Starting phenix.real_space_refine on Mon Jun 23 01:10:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t9n_25763/06_2025/7t9n_25763_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t9n_25763/06_2025/7t9n_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_25763/06_2025/7t9n_25763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t9n_25763/06_2025/7t9n_25763.map" model { file = "/net/cci-nas-00/data/ceres_data/7t9n_25763/06_2025/7t9n_25763_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t9n_25763/06_2025/7t9n_25763_trim.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 78 5.16 5 C 8538 2.51 5 N 2266 2.21 5 O 2507 1.98 5 H 13037 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26426 Number of models: 1 Model: "" Number of chains: 8 Chain: "L" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 3122 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 196} Chain: "H" Number of atoms: 3230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 3230 Classifications: {'peptide': 215} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 200} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1889 Classifications: {'peptide': 126} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 119} Chain: "R" Number of atoms: 8866 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 8866 Classifications: {'peptide': 555} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 529} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 3257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3257 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 8, 'ASN:plan1': 4, 'ARG:plan': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 102 Chain: "Y" Number of atoms: 5109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5109 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "Z" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 82 Unusual residues: {'NAG': 3, 'Z41': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 12.50, per 1000 atoms: 0.47 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: 6.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3240 Finding SS restraints... 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: 2.29 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: 10.40 Time building geometry restraints manager: 8.19 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: 4.400 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: 0.440 Extract box with map and model: 1.030 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 55.580 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:22.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.530 ------------------------------------------------------------------------------- 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 : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.21 % Allowed : 0.55 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1699 helix: 2.02 (0.26), residues: 425 sheet: 0.14 (0.25), residues: 474 loop : -0.14 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 234 HIS 0.013 0.001 HIS X 357 PHE 0.016 0.001 PHE Y 234 TYR 0.014 0.001 TYR Y 105 ARG 0.002 0.000 ARG N 67 Details of bonding type rmsd link_NAG-ASN : bond 0.08155 ( 3) link_NAG-ASN : angle 9.48929 ( 9) hydrogen bonds : bond 0.18859 ( 614) hydrogen bonds : angle 7.80328 ( 1728) SS BOND : bond 0.00437 ( 7) SS BOND : angle 0.57585 ( 14) covalent geometry : bond 0.00599 (13686) covalent geometry : angle 0.72168 (18598) *********************** 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 : 2.055 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "SER H 113 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 30 ASN cc_start: 0.7536 (m-40) cc_final: 0.7236 (m-40) REVERT: L 78 LEU cc_start: 0.6997 (mp) cc_final: 0.6491 (mp) REVERT: L 82 ASP cc_start: 0.6855 (m-30) cc_final: 0.6625 (m-30) REVERT: H 72 ASP cc_start: 0.7187 (t0) cc_final: 0.6821 (t0) REVERT: N 3 GLN cc_start: 0.7157 (tt0) cc_final: 0.6713 (tm-30) REVERT: N 5 GLN cc_start: 0.6786 (tp40) cc_final: 0.6400 (tm-30) REVERT: R 48 PRO cc_start: 0.7621 (Cg_endo) cc_final: 0.7141 (Cg_exo) REVERT: R 61 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6704 (tt0) REVERT: R 102 LYS cc_start: 0.7164 (mttt) cc_final: 0.6903 (mtpp) REVERT: R 160 ASP cc_start: 0.6992 (m-30) cc_final: 0.6563 (t70) REVERT: R 219 ASP cc_start: 0.7521 (m-30) cc_final: 0.7303 (m-30) REVERT: R 251 GLU cc_start: 0.7514 (tt0) cc_final: 0.7269 (tt0) REVERT: R 274 ARG cc_start: 0.7794 (mtp-110) cc_final: 