Starting phenix.real_space_refine (version: dev) on Mon Feb 20 14:18:03 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/02_2023/8a5d_15165_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 Process input model Symmetric amino acids flipped Residue "G TYR 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 785": "OD1" <-> "OD2" Residue "G GLU 805": "OE1" <-> "OE2" Residue "U GLU 7": "OE1" <-> "OE2" Residue "U ASP 102": "OD1" <-> "OD2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U ASP 194": "OD1" <-> "OD2" Residue "U GLU 204": "OE1" <-> "OE2" Residue "U TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 278": "OE1" <-> "OE2" Residue "U ASP 282": "OD1" <-> "OD2" Residue "U TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 365": "OE1" <-> "OE2" Residue "U ASP 383": "OD1" <-> "OD2" Residue "U GLU 386": "OE1" <-> "OE2" Residue "U ASP 401": "OD1" <-> "OD2" Residue "U PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 675": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 705": "OE1" <-> "OE2" Residue "U ASP 723": "OD1" <-> "OD2" Residue "U GLU 730": "OE1" <-> "OE2" Residue "V GLU 4": "OE1" <-> "OE2" Residue "V ASP 51": "OD1" <-> "OD2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V ASP 80": "OD1" <-> "OD2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 167": "OE1" <-> "OE2" Residue "V ARG 196": "NH1" <-> "NH2" Residue "V GLU 207": "OE1" <-> "OE2" Residue "V ARG 210": "NH1" <-> "NH2" Residue "V ASP 211": "OD1" <-> "OD2" Residue "V GLU 214": "OE1" <-> "OE2" Residue "V TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 222": "OD1" <-> "OD2" Residue "V PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 226": "OE1" <-> "OE2" Residue "V GLU 241": "OE1" <-> "OE2" Residue "V PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 334": "OE1" <-> "OE2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "V PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 14": "OD1" <-> "OD2" Residue "W TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 143": "OE1" <-> "OE2" Residue "W PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 264": "OD1" <-> "OD2" Residue "W ASP 276": "OD1" <-> "OD2" Residue "W PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 284": "OE1" <-> "OE2" Residue "W PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 322": "OE1" <-> "OE2" Residue "W PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 325": "OD1" <-> "OD2" Residue "W ASP 344": "OD1" <-> "OD2" Residue "W ASP 402": "OD1" <-> "OD2" Residue "W GLU 464": "OE1" <-> "OE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 12222 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 729 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "U" Number of atoms: 4876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4876 Classifications: {'peptide': 600} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 571} Chain breaks: 2 Chain: "V" Number of atoms: 2831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2831 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "W" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3377 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 31, 'TRANS': 400} Chain breaks: 1 Chain: "X" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 313 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.08, per 1000 atoms: 0.58 Number of scatterers: 12222 At special positions: 0 Unit cell: (85.779, 105.9, 160.968, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 9 15.00 Mg 3 11.99 O 2288 8.00 N 2139 7.00 C 7719 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 1.9 seconds 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2846 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 14 sheets defined 42.3% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'G' and resid 725 through 740 Processing helix chain 'G' and resid 742 through 776 removed outlier: 3.564A pdb=" N LYS G 773 " --> pdb=" O SER G 769 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N TRP G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLN G 776 " --> pdb=" O ALA G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 780 through 807 removed outlier: 3.955A pdb=" N ARG G 806 " --> pdb=" O LYS G 802 " (cutoff:3.500A) Processing helix chain 'U' and resid 7 through 13 Processing helix chain 'U' and resid 46 