Y 47 " --> pdb=" O ASN Y 340 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN Y 340 " --> pdb=" O THR Y 47 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS Y 337 " --> pdb=" O THR Y 329 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 58 through 63 removed outlier: 3.673A pdb=" N ALA Y 60 " --> pdb=" O ALA Y 73 " (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=AC3, 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: 4.306A pdb=" N GLY Y 116 " --> pdb=" O ILE Y 120 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ILE Y 120 " --> pdb=" O GLY Y 116 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N CYS Y 121 " --> pdb=" O GLU Y 138 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU Y 138 " --> pdb=" O CYS Y 121 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE Y 123 " --> pdb=" O SER Y 136 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG Y 134 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Y' and resid 146 through 151 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=AC5, first strand: chain 'Y' and resid 187 through 192 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=AC6, first strand: chain 'Y' and resid 229 through 234 removed outlier: 6.486A pdb=" N CYS Y 250 " --> pdb=" O THR Y 263 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N THR Y 263 " --> pdb=" O CYS Y 250 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU Y 252 " --> pdb=" O LEU Y 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Y' and resid 273 through 278 removed outlier: 3.620A pdb=" N SER Y 275 " --> pdb=" O GLY Y 288 " (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) 643 hydrogen bonds defined for protein. 1728 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: 6.78 Time building geometry restraints manager: 3.17 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: 0.00 - 6.97: 48055 6.97 - 13.95: 21 13.95 - 20.92: 4 20.92 - 27.89: 3 27.89 - 34.86: 5 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: 689 2.12 - 2.74: 48141 2.74 - 3.36: 77350 3.36 - 3.98: 101792 3.98 - 4.60: 158708 Nonbonded interactions: 386680 Sorted by model distance: nonbonded pdb=" OH TYR H 59 " pdb=" H VAL H 69 " model vdw 1.495 2.450 nonbonded pdb=" H TYR R 195 " pdb=" O ASP R 219 " model vdw 1.498 2.450 nonbonded pdb=" OD2 ASP R 410 " pdb="HH22 ARG R 418 " model vdw 1.527 2.450 nonbonded pdb=" O ILE Y 58 " pdb=" HG SER Y 316 " model vdw 1.586 2.450 nonbonded pdb=" O VAL H 11 " pdb=" HZ1 LYS H 13 " model vdw 1.592 2.450 ... (remaining 386675 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 5.040 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: 0.160 Extract box with map and model: 0.280 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 25.380 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- 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 13696 Z= 0.338 Angle : 0.751 19.506 18621 Z= 0.428 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 : 6.02 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.002 0.000 ARG N 67 TYR 0.014 0.001 TYR Y 105 PHE 0.016 0.001 PHE Y 234 TRP 0.010 0.001 TRP X 234 HIS 0.013 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00599 (13686) covalent geometry : angle 0.72168 (18598) SS BOND : bond 0.00437 ( 7) SS BOND : angle 0.57585 ( 14) hydrogen bonds : bond 0.18859 ( 614) hydrogen bonds : angle 7.80328 ( 1728) link_NAG-ASN : bond 0.08155 ( 3) link_NAG-ASN : angle 9.48929 ( 9) *********************** 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 to be fit. rotamer outliers: 3 poor density : 238 time to evaluate : 0.648 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: 0.7288 (m110) 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: 0.7437 (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: 1.3282 time to fit residues: 348.2917 Evaluate side-chains 169 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 167 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 26 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 173 GLN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 278 ASN Y 32 GLN Y 266 HIS ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.129951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.105460 