0.7436 (ttt90) REVERT: R 461 PHE cc_start: 0.7382 (t80) cc_final: 0.7163 (t80) REVERT: R 535 LEU cc_start: 0.7674 (tp) cc_final: 0.7056 (tm) REVERT: R 536 ARG cc_start: 0.6832 (mtt180) cc_final: 0.6541 (mmt180) REVERT: R 539 CYS cc_start: 0.7333 (t) cc_final: 0.6501 (m) REVERT: X 211 LYS cc_start: 0.7133 (mttp) cc_final: 0.6904 (mtpp) REVERT: X 392 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7006 (mm-30) REVERT: Y 59 TYR cc_start: 0.7793 (m-80) cc_final: 0.7570 (m-80) REVERT: Y 226 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7474 (mt-10) REVERT: Y 336 LEU cc_start: 0.8455 (mp) cc_final: 0.8229 (mt) REVERT: Z 46 LYS cc_start: 0.8170 (mmmt) cc_final: 0.7835 (mppt) outliers start: 3 outliers final: 2 residues processed: 241 average time/residue: 2.6731 time to fit residues: 706.6072 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 : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 113 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 0.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.129415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.104870 restraints weight = 69011.453| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.92 r_work: 0.3373 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13696 Z= 0.215 Angle : 0.613 11.205 18621 Z= 0.321 Chirality : 0.057 1.655 2141 Planarity : 0.004 0.045 2349 Dihedral : 7.089 60.122 1964 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.21), residues: 1699 helix: 2.01 (0.26), residues: 419 sheet: -0.03 (0.25), residues: 438 loop : -0.39 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.007 0.001 HIS X 357 PHE 0.013 0.001 PHE N 108 TYR 0.012 0.002 TYR R 116 ARG 0.004 0.000 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00911 ( 3) link_NAG-ASN : angle 4.17932 ( 9) hydrogen bonds : bond 0.05114 ( 614) hydrogen bonds : angle 5.87847 ( 1728) SS BOND : bond 0.00671 ( 7) SS BOND : angle 0.85606 ( 14) covalent geometry : bond 0.00487 (13686) covalent geometry : angle 0.60644 (18598) *********************** 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: 18 poor density : 180 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7771 (p0) cc_final: 0.7503 (p0) REVERT: L 61 ARG cc_start: 0.7683 (mtm110) cc_final: 0.7051 (mtm-85) REVERT: L 82 ASP cc_start: 0.7607 (m-30) cc_final: 0.7384 (m-30) REVERT: H 17 SER cc_start: 0.8870 (p) cc_final: 0.8577 (t) REVERT: N 3 GLN cc_start: 0.7705 (tt0) cc_final: 0.7426 (tm-30) REVERT: R 48 PRO cc_start: 0.7649 (Cg_endo) cc_final: 0.7205 (Cg_exo) REVERT: R 140 MET cc_start: 0.6956 (tmt) cc_final: 0.6712 (tmt) REVERT: R 535 LEU cc_start: 0.8080 (tp) cc_final: 0.7850 (tp) REVERT: R 536 ARG cc_start: 0.7571 (mtt180) cc_final: 0.7173 (mmt180) REVERT: R 539 CYS cc_start: 0.7927 (t) cc_final: 0.7202 (m) REVERT: R 624 LYS cc_start: 0.7329 (mmpt) cc_final: 0.6465 (mmmt) REVERT: R 682 THR cc_start: 0.7475 (p) cc_final: 0.7110 (p) REVERT: X 392 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7826 (mm-30) REVERT: Y 197 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7442 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8807 (mp) cc_final: 0.8568 (mt) outliers start: 18 outliers final: 5 residues processed: 190 average time/residue: 2.9581 time to fit residues: 621.2728 Evaluate side-chains 159 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 154 time to evaluate : 2.168 ------------------------------------------------------------------------------- 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 22 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 157 optimal weight: 0.7980 chunk 81 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN R 173 GLN 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 = 0.3933 r_free = 0.3933 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.107527 restraints weight = 68633.140| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.95 r_work: 0.3356 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13696 Z= 0.176 Angle : 0.566 10.971 18621 Z= 0.296 Chirality : 0.056 1.661 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.845 48.635 1962 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.10 % Allowed : 10.08 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.21), residues: 1699 helix: 2.01 (0.26), residues: 419 sheet: -0.07 (0.25), residues: 439 loop : -0.47 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR R 482 ARG 0.006 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00107 ( 3) link_NAG-ASN : angle 1.93406 ( 9) hydrogen bonds : bond 0.04671 ( 614) hydrogen bonds : angle 5.53136 ( 1728) SS BOND : bond 0.00426 ( 7) SS BOND : angle 2.12877 ( 14) covalent geometry : bond 0.00403 (13686) covalent geometry : angle 0.56144 (18598) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3398 Ramachandran restraints generated. 