through 48 No H-bonds generated for 'chain 'U' and resid 46 through 48' Processing helix chain 'U' and resid 50 through 63 Processing helix chain 'U' and resid 103 through 105 No H-bonds generated for 'chain 'U' and resid 103 through 105' Processing helix chain 'U' and resid 158 through 161 No H-bonds generated for 'chain 'U' and resid 158 through 161' Processing helix chain 'U' and resid 164 through 183 Processing helix chain 'U' and resid 192 through 201 Processing helix chain 'U' and resid 237 through 241 Processing helix chain 'U' and resid 264 through 266 No H-bonds generated for 'chain 'U' and resid 264 through 266' Processing helix chain 'U' and resid 270 through 287 Processing helix chain 'U' and resid 294 through 299 removed outlier: 4.292A pdb=" N LYS U 298 " --> pdb=" O ALA U 295 " (cutoff:3.500A) Processing helix chain 'U' and resid 312 through 324 Processing helix chain 'U' and resid 336 through 344 Processing helix chain 'U' and resid 371 through 373 No H-bonds generated for 'chain 'U' and resid 371 through 373' Processing helix chain 'U' and resid 381 through 394 Processing helix chain 'U' and resid 407 through 420 Processing helix chain 'U' and resid 425 through 427 No H-bonds generated for 'chain 'U' and resid 425 through 427' Processing helix chain 'U' and resid 454 through 463 Proline residue: U 459 - end of helix removed outlier: 4.713A pdb=" N PHE U 462 " --> pdb=" O ALA U 458 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TYR U 463 " --> pdb=" O PRO U 459 " (cutoff:3.500A) Processing helix chain 'U' and resid 465 through 467 No H-bonds generated for 'chain 'U' and resid 465 through 467' Processing helix chain 'U' and resid 499 through 508 removed outlier: 3.509A pdb=" N VAL U 508 " --> pdb=" O ILE U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 621 through 628 Processing helix chain 'U' and resid 637 through 649 Processing helix chain 'U' and resid 653 through 662 removed outlier: 3.684A pdb=" N SER U 662 " --> pdb=" O GLU U 658 " (cutoff:3.500A) Processing helix chain 'U' and resid 668 through 671 Processing helix chain 'U' and resid 675 through 686 Processing helix chain 'U' and resid 708 through 718 Processing helix chain 'U' and resid 728 through 742 removed outlier: 8.618A pdb=" N SER U 736 " --> pdb=" O LYS U 732 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N ARG U 737 " --> pdb=" O MET U 733 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N CYS U 738 " --> pdb=" O LEU U 734 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ILE U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR U 740 " --> pdb=" O SER U 736 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET U 741 " --> pdb=" O ARG U 737 " (cutoff:3.500A) Processing helix chain 'V' and resid 55 through 60 Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'V' and resid 79 through 91 Processing helix chain 'V' and resid 98 through 100 No H-bonds generated for 'chain 'V' and resid 98 through 100' Processing helix chain 'V' and resid 113 through 125 removed outlier: 3.590A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 144 Processing helix chain 'V' and resid 172 through 174 No H-bonds generated for 'chain 'V' and resid 172 through 174' Processing helix chain 'V' and resid 182 through 195 Processing helix chain 'V' and resid 203 through 216 Processing helix chain 'V' and resid 223 through 231 removed outlier: 4.091A pdb=" N ALA V 231 " --> pdb=" O ILE V 227 " (cutoff:3.500A) Processing helix chain 'V' and resid 252 through 261 removed outlier: 3.795A pdb=" N ARG V 256 " --> pdb=" O GLU V 253 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA V 257 " --> pdb=" O ARG V 254 " (cutoff:3.500A) Proline residue: V 258 - end of helix Processing helix chain 'V' and resid 264 through 267 Processing helix chain 'V' and resid 274 through 284 Processing helix chain 'V' and resid 290 through 296 removed outlier: 3.605A pdb=" N ASN V 296 " --> pdb=" O ASP V 292 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 304 No H-bonds generated for 'chain 'V' and resid 302 through 304' Processing helix chain 'V' and resid 309 through 320 removed outlier: 3.503A pdb=" N LEU V 320 " --> pdb=" O GLU V 316 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 348 removed outlier: 3.581A pdb=" N SER V 338 " --> pdb=" O ARG V 335 