restraints weight = 69302.497| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.07 r_work: 0.3368 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13696 Z= 0.183 Angle : 0.604 12.107 18621 Z= 0.314 Chirality : 0.057 1.655 2141 Planarity : 0.004 0.045 2349 Dihedral : 6.951 58.552 1964 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.04 % Allowed : 7.87 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.21), residues: 1699 helix: 2.06 (0.26), residues: 418 sheet: -0.04 (0.25), residues: 438 loop : -0.37 (0.22), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 98 TYR 0.012 0.001 TYR R 116 PHE 0.013 0.001 PHE Y 234 TRP 0.014 0.002 TRP Y 82 HIS 0.006 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00415 (13686) covalent geometry : angle 0.59521 (18598) SS BOND : bond 0.00441 ( 7) SS BOND : angle 0.82980 ( 14) hydrogen bonds : bond 0.04967 ( 614) hydrogen bonds : angle 5.81326 ( 1728) link_NAG-ASN : bond 0.00469 ( 3) link_NAG-ASN : angle 4.71893 ( 9) *********************** 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 198 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7671 (mtm110) cc_final: 0.7092 (mtm-85) REVERT: L 82 ASP cc_start: 0.7580 (m-30) cc_final: 0.7316 (m-30) REVERT: H 17 SER cc_start: 0.8881 (p) cc_final: 0.8581 (t) REVERT: N 3 GLN cc_start: 0.7708 (tt0) cc_final: 0.7422 (tm-30) REVERT: R 48 PRO cc_start: 0.7645 (Cg_endo) cc_final: 0.7201 (Cg_exo) REVERT: R 140 MET cc_start: 0.7004 (tmt) cc_final: 0.6758 (tmt) REVERT: R 474 ASP cc_start: 0.6535 (t70) cc_final: 0.5979 (t0) REVERT: R 535 LEU cc_start: 0.8054 (tp) cc_final: 0.7825 (tp) REVERT: R 536 ARG cc_start: 0.7572 (mtt180) cc_final: 0.7144 (mmt180) REVERT: R 539 CYS cc_start: 0.7943 (t) cc_final: 0.7191 (m) REVERT: R 624 LYS cc_start: 0.7286 (mmpt) cc_final: 0.6437 (mmmt) REVERT: Y 197 ARG cc_start: 0.7738 (tpp80) cc_final: 0.7435 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8805 (mp) cc_final: 0.8551 (mt) outliers start: 15 outliers final: 5 residues processed: 192 average time/residue: 1.3924 time to fit residues: 290.8692 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 19 optimal weight: 40.0000 chunk 3 optimal weight: 2.9990 chunk 125 optimal weight: 0.0980 chunk 54 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN R 113 ASN Y 32 GLN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.131609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.107125 restraints weight = 68816.929| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 2.00 r_work: 0.3366 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13696 Z= 0.202 Angle : 0.582 10.958 18621 Z= 0.303 Chirality : 0.057 1.659 2141 Planarity : 0.004 0.048 2349 Dihedral : 5.850 53.329 1962 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.38 % Allowed : 10.43 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.21), residues: 1699 helix: 1.96 (0.26), residues: 419 sheet: -0.15 (0.25), residues: 441 loop : -0.46 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 18 TYR 0.016 0.002 TYR Y 105 PHE 0.014 0.002 PHE N 108 TRP 0.013 0.002 TRP Y 82 HIS 0.005 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00464 (13686) covalent geometry : angle 0.57884 (18598) SS BOND : bond 0.00687 ( 7) SS BOND : angle 1.85643 ( 14) hydrogen bonds : bond 0.04729 ( 614) hydrogen bonds : angle 5.48322 ( 1728) link_NAG-ASN : bond 0.00105 ( 3) link_NAG-ASN : angle 1.79795 ( 9) *********************** 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 186 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7699 (mtm110) cc_final: 0.7376 (mtm110) REVERT: H 17 SER cc_start: 0.8845 (p) cc_final: 0.8559 (t) REVERT: N 3 GLN cc_start: 0.7759 (tt0) cc_final: 0.7434 (tm-30) REVERT: R 48 PRO cc_start: 0.7718 (Cg_endo) cc_final: 0.7274 (Cg_exo) REVERT: R 140 MET cc_start: 0.7099 (tmt) cc_final: 0.6841 (tmt) REVERT: R 165 THR cc_start: 0.8871 (m) cc_final: 0.8640 (m) REVERT: R 474 ASP cc_start: 0.6423 (t70) cc_final: 0.6147 (t0) REVERT: R 523 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8278 (mt) REVERT: R 535 LEU cc_start: 0.7935 (tp) cc_final: 0.7682 (tp) REVERT: R 536 