1699 Oldfield, 0 Emsley, 1699 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 262 is missing expected H atoms. Skipping. Residue LEU 265 is missing expected H atoms. Skipping. Residue MET 396 is missing expected H atoms. Skipping. Residue VAL 397 is missing expected H atoms. Skipping. Residue LYS 401 is missing expected H atoms. Skipping. Residue LYS 621 is missing expected H atoms. Skipping. Residue LYS 17 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 25 is missing expected H atoms. Skipping. Residue LYS 28 is missing expected H atoms. Skipping. Residue LYS 32 is missing expected H atoms. Skipping. Residue SER 54 is missing expected H atoms. Skipping. Residue THR 55 is missing expected H atoms. Skipping. Residue LYS 58 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LYS 274 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue SER 306 is missing expected H atoms. Skipping. Residue LYS 307 is missing expected H atoms. Skipping. Residue LEU 308 is missing expected H atoms. Skipping. Residue SER 352 is missing expected H atoms. Skipping. Evaluate side-chains 180 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 17 SER cc_start: 0.8831 (p) cc_final: 0.8546 (t) REVERT: N 3 GLN cc_start: 0.7713 (tt0) cc_final: 0.7414 (tm-30) REVERT: R 48 PRO cc_start: 0.7670 (Cg_endo) cc_final: 0.7220 (Cg_exo) REVERT: R 140 MET cc_start: 0.6956 (tmt) cc_final: 0.6683 (tmt) REVERT: R 474 ASP cc_start: 0.6354 (t70) cc_final: 0.6122 (t0) REVERT: R 535 LEU cc_start: 0.7989 (tp) cc_final: 0.7753 (tp) REVERT: R 536 ARG cc_start: 0.7496 (mtt180) cc_final: 0.7108 (mmt180) REVERT: R 539 CYS cc_start: 0.7885 (t) cc_final: 0.7127 (m) REVERT: R 624 LYS cc_start: 0.7404 (mmpt) cc_final: 0.6583 (mmmt) REVERT: R 682 THR cc_start: 0.7279 (p) cc_final: 0.6896 (p) REVERT: X 392 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7869 (mm-30) REVERT: Y 197 ARG cc_start: 0.7768 (tpp80) cc_final: 0.7471 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8845 (mp) cc_final: 0.8510 (mt) outliers start: 16 outliers final: 9 residues processed: 172 average time/residue: 2.9496 time to fit residues: 561.3858 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 562 SER Chi-restraints excluded: chain X residue 285 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 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 31 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 157 optimal weight: 0.0970 chunk 74 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN 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 = 0.3918 r_free = 0.3918 target = 0.131220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106490 restraints weight = 68980.918| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.01 r_work: 0.3357 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2652 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= 0.210 Angle : 0.580 10.851 18621 Z= 0.303 Chirality : 0.056 1.658 2141 Planarity : 0.004 0.039 2349 Dihedral : 5.734 55.529 1962 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.45 % Allowed : 11.33 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.21), residues: 1699 helix: 1.86 (0.25), residues: 420 sheet: -0.21 (0.25), residues: 443 loop : -0.53 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP X 234 HIS 0.005 0.001 HIS X 357 PHE 0.014 0.001 PHE N 108 TYR 0.013 0.001 TYR Y 105 ARG 0.004 0.000 ARG R 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00052 ( 3) link_NAG-ASN : angle 2.26226 ( 9) hydrogen bonds : bond 0.04542 ( 614) hydrogen bonds : angle 5.36512 ( 1728) SS BOND : bond 0.00448 ( 7) SS BOND : angle 1.06596 ( 14) covalent geometry : bond 0.00484 (13686) covalent geometry : angle 0.57707 (18598) *********************** 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 183 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7911 (p0) cc_final: 0.7586 (p0) REVERT: H 17 SER cc_start: 0.8840 (p) cc_final: 0.8535 (t) REVERT: H 79 TYR cc_start: 0.8104 (m-80) cc_final: 0.7879 (m-10) REVERT: N 3 GLN cc_start: 0.7825 (tt0) cc_final: 0.7485 (tm-30) REVERT: R 48 PRO cc_start: 0.7711 (Cg_endo) cc_final: 0.7272 (Cg_exo) REVERT: R 140 MET cc_start: 0.7200 (tmt) cc_final: 0.6950 (tmt) REVERT: R 165 THR cc_start: 0.8862 (m) cc_final: 0.8620 (m) REVERT: R 535 LEU cc_start: 0.7927 (tp) cc_final: 0.7695 (tp) REVERT: R 539 CYS cc_start: 0.7828 (t) cc_final: 0.7105 (m) REVERT: R 682 THR cc_start: 0.7235 (p) cc_final: 0.6888 (p) REVERT: X 392 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7921 (mm-30) REVERT: Y 59 TYR cc_start: 0.8904 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: Y 197 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7578 (tpp-160) REVERT: Y 336 LEU cc_start: 0.8883 (mp) cc_final: 0.8512 (mt) outliers start: 21 outliers final: 10 residues processed: 171 average time/residue: 2.4669 time to fit residues: 466.3376 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 X residue 365 CYS Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 262 MET Chi-restraints excluded: chain Z residue 57 SER 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 38 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 129 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN R 173 GLN Y 32 GLN Y 88 ASN ** 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 = 0.3920 r_free = 0.3920 target = 0.131144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.105118 restraints weight = 68746.737| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.63 r_work: 0.3367 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13696 Z= 0.194 Angle : 0.570 10.769 18621 Z= 0.297 Chirality : 0.056 1.661 2141 Planarity : 0.004 0.040 2349 Dihedral : 5.647 59.059 1962 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.59 % Allowed : 11.88 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.21), residues: 1699 helix: 1.82 (0.25), residues: 420 sheet: -0.23 (0.24), residues: 453 loop : -0.54 (0.22), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 PHE 0.012 0.001 PHE N 108 TYR 0.010 0.001 TYR L 49 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00045 ( 3) link_NAG-ASN : angle 2.29221 ( 9) hydrogen bonds : bond 0.04385 ( 614) hydrogen bonds : angle 5.26785 ( 1728) SS BOND : bond 0.00434 ( 7) SS BOND : angle 2.31914 ( 14) covalent geometry : bond 0.00450 (13686) covalent geometry : angle 0.56483 (18598) *********************** 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 180 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 157 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7796 (p0) cc_final: 0.7567 (p0) REVERT: L 83 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: H 17 SER cc_start: 0.8795 (p) cc_final: 0.8501 (t) REVERT: N 3 GLN cc_start: 0.7697 (tt0) cc_final: 0.7366 (tm-30) REVERT: R 48 PRO cc_start: 0.7726 (Cg_endo) cc_final: 0.7309 (Cg_exo) REVERT: R 165 THR cc_start: 0.8847 (m) cc_final: 0.8611 (m) REVERT: R 535 LEU cc_start: 0.7948 (tp) cc_final: 0.7692 (tp) REVERT: R 539 CYS cc_start: 0.7815 (t) cc_final: 0.7139 (m) REVERT: R 624 LYS cc_start: 0.7445 (mmpt) cc_final: 0.6632 (mmmt) REVERT: R 682 THR cc_start: 0.7297 (p) cc_final: 0.7019 (p) REVERT: X 392 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7957 (mm-30) REVERT: Y 59 TYR cc_start: 0.8934 (OUTLIER) cc_final: 0.8163 (m-80) REVERT: Y 197 ARG cc_start: 0.7736 (tpp80) cc_final: 0.7449 (tpp-160) outliers start: 23 outliers final: 13 residues processed: 171 average time/residue: 2.4741 time to fit residues: 467.9013 Evaluate side-chains 169 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU 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 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 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 55 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 117 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 35 ASN R 173 GLN X 271 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 = 0.3927 r_free = 0.3927 target = 0.131579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.105702 restraints weight = 68391.964| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 1.60 r_work: 0.3371 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.2997 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= 0.161 Angle : 0.549 10.718 18621 Z= 0.285 Chirality : 0.056 1.660 2141 Planarity : 0.004 0.040 2349 Dihedral : 5.504 54.757 1962 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.66 % Allowed : 12.22 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1699 helix: 1.85 (0.25), residues: 424 sheet: -0.26 (0.24), residues: 453 loop : -0.46 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 82 HIS 0.004 0.001 HIS X 357 