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL V 339 " --> pdb=" O LYS V 336 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA V 347 " --> pdb=" O SER V 344 " (cutoff:3.500A) Processing helix chain 'V' and resid 350 through 354 Processing helix chain 'V' and resid 359 through 365 Processing helix chain 'V' and resid 367 through 373 Processing helix chain 'W' and resid 86 through 97 Processing helix chain 'W' and resid 156 through 170 removed outlier: 3.620A pdb=" N TRP W 170 " --> pdb=" O VAL W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'W' and resid 215 through 217 No H-bonds generated for 'chain 'W' and resid 215 through 217' Processing helix chain 'W' and resid 225 through 238 Processing helix chain 'W' and resid 248 through 250 No H-bonds generated for 'chain 'W' and resid 248 through 250' Processing helix chain 'W' and resid 276 through 291 removed outlier: 3.748A pdb=" N ARG W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 309 through 315 removed outlier: 3.867A pdb=" N THR W 315 " --> pdb=" O ASP W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 342 removed outlier: 4.624A pdb=" N ALA W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N GLY W 341 " --> pdb=" O ARG W 337 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N MET W 342 " --> pdb=" O VAL W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 363 No H-bonds generated for 'chain 'W' and resid 361 through 363' Processing helix chain 'W' and resid 365 through 375 removed outlier: 3.704A pdb=" N GLY W 375 " --> pdb=" O ALA W 371 " (cutoff:3.500A) Processing helix chain 'W' and resid 378 through 387 Proline residue: W 382 - end of helix Processing helix chain 'W' and resid 393 through 396 Processing helix chain 'W' and resid 400 through 411 Processing helix chain 'W' and resid 432 through 441 removed outlier: 3.587A pdb=" N SER W 441 " --> pdb=" O SER W 437 " (cutoff:3.500A) Processing helix chain 'W' and resid 443 through 447 removed outlier: 3.981A pdb=" N GLN W 447 " --> pdb=" O THR W 444 " (cutoff:3.500A) Processing helix chain 'W' and resid 452 through 456 Processing helix chain 'W' and resid 461 through 465 Processing sheet with id= A, first strand: chain 'U' and resid 127 through 130 removed outlier: 6.527A pdb=" N SER U 301 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N ILE U 109 " --> pdb=" O SER U 301 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N VAL U 303 " --> pdb=" O ILE U 109 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'U' and resid 133 through 136 Processing sheet with id= C, first strand: chain 'U' and resid 696 through 698 removed outlier: 6.596A pdb=" N ILE U 663 " --> pdb=" O SER U 697 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N MET U 664 " --> pdb=" O GLN U 348 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N CYS U 350 " --> pdb=" O MET U 664 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N VAL U 666 " --> pdb=" O CYS U 350 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL U 352 " --> pdb=" O VAL U 666 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 431 through 437 Processing sheet with id= E, first strand: chain 'V' and resid 132 through 136 removed outlier: 6.552A pdb=" N VAL V 103 " --> pdb=" O TYR V 133 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N SER V 135 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU V 105 " --> pdb=" O SER V 135 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 8.249A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'V' and resid 35 through 38 Processing sheet with id= G, first strand: chain 'V' and resid 297 through 300 removed outlier: 6.205A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'V' and resid 238 through 241 removed outlier: 3.639A pdb=" N LYS V 238 " --> pdb=" O ILE V 250 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'W' and resid 175 through 179 removed outlier: 6.390A pdb=" N LEU W 146 " --> pdb=" O TRP W 176 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N SER W 178 " --> pdb=" O LEU W 146 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET W 148 " --> pdb=" O SER W 178 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU W 24 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N THR W 149 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU W 26 " --> pdb=" O THR W 