ARG cc_start: 0.7447 (mtt180) cc_final: 0.7027 (mmt180) REVERT: R 539 CYS cc_start: 0.7851 (t) cc_final: 0.7088 (m) REVERT: R 624 LYS cc_start: 0.7364 (mmpt) cc_final: 0.6537 (mmmt) REVERT: X 392 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7892 (mm-30) REVERT: Y 59 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8171 (m-80) REVERT: Y 197 ARG cc_start: 0.7822 (tpp80) cc_final: 0.7520 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8871 (mp) cc_final: 0.8534 (mt) outliers start: 20 outliers final: 8 residues processed: 175 average time/residue: 1.2311 time to fit residues: 235.4059 Evaluate side-chains 164 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 12 VAL Chi-restraints excluded: chain R residue 90 GLN 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 41 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 152 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN ** R 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 GLN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.131799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.106052 restraints weight = 68596.518| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.62 r_work: 0.3371 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13696 Z= 0.157 Angle : 0.548 10.842 18621 Z= 0.286 Chirality : 0.056 1.662 2141 Planarity : 0.004 0.038 2349 Dihedral : 5.550 53.290 1962 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.31 % Allowed : 11.26 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1699 helix: 1.99 (0.26), residues: 420 sheet: -0.21 (0.25), residues: 439 loop : -0.41 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.009 0.001 TYR N 95 PHE 0.012 0.001 PHE N 108 TRP 0.014 0.001 TRP Y 82 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00359 (13686) covalent geometry : angle 0.54507 (18598) SS BOND : bond 0.00374 ( 7) SS BOND : angle 1.00249 ( 14) hydrogen bonds : bond 0.04274 ( 614) hydrogen bonds : angle 5.25150 ( 1728) link_NAG-ASN : bond 0.00094 ( 3) link_NAG-ASN : angle 2.20117 ( 9) *********************** 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 182 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7714 (p0) cc_final: 0.7432 (p0) REVERT: L 61 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7490 (mtm110) REVERT: H 17 SER cc_start: 0.8787 (p) cc_final: 0.8495 (t) REVERT: N 3 GLN cc_start: 0.7652 (tt0) cc_final: 0.7338 (tm-30) REVERT: R 48 PRO cc_start: 0.7739 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: R 140 MET cc_start: 0.6940 (tmt) cc_final: 0.6679 (tmt) REVERT: R 165 THR cc_start: 0.8856 (m) cc_final: 0.8625 (m) REVERT: R 274 ARG cc_start: 0.7854 (mtp-110) cc_final: 0.7545 (ttt90) REVERT: R 416 PHE cc_start: 0.6424 (p90) cc_final: 0.6169 (p90) REVERT: R 474 ASP cc_start: 0.6313 (t70) cc_final: 0.6044 (t0) REVERT: R 523 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8252 (mt) REVERT: R 535 LEU cc_start: 0.7920 (tp) cc_final: 0.7710 (tp) REVERT: R 539 CYS cc_start: 0.7781 (t) cc_final: 0.7091 (m) REVERT: R 682 THR cc_start: 0.7454 (p) cc_final: 0.6971 (p) REVERT: X 392 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7837 (mm-30) REVERT: Y 59 TYR cc_start: 0.8798 (OUTLIER) cc_final: 0.8170 (m-80) REVERT: Y 197 ARG cc_start: 0.7720 (tpp80) cc_final: 0.7444 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8852 (mp) cc_final: 0.8459 (mt) outliers start: 19 outliers final: 9 residues processed: 173 average time/residue: 1.3007 time to fit residues: 246.8400 Evaluate side-chains 164 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.702 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 523 ILE Chi-restraints excluded: chain X residue 20 ARG 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 262 MET Chi-restraints excluded: chain Z residue 62 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 67 optimal weight: 0.1980 chunk 13 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 156 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 39 optimal weight: 8.9990 chunk 151 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 GLN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.132322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107058 restraints weight = 68472.067| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.87 r_work: 0.3362 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13696 Z= 0.135 Angle : 0.530 10.739 18621 Z= 0.276 Chirality : 0.055 1.662 2141 Planarity : 0.003 0.039 2349 Dihedral : 5.335 55.679 1962 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.10 % Allowed : 11.