PHE 0.011 0.001 PHE N 108 TYR 0.009 0.001 TYR N 95 ARG 0.003 0.000 ARG N 98 Details of bonding type rmsd link_NAG-ASN : bond 0.00032 ( 3) link_NAG-ASN : angle 2.16248 ( 9) hydrogen bonds : bond 0.04173 ( 614) hydrogen bonds : angle 5.13474 ( 1728) SS BOND : bond 0.00509 ( 7) SS BOND : angle 1.25555 ( 14) covalent geometry : bond 0.00372 (13686) covalent geometry : angle 0.54589 (18598) *********************** 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 180 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: H 17 SER cc_start: 0.8784 (p) cc_final: 0.8499 (t) REVERT: N 3 GLN cc_start: 0.7728 (tt0) cc_final: 0.7388 (tm-30) REVERT: R 48 PRO cc_start: 0.7726 (Cg_endo) cc_final: 0.7316 (Cg_exo) REVERT: R 165 THR cc_start: 0.8856 (m) cc_final: 0.8618 (m) REVERT: R 535 LEU cc_start: 0.7933 (tp) cc_final: 0.7681 (tp) REVERT: R 539 CYS cc_start: 0.7776 (t) cc_final: 0.7095 (m) REVERT: R 624 LYS cc_start: 0.7415 (mmpt) cc_final: 0.6597 (mmmt) REVERT: R 682 THR cc_start: 0.7307 (p) cc_final: 0.7056 (p) REVERT: X 392 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7953 (mm-30) REVERT: Y 59 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.7797 (m-10) REVERT: Y 82 TRP cc_start: 0.8761 (OUTLIER) cc_final: 0.6756 (m-90) REVERT: Y 197 ARG cc_start: 0.7760 (tpp80) cc_final: 0.7483 (tpp-160) outliers start: 24 outliers final: 10 residues processed: 169 average time/residue: 2.9289 time to fit residues: 552.8538 Evaluate side-chains 161 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 12 VAL 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 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 Z residue 57 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN R 173 GLN 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 = 0.3915 r_free = 0.3915 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.106642 restraints weight = 68338.161| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.96 r_work: 0.3324 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13696 Z= 0.220 Angle : 0.586 10.688 18621 Z= 0.304 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.041 2349 Dihedral : 5.649 47.523 1962 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.24 % Allowed : 12.50 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.21), residues: 1699 helix: 1.83 (0.25), residues: 413 sheet: -0.25 (0.24), residues: 449 loop : -0.49 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 234 HIS 0.005 0.001 HIS X 357 PHE 0.013 0.002 PHE N 108 TYR 0.012 0.001 TYR L 49 ARG 0.004 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00170 ( 3) link_NAG-ASN : angle 2.30725 ( 9) hydrogen bonds : bond 0.04377 ( 614) hydrogen bonds : angle 5.19765 ( 1728) SS BOND : bond 0.00482 ( 7) SS BOND : angle 2.35702 ( 14) covalent geometry : bond 0.00510 (13686) covalent geometry : angle 0.58076 (18598) *********************** 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 170 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 152 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7890 (p0) cc_final: 0.7556 (p0) REVERT: L 83 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: H 17 SER cc_start: 0.8853 (p) cc_final: 0.8546 (t) REVERT: N 3 GLN cc_start: 0.7797 (tt0) cc_final: 0.7449 (tm-30) REVERT: R 48 PRO cc_start: 0.7736 (Cg_endo) cc_final: 0.7320 (Cg_exo) REVERT: R 535 LEU cc_start: 0.7975 (tp) cc_final: 0.7725 (tp) REVERT: R 539 CYS cc_start: 0.7868 (t) cc_final: 0.7228 (m) REVERT: R 624 LYS cc_start: 0.7389 (mmpt) cc_final: 0.6608 (mmmt) REVERT: R 682 THR cc_start: 0.7261 (p) cc_final: 0.6941 (p) REVERT: X 392 GLU cc_start: 0.8244 (mm-30) cc_final: 0.8003 (mm-30) REVERT: Y 59 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.7820 (m-10) REVERT: Y 197 ARG cc_start: 0.7831 (tpp80) cc_final: 0.7541 (tpp-160) outliers start: 18 outliers final: 10 residues processed: 162 average time/residue: 2.6043 time to fit residues: 465.6289 Evaluate side-chains 159 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 12 VAL 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 R residue 691 ILE Chi-restraints excluded: chain X residue 20 ARG Chi-restraints excluded: chain X residue 390 GLN Chi-restraints excluded: chain Y residue 59 TYR 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 129 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 81 optimal weight: 0.0570 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3917 r_free = 0.3917 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106629 restraints