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.21), residues: 1699 helix: 2.04 (0.26), residues: 424 sheet: -0.17 (0.25), residues: 435 loop : -0.33 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 18 TYR 0.010 0.001 TYR H 79 PHE 0.010 0.001 PHE N 108 TRP 0.013 0.001 TRP X 234 HIS 0.003 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00308 (13686) covalent geometry : angle 0.52699 (18598) SS BOND : bond 0.00291 ( 7) SS BOND : angle 1.57513 ( 14) hydrogen bonds : bond 0.04069 ( 614) hydrogen bonds : angle 5.08054 ( 1728) link_NAG-ASN : bond 0.00064 ( 3) link_NAG-ASN : angle 2.08017 ( 9) *********************** 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 177 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7446 (mtm110) REVERT: H 17 SER cc_start: 0.8802 (p) cc_final: 0.8506 (t) REVERT: N 3 GLN cc_start: 0.7719 (tt0) cc_final: 0.7402 (tm-30) REVERT: N 99 CYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7897 (t) REVERT: R 48 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7340 (Cg_exo) REVERT: R 165 THR cc_start: 0.8842 (m) cc_final: 0.8597 (m) REVERT: R 474 ASP cc_start: 0.6379 (t70) cc_final: 0.6123 (t0) REVERT: R 535 LEU cc_start: 0.7892 (tp) cc_final: 0.7635 (tp) REVERT: R 539 CYS cc_start: 0.7839 (t) cc_final: 0.7129 (m) REVERT: R 624 LYS cc_start: 0.7412 (mmpt) cc_final: 0.6630 (mmmt) REVERT: R 682 THR cc_start: 0.7422 (p) cc_final: 0.7041 (p) REVERT: Y 59 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8226 (m-80) REVERT: Y 161 SER cc_start: 0.8685 (t) cc_final: 0.8340 (m) REVERT: Y 197 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7557 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8826 (mp) cc_final: 0.8487 (mt) outliers start: 16 outliers final: 10 residues processed: 171 average time/residue: 1.2530 time to fit residues: 235.0671 Evaluate side-chains 163 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 90 GLN 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 X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Z residue 57 SER Chi-restraints excluded: chain Z residue 62 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 19 optimal weight: 30.0000 chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 80 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27BASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 173 GLN X 271 ASN Y 32 GLN Y 88 ASN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.127401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102577 restraints weight = 68738.971| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.05 r_work: 0.3312 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13696 Z= 0.324 Angle : 0.649 10.663 18621 Z= 0.339 Chirality : 0.059 1.651 2141 Planarity : 0.005 0.042 2349 Dihedral : 5.999 46.530 1962 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.80 % Allowed : 11.88 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.20), residues: 1699 helix: 1.55 (0.25), residues: 418 sheet: -0.26 (0.24), residues: 458 loop : -0.66 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 50 TYR 0.019 0.002 TYR L 49 PHE 0.026 0.002 PHE X 212 TRP 0.014 0.002 TRP X 234 HIS 0.007 0.002 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00758 (13686) covalent geometry : angle 0.64469 (18598) SS BOND : bond 0.00701 ( 7) SS BOND : angle 1.54054 ( 14) hydrogen bonds : bond 0.04864 ( 614) hydrogen bonds : angle 5.42134 ( 1728) link_NAG-ASN : bond 0.00394 ( 3) link_NAG-ASN : angle 2.89046 ( 9) *********************** 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 181 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.8107 (p0) cc_final: 0.7744 (p0) REVERT: H 17 SER cc_start: 0.8778 (p) cc_final: 0.8490 (t) REVERT: H 40 LEU cc_start: 0.4781 (mp) cc_final: 0.4563 (mt) REVERT: N 3 GLN cc_start: 0.7796 (tt0) cc_final: 0.7448 (tm-30) REVERT: R 48 PRO cc_start: 0.7713 (Cg_endo) cc_final: 0.7310 (Cg_exo) REVERT: R 165 THR cc_start: 0.8870 (m) cc_final: 0.8641 (m) REVERT: R 474 ASP cc_start: 0.6547 (t70) cc_final: 0.6330 (t0) REVERT: R 535 LEU cc_start: 0.8011 (tp) cc_final: 0.7773 (tp) REVERT: R 539 CYS cc_start: 0.7879 (t) cc_final: 0.7277 (m) REVERT: R 624 LYS cc_start: 0.7435 (mmpt) cc_final: 0.6649 (mmmt) REVERT: R 682 THR cc_start: 0.7440 (p) cc_final: 0.7027 (p) REVERT: Y 59 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.7894 (m-10) REVERT: Y 197 ARG cc_start: 0.7885 (tpp80) cc_final: 0.7566 (tpp-160) outliers start: 26 outliers final: 14 residues processed: 169 average time/residue: 1.3870 time to fit residues: 256.5798 Evaluate side-chains 163 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.711 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 496 THR 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 262 MET 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 75 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 19 optimal weight: 30.0000 chunk 51 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.130343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.105607 restraints weight = 68283.614| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.10 r_work: 0.3321 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3190 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13696 Z= 0.201 Angle : 0.576 10.618 18621 Z= 0.302 Chirality : 0.056 1.658 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.787 44.687 1962 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.52 % Allowed : 12.71 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1699 helix: 1.71 (0.25), residues: 413 sheet: -0.23 (0.24), residues: 451 loop : -0.57 (0.22), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 50 TYR 0.012 0.001 TYR H 59 PHE 0.012 0.001 PHE X 212 TRP 0.014 0.002 TRP H 33 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00463 (13686) covalent geometry : angle 0.57339 (18598) SS BOND : bond 0.00492 ( 7) SS BOND : angle 1.09546 ( 14) hydrogen bonds : bond 0.04360 ( 614) hydrogen bonds : angle 5.23526 ( 1728) link_NAG-ASN : bond 0.00082 ( 3) link_NAG-ASN : angle 2.24910 ( 9) *********************** 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 to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7848 (p0) cc_final: 0.7543 (p0) REVERT: L 61 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7424 (mtm110) REVERT: H 17 SER cc_start: 0.8804 (p) cc_final: 0.8519 (t) REVERT: N 3 GLN cc_start: 0.7865 (tt0) cc_final: 0.7499 (tm-30) REVERT: R 48 PRO cc_start: 0.7738 (Cg_endo) cc_final: 0.7334 (Cg_exo) REVERT: R 165 THR cc_start: 0.8872 (m) cc_final: 0.8625 (m) REVERT: R 416 PHE cc_start: 0.6550 (p90) cc_final: 0.6272 (p90) REVERT: R 535 LEU cc_start: 0.7984 (tp) cc_final: 0.7754 (tp) REVERT: R 539 CYS cc_start: 0.7833 (t) cc_final: 0.7214 (m) REVERT: R 624 LYS cc_start: 0.7414 (mmpt) cc_final: 0.6643 (mmmt) REVERT: R 682 THR cc_start: 0.7385 (p) cc_final: 0.7180 (p) REVERT: Y 59 TYR cc_start: 0.8986 (OUTLIER) cc_final: 0.7879 (m-10) REVERT: Y 82 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.6759 (m-90) REVERT: Y 197 ARG cc_start: 0.7903 (tpp80) cc_final: 0.7604 (tpp-160) outliers start: 22 outliers final: 13 residues processed: 167 average time/residue: 1.3965 time to fit residues: 255.1750 Evaluate side-chains 164 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 496 THR 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 82 TRP Chi-restraints excluded: chain Y residue 262 MET 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 32 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.0020 chunk 117 optimal weight: 1.9990 chunk 37 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 128 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 overall best weight: 1.0392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN N 35 ASN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105101 restraints weight = 68240.137| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.62 r_work: 0.3356 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13696 Z= 0.186 Angle : 0.566 10.670 18621 Z= 0.296 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.736 51.085 1962 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.17 % Allowed : 13.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1699 helix: 1.79 (0.26), residues: 413 sheet: -0.25 (0.24), residues: 456 loop : -0.58 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 50 TYR 0.011 0.001 TYR R 521 PHE 0.013 0.001 PHE R 37 TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00431 (13686) covalent geometry : angle 0.56365 (18598) SS BOND : bond 0.00458 ( 7) SS BOND : angle 1.04424 ( 14) hydrogen bonds : bond 0.04232 ( 614) hydrogen bonds : angle 5.14251 ( 1728) link_NAG-ASN : bond 0.00125 ( 3) link_NAG-ASN : angle 2.08042 ( 9) *********************** 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 170 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8810 (p) cc_final: 0.8509 (t) REVERT: N 3 GLN cc_start: 0.7749 (tt0) cc_final: 0.7393 (tm-30) REVERT: R 48 PRO cc_start: 0.7764 (Cg_endo) cc_final: 0.7374 (Cg_exo) REVERT: R 165 THR cc_start: 0.8840 (m) cc_final: 0.8610 (m) REVERT: R 535 LEU cc_start: 0.7979 (tp) cc_final: 0.7739 (tp) REVERT: R 539 CYS cc_start: 0.7786 (t) cc_final: 0.7184 (m) REVERT: R 624 LYS cc_start: 0.7360 (mmpt) cc_final: 0.6612 (mmmt) REVERT: Y 59 TYR cc_start: 0.8976 (OUTLIER) cc_final: 0.7875 (m-10) REVERT: Y 82 TRP cc_start: 0.8786 (OUTLIER) cc_final: 0.6805 (m-90) REVERT: Y 197 ARG cc_start: 0.7752 (tpp80) cc_final: 0.7469 (tpp-160) outliers start: 17 outliers final: 13 residues processed: 161 average time/residue: 1.4199 time to fit residues: 249.6076 Evaluate side-chains 164 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 149 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 496 THR 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 262 MET 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 154 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.130722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106256 restraints weight = 68482.771| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.02 r_work: 0.3335 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13696 Z= 0.187 Angle : 0.564 10.658 18621 Z= 0.295 Chirality : 0.056 1.657 2141 Planarity : 0.004 0.038 2349 Dihedral : 5.765 57.016 1962 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.38 % Allowed : 13.33 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.21), residues: 1699 helix: 1.81 (0.26), residues: 413 sheet: -0.25 (0.24), residues: 456 loop : -0.58 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 62 TYR 0.012 0.001 TYR R 521 PHE 0.013 0.001 PHE R 37 TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00432 (13686) covalent geometry : angle 0.56215 (18598) SS BOND : bond 0.00449 ( 7) SS BOND : angle 1.01545 ( 14) hydrogen bonds : bond 0.04212 ( 614) hydrogen bonds : angle 5.10807 ( 1728) link_NAG-ASN : bond 0.00123 ( 3) link_NAG-ASN : angle 1.97852 ( 9) *********************** 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 174 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.737 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 52 ASP cc_start: 0.7841 (p0) cc_final: 0.7519 (p0) REVERT: H 17 SER cc_start: 0.8791 (p) cc_final: 0.8488 (t) REVERT: N 3 GLN cc_start: 0.7826 (tt0) cc_final: 0.7459 (tm-30) REVERT: R 48 PRO cc_start: 0.7771 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: R 165 THR cc_start: 0.8867 (m) cc_final: 0.8628 (m) REVERT: R 535 LEU cc_start: 0.7946 (tp) cc_final: 0.7702 (tp) REVERT: R 539 CYS cc_start: 0.7688 (t) cc_final: 0.7098 (m) REVERT: R 554 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6222 (tt) REVERT: R 624 LYS cc_start: 0.7353 (mmpt) cc_final: 0.6590 (mmmt) REVERT: Y 59 TYR cc_start: 0.9004 (OUTLIER) cc_final: 0.7908 (m-10) REVERT: Y 82 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.6785 (m-90) REVERT: Y 197 ARG cc_start: 0.7884 (tpp80) cc_final: 0.7569 (tpp-160) outliers start: 20 outliers final: 15 residues processed: 163 average time/residue: 1.4614 time to fit residues: 259.8772 Evaluate side-chains 169 