weight = 68481.923| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.89 r_work: 0.3353 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13696 Z= 0.207 Angle : 0.576 10.663 18621 Z= 0.300 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.040 2349 Dihedral : 5.675 44.919 1962 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.10 % Allowed : 12.91 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.21), residues: 1699 helix: 1.77 (0.25), residues: 414 sheet: -0.26 (0.24), residues: 454 loop : -0.53 (0.22), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS Z 44 PHE 0.013 0.001 PHE R 37 TYR 0.013 0.001 TYR R 521 ARG 0.003 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00137 ( 3) link_NAG-ASN : angle 2.18379 ( 9) hydrogen bonds : bond 0.04325 ( 614) hydrogen bonds : angle 5.17250 ( 1728) SS BOND : bond 0.00471 ( 7) SS BOND : angle 1.93571 ( 14) covalent geometry : bond 0.00480 (13686) covalent geometry : angle 0.57192 (18598) *********************** 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 164 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7830 (p0) cc_final: 0.7566 (p0) REVERT: L 83 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6516 (tm-30) REVERT: H 17 SER cc_start: 0.8832 (p) cc_final: 0.8534 (t) REVERT: N 3 GLN cc_start: 0.7822 (tt0) cc_final: 0.7467 (tm-30) REVERT: R 48 PRO cc_start: 0.7757 (Cg_endo) cc_final: 0.7353 (Cg_exo) REVERT: R 535 LEU cc_start: 0.7949 (tp) cc_final: 0.7695 (tp) REVERT: R 539 CYS cc_start: 0.7759 (t) cc_final: 0.7158 (m) REVERT: R 624 LYS cc_start: 0.7374 (mmpt) cc_final: 0.6596 (mmmt) REVERT: R 682 THR cc_start: 0.7255 (p) cc_final: 0.7021 (p) REVERT: Y 59 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.7936 (m-10) REVERT: Y 82 TRP cc_start: 0.8802 (OUTLIER) cc_final: 0.6792 (m-90) REVERT: Y 197 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7608 (tpp-160) outliers start: 16 outliers final: 10 residues processed: 157 average time/residue: 3.0543 time to fit residues: 532.8688 Evaluate side-chains 158 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 145 time to evaluate : 2.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 12 VAL 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 Z residue 57 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3918 r_free = 0.3918 target = 0.131258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.106612 restraints weight = 68169.119| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.90 r_work: 0.3344 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3323 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= 0.193 Angle : 0.567 10.672 18621 Z= 0.296 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.041 2349 Dihedral : 5.700 51.321 1962 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.04 % Allowed : 13.40 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1699 helix: 1.82 (0.25), residues: 413 sheet: -0.25 (0.24), residues: 449 loop : -0.51 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP Y 82 HIS 0.004 0.001 HIS X 357 PHE 0.013 0.001 PHE R 37 TYR 0.016 0.001 TYR R 521 ARG 0.003 0.000 ARG H 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00118 ( 3) link_NAG-ASN : angle 2.03022 ( 9) hydrogen bonds : bond 0.04252 ( 614) hydrogen bonds : angle 5.12367 ( 1728) SS BOND : bond 0.00462 ( 7) SS BOND : angle 1.73019 ( 14) covalent geometry : bond 0.00448 (13686) covalent geometry : angle 0.56324 (18598) *********************** 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 166 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 52 ASP cc_start: 0.7766 (p0) cc_final: 0.7513 (p0) REVERT: L 83 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.6280 (tm-30) REVERT: H 17 SER cc_start: 0.8766 (p) cc_final: 0.8505 (t) REVERT: N 3 GLN cc_start: 0.7734 (tt0) cc_final: 0.7362 (tm-30) REVERT: R 48 PRO cc_start: 0.7663 (Cg_endo) cc_final: 0.7273 (Cg_exo) REVERT: R 535 LEU cc_start: 0.7981 (tp) cc_final: 0.7758 (tp) REVERT: R 539 CYS cc_start: 0.7734 (t) cc_final: 0.7197 (m) REVERT: R 624 LYS cc_start: 0.7351 (mmpt) cc_final: 0.6636 (mmmt) REVERT: R 682 THR cc_start: 0.7338 (p) cc_final: 0.6984 (p) REVERT: X 392 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7799 (mm-30) REVERT: Y 59 TYR cc_start: 0.9013 (OUTLIER) cc_final: 0.7954 (m-10) REVERT: Y 82 TRP cc_start: 0.8826 (OUTLIER) cc_final: 0.6787 (m-90) REVERT: Y 197 ARG cc_start: 0.7799 (tpp80) cc_final: 0.7509 (tpp-160) outliers start: 15 outliers final: 12 residues processed: 160 average