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 486 ILE Chi-restraints excluded: chain R residue 496 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 262 MET 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 167 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 30 ASN ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.128570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.104057 restraints weight = 68275.486| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.95 r_work: 0.3349 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3203 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13696 Z= 0.203 Angle : 0.576 10.676 18621 Z= 0.302 Chirality : 0.056 1.656 2141 Planarity : 0.004 0.037 2349 Dihedral : 5.805 59.186 1962 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.45 % Allowed : 13.67 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.21), residues: 1699 helix: 1.81 (0.25), residues: 413 sheet: -0.26 (0.24), residues: 456 loop : -0.60 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Z 62 TYR 0.016 0.001 TYR R 521 PHE 0.013 0.001 PHE R 37 TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00471 (13686) covalent geometry : angle 0.57423 (18598) SS BOND : bond 0.00480 ( 7) SS BOND : angle 1.03185 ( 14) hydrogen bonds : bond 0.04264 ( 614) hydrogen bonds : angle 5.11359 ( 1728) link_NAG-ASN : bond 0.00158 ( 3) link_NAG-ASN : angle 1.95186 ( 9) ********************** 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 to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.863 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 52 ASP cc_start: 0.7868 (p0) cc_final: 0.7540 (p0) REVERT: H 17 SER cc_start: 0.8820 (p) cc_final: 0.8524 (t) REVERT: N 3 GLN cc_start: 0.7884 (tt0) cc_final: 0.7543 (tm-30) REVERT: R 48 PRO cc_start: 0.7866 (Cg_endo) cc_final: 0.7477 (Cg_exo) REVERT: R 165 THR cc_start: 0.8862 (m) cc_final: 0.8626 (m) REVERT: R 535 LEU cc_start: 0.7975 (tp) cc_final: 0.7748 (tp) REVERT: R 539 CYS cc_start: 0.7782 (t) cc_final: 0.7192 (m) REVERT: R 624 LYS cc_start: 0.7409 (mmpt) cc_final: 0.6650 (mmmt) REVERT: Y 59 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.7947 (m-10) REVERT: Y 82 TRP cc_start: 0.8787 (OUTLIER) cc_final: 0.6776 (m-90) REVERT: Y 197 ARG cc_start: 0.7940 (tpp80) cc_final: 0.7640 (tpp-160) outliers start: 21 outliers final: 15 residues processed: 161 average time/residue: 1.3842 time to fit residues: 244.0559 Evaluate side-chains 166 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 90 GLN Chi-restraints excluded: chain R residue 150 THR Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 496 THR 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 262 MET 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 149 optimal weight: 0.9990 chunk 20 optimal weight: 9.9990 chunk 117 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 163 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.129113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.104855 restraints weight = 68087.004| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.89 r_work: 0.3366 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13696 Z= 0.162 Angle : 0.555 10.683 18621 Z= 0.290 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.038 2349 Dihedral : 5.713 57.249 1962 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.24 % Allowed : 13.81 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.21), residues: 1699 helix: 1.91 (0.26), residues: 413 sheet: -0.24 (0.24), residues: 456 loop : -0.55 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Z 62 TYR 0.016 0.001 TYR R 521 PHE 0.014 0.001 PHE R 37 TRP 0.014 0.001 TRP Y 82 HIS 0.003 0.001 HIS X 357 Details of bonding type rmsd covalent geometry : bond 0.00373 (13686) covalent geometry : angle 0.55330 (18598) SS BOND : bond 0.00403 ( 7) SS BOND : angle 0.94675 ( 14) hydrogen bonds : bond 0.04083 ( 614) hydrogen bonds : angle 5.01843 ( 1728) link_NAG-ASN : bond 0.00073 ( 3) link_NAG-ASN : angle 1.69796 ( 9) =============================================================================== Job complete usr+sys time: 9808.94 seconds wall clock time: 166 minutes 31.91 seconds (9991.91 seconds total)