time/residue: 3.5390 time to fit residues: 654.3595 Evaluate side-chains 160 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 12 VAL 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 276 ASP Chi-restraints excluded: chain R residue 486 ILE 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 Z residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 49 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.129024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.104678 restraints weight = 68493.412| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 1.95 r_work: 0.3353 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3360 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= 0.161 Angle : 0.555 10.664 18621 Z= 0.289 Chirality : 0.056 1.659 2141 Planarity : 0.004 0.041 2349 Dihedral : 5.669 53.688 1962 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.24 % Allowed : 13.60 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.21), residues: 1699 helix: 1.90 (0.26), residues: 413 sheet: -0.24 (0.24), residues: 449 loop : -0.47 (0.22), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 82 HIS 0.003 0.001 HIS X 357 PHE 0.014 0.001 PHE R 37 TYR 0.018 0.001 TYR R 521 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd link_NAG-ASN : bond 0.00072 ( 3) link_NAG-ASN : angle 1.88708 ( 9) hydrogen bonds : bond 0.04134 ( 614) hydrogen bonds : angle 5.06932 ( 1728) SS BOND : bond 0.00400 ( 7) SS BOND : angle 1.58697 ( 14) covalent geometry : bond 0.00371 (13686) covalent geometry : angle 0.55208 (18598) ********************** 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 166 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 148 time to evaluate : 1.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 83 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: H 17 SER cc_start: 0.8815 (p) cc_final: 0.8532 (t) REVERT: N 3 GLN cc_start: 0.7781 (tt0) cc_final: 0.7434 (tm-30) REVERT: R 48 PRO cc_start: 0.7737 (Cg_endo) cc_final: 0.7342 (Cg_exo) REVERT: R 535 LEU cc_start: 0.7954 (tp) cc_final: 0.7720 (tp) REVERT: R 539 CYS cc_start: 0.7787 (t) cc_final: 0.7196 (m) REVERT: R 554 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6140 (tt) REVERT: R 624 LYS cc_start: 0.7395 (mmpt) cc_final: 0.6656 (mmmt) REVERT: R 682 THR cc_start: 0.7339 (p) cc_final: 0.6986 (p) REVERT: X 392 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7852 (mm-30) REVERT: Y 59 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.7906 (m-10) REVERT: Y 82 TRP cc_start: 0.8800 (OUTLIER) cc_final: 0.6761 (m-90) REVERT: Y 197 ARG cc_start: 0.7771 (tpp80) cc_final: 0.7489 (tpp-160) outliers start: 18 outliers final: 12 residues processed: 159 average time/residue: 2.5798 time to fit residues: 452.4751 Evaluate side-chains 162 residues out of total 1495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 83 GLU Chi-restraints excluded: chain N residue 12 VAL 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 276 ASP 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 Z residue 57 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 52 optimal weight: 0.0470 chunk 144 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3928 r_free = 0.3928 target = 0.131764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.105920 restraints weight = 68257.991| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.62 r_work: 0.3371 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13696 Z= 0.147 Angle : 0.546 10.664 18621 Z= 0.285 Chirality : 0.056 1.660 2141 Planarity : 0.004 0.040 2349 Dihedral : 5.630 55.754 1962 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.10 % Allowed : 13.88 % Favored : 85.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.21), residues: 1699 helix: 1.96 (0.25), residues: 417 sheet: -0.25 (0.24), residues: 449 loop : -0.45 (0.22), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 82 HIS 0.003 0.001 HIS X 357 PHE 0.014 0.001 PHE R 37 TYR 0.019 0.001 TYR R 521 ARG 0.003 0.000 ARG Z 62 Details of bonding type rmsd link_NAG-ASN : bond 0.00054 ( 3) link_NAG-ASN : angle 1.77511 ( 9) hydrogen bonds : bond 0.04051 ( 614) hydrogen bonds : angle 5.01293 ( 1728) SS BOND : bond 0.00369 ( 7) SS BOND : angle 1.49287 ( 14) covalent geometry : bond 0.00338 (13686) covalent geometry : angle 0.54382 (18598) =============================================================================== Job complete usr+sys time: 20025.61 seconds wall clock time: 349 minutes 9.25 seconds (20949.25 seconds total)