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'W' and resid 50 through 53 Processing sheet with id= K, first strand: chain 'W' and resid 419 through 421 removed outlier: 6.585A pdb=" N VAL W 388 " --> pdb=" O HIS W 420 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU W 194 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N THR W 391 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE W 196 " --> pdb=" O THR W 391 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'W' and resid 319 through 322 Processing sheet with id= M, first strand: chain 'W' and resid 251 through 254 removed outlier: 7.090A pdb=" N ARG W 266 " --> pdb=" O GLU W 252 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'X' and resid 171 through 179 446 hydrogen bonds defined for protein. 1209 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: 3.78 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 2037 1.30 - 1.44: 3314 1.44 - 1.58: 7031 1.58 - 1.72: 8 1.72 - 1.86: 111 Bond restraints: 12501 Sorted by residual: bond pdb=" PG AGS U 900 " pdb=" S1G AGS U 900 " ideal model delta sigma weight residual 1.949 1.795 0.154 2.00e-02 2.50e+03 5.95e+01 bond pdb=" O2B AGS V 500 " pdb=" PB AGS V 500 " ideal model delta sigma weight residual 1.531 1.413 0.118 1.60e-02 3.91e+03 5.48e+01 bond pdb=" C SER V 155 " pdb=" O SER V 155 " ideal model delta sigma weight residual 1.235 1.309 -0.075 1.13e-02 7.83e+03 4.36e+01 bond pdb=" O2B AGS W 500 " pdb=" PB AGS W 500 " ideal model delta sigma weight residual 1.531 1.436 0.095 1.60e-02 3.91e+03 3.55e+01 bond pdb=" C PRO V 164 " pdb=" O PRO V 164 " ideal model delta sigma weight residual 1.233 1.168 0.065 1.10e-02 8.26e+03 3.52e+01 ... (remaining 12496 not shown) Histogram of bond angle deviations from ideal: 85.69 - 95.62: 4 95.62 - 105.55: 444 105.55 - 115.48: 7314 115.48 - 125.40: 8709 125.40 - 135.33: 476 Bond angle restraints: 16947 Sorted by residual: angle pdb=" O3A AGS W 500 " pdb=" PB AGS W 500 " pdb=" O3B AGS W 500 " ideal model delta sigma weight residual 109.69 85.69 24.00 3.00e+00 1.11e-01 6.40e+01 angle pdb=" C PRO W 28 " pdb=" N GLY W 29 " pdb=" CA GLY W 29 " ideal model delta sigma weight residual 121.48 127.73 -6.25 1.06e+00 8.90e-01 3.47e+01 angle pdb=" O3A AGS U 900 " pdb=" PB AGS U 900 " pdb=" O3B AGS U 900 " ideal model delta sigma weight residual 109.69 92.05 17.64 3.00e+00 1.11e-01 3.46e+01 angle pdb=" C GLN W 334 " pdb=" N ARG W 335 " pdb=" CA ARG W 335 " ideal model delta sigma weight residual 120.38 127.85 -7.47 1.37e+00 5.33e-01 2.98e+01 angle pdb=" C ALA W 460 " pdb=" N GLY W 461 " pdb=" CA GLY W 461 " ideal model delta sigma weight residual 120.13 126.99 -6.86 1.26e+00 6.30e-01 2.97e+01 ... (remaining 16942 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6927 17.96 - 35.92: 482 35.92 - 53.88: 90 53.88 - 71.85: 21 71.85 - 89.81: 16 Dihedral angle restraints: 7536 sinusoidal: 3127 harmonic: 4409 Sorted by residual: dihedral pdb=" CA ARG U 406 " pdb=" C ARG U 406 " pdb=" N ARG U 407 " pdb=" CA ARG U 407 " ideal model delta harmonic sigma weight residual 180.00 -153.76 -26.24 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA ASP W 240 " pdb=" C ASP W 240 " pdb=" N PRO W 241 " pdb=" CA PRO W 241 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA ASN W 169 " pdb=" C ASN W 169 " pdb=" N TRP W 170 " pdb=" CA TRP W 170 " ideal model delta harmonic sigma weight residual -180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 7533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 938 0.065 - 0.129: 613 0.129 - 0.194: 214 0.194 - 0.258: 55 0.258 - 0.323: 12 Chirality restraints: 1832 Sorted by residual: chirality pdb=" CA VAL U 30 " pdb=" N VAL U 30 " pdb=" C VAL U 30 " pdb=" CB VAL U 30 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.61e+00 chirality pdb=" CA SER V 281 " pdb=" N SER V 281 " pdb=" C SER V 281 " pdb=" CB SER V 281 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA SER W 178 " pdb=" N SER W 178 " pdb=" C SER W 178 " pdb=" CB SER W 178 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1829 not shown) Planarity restraints: 2185 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP W 433 " 0.100 2.00e-02 2.50e+03 5.92e-02 8.76e+01 pdb=" CG TRP W 433 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP W 433 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP W 433 " -0.075 2.00e-02 2.50e+03 pdb=" NE1 TRP W 433 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP W 433 " -0.047 2.00e-02 2.50e+03 pdb=" CE3 TRP W 433 " -0.088 2.00e-02 2.50e+03 pdb=" CZ2 TRP W 433 " 0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP W 433 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP W 433 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' AGS W 500 " 0.077 2.00e-02 2.50e+03 3.71e-02 3.79e+01 pdb=" C2 AGS W 500 " 0.016 2.00e-02 2.50e+03 pdb=" C4 AGS W 500 " -0.022 2.00e-02 2.50e+03 pdb=" C5 AGS W 500 " -0.015 2.00e-02 2.50e+03 pdb=" C6 AGS W 500 " -0.037 2.00e-02 2.50e+03 pdb=" C8 AGS W 500 " -0.008 2.00e-02 2.50e+03 pdb=" N1 AGS W 500 " -0.000 2.00e-02 2.50e+03 pdb=" N3 AGS W 500 " -0.020 2.00e-02 2.50e+03 pdb=" N6 AGS W 500 " 0.064 2.00e-02 2.50e+03 pdb=" N7 AGS W 500 " -0.007 2.00e-02 2.50e+03 pdb=" N9 AGS W 500 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 340 " 0.062 2.00e-02 2.50e+03 3.77e-02 3.55e+01 pdb=" CG TRP V 340 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TRP V 340 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 TRP V 340 " -0.043 2.00e-02 2.50e+03 pdb=" NE1 TRP V 340 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP V 340 " -0.031 2.00e-02 2.50e+03 pdb=" CE3 TRP V 340 " -0.060 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 340 " 0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 340 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP V 340 " 0.059 2.00e-02 2.50e+03 ... (remaining 2182 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 14 2.58 - 3.16: 9701 3.16 - 3.74: 17913 3.74 - 4.32: 27181 4.32 - 4.90: 44214 Nonbonded interactions: 99023 Sorted by model distance: nonbonded pdb=" O3G AGS U 900 " pdb="MG MG U 901 " model vdw 2.001 2.170 nonbonded pdb=" O2G AGS W 500 " pdb="MG MG W 501 " model vdw 2.007 2.170 nonbonded pdb=" O2G AGS V 500 " pdb="MG MG V 501 " model vdw 2.013 2.170 nonbonded pdb=" O1B AGS V 500 " pdb="MG MG V 501 " model vdw 2.221 2.170 nonbonded pdb=" OD1 ASP U 276 " pdb=" ND1 HIS V 235 " model vdw 2.247 2.520 ... (remaining 99018 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 64 5.16 5 C 7719 2.51 5 N 2139 2.21 5 O 2288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 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: 0.010 Extract box with map and model: 4.410 Check model and map are aligned: 0.220 Process input model: 34.980 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.130 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 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 : 0.016 0.154 12501 Z= 1.041 Angle : 1.878 23.997 16947 Z= 1.296 Chirality : 0.093 0.323 1832 Planarity : 0.011 0.065 2185 Dihedral : 13.807 89.808 4690 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.60 % Favored : 97.27 % Rotamer Outliers : 0.23 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1501 helix: -1.11 (0.18), residues: 617 sheet: 0.08 (0.34), residues: 201 loop : 0.07 (0.23), residues: 683 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 1.419 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 1.5692 time to fit residues: 409.0999 Evaluate side-chains 141 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 1.427 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 4.9990 chunk 113 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 259 HIS U 436 HIS U 442 GLN V 92 ASN V 128 ASN V 246 GLN V 275 HIS W 316 GLN W 458 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 12501 Z= 0.235 Angle : 0.616 9.637 16947 Z= 0.324 Chirality : 0.045 0.156 1832 Planarity : 0.004 0.038 2185 Dihedral : 6.710 62.790 1695 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.22), residues: 1501 helix: 0.92 (0.21), residues: 627 sheet: 0.44 (0.33), residues: 205 loop : 0.69 (0.25), residues: 669 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 182 average time/residue: 1.4872 time to fit residues: 291.8312 Evaluate side-chains 146 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.505 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 5 average time/residue: 0.8865 time to fit residues: 6.9120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 chunk 109 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 78 ASN V 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 12501 Z= 0.215 Angle : 0.542 8.465 16947 Z= 0.283 Chirality : 0.044 0.151 1832 Planarity : 0.004 0.043 2185 Dihedral : 6.289 61.708 1695 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.22), residues: 1501 helix: 1.35 (0.21), residues: 627 sheet: 0.52 (0.34), residues: 205 loop : 0.68 (0.25), residues: 669 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.614 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 20 residues processed: 166 average time/residue: 1.5000 time to fit residues: 268.6553 Evaluate side-chains 145 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 1.454 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 15 residues processed: 6 average time/residue: 0.7100 time to fit residues: 7.1811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 39 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.031 12501 Z= 0.156 Angle : 0.488 7.311 16947 Z= 0.253 Chirality : 0.042 0.143 1832 Planarity : 0.004 0.043 2185 Dihedral : 5.994 56.312 1695 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.22), residues: 1501 helix: 1.51 (0.22), residues: 621 sheet: 0.42 (0.34), residues: 213 loop : 0.76 (0.25), residues: 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 132 time to evaluate : 1.647 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 162 average time/residue: 1.4197 time to fit residues: 247.7570 Evaluate side-chains 146 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 19 residues processed: 5 average time/residue: 0.6248 time to fit residues: 5.4205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.0010 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.0270 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 overall best weight: 0.5446 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 320 HIS V 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 12501 Z= 0.141 Angle : 0.465 6.523 16947 Z= 0.240 Chirality : 0.041 0.138 1832 Planarity : 0.004 0.041 2185 Dihedral : 5.788 56.242 1695 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.22), residues: 1501 helix: 1.67 (0.22), residues: 614 sheet: 0.49 (0.34), residues: 213 loop : 0.80 (0.25), residues: 674 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 131 time to evaluate : 1.577 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 19 residues processed: 162 average time/residue: 1.6314 time to fit residues: 284.5218 Evaluate side-chains 142 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.480 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 17 residues processed: 3 average time/residue: 0.7356 time to fit residues: 4.4974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12501 Z= 0.230 Angle : 0.506 7.610 16947 Z= 0.259 Chirality : 0.043 0.145 1832 Planarity : 0.004 0.043 2185 Dihedral : 5.859 54.596 1695 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 3.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1501 helix: 1.48 (0.22), residues: 620 sheet: 0.41 (0.33), residues: 213 loop : 0.76 (0.25), residues: 668 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 128 time to evaluate : 1.689 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 157 average time/residue: 1.5887 time to fit residues: 268.4237 Evaluate side-chains 152 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 125 time to evaluate : 1.728 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 22 residues processed: 6 average time/residue: 0.9310 time to fit residues: 8.4130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 0.0370 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 232 GLN V 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 12501 Z= 0.162 Angle : 0.469 7.150 16947 Z= 0.241 Chirality : 0.041 0.135 1832 Planarity : 0.004 0.042 2185 Dihedral : 5.766 56.294 1695 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1501 helix: 1.52 (0.22), residues: 621 sheet: 0.45 (0.34), residues: 215 loop : 0.82 (0.25), residues: 665 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.681 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 23 residues processed: 153 average time/residue: 1.5788 time to fit residues: 259.8389 Evaluate side-chains 146 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 123 time to evaluate : 1.464 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 3 average time/residue: 0.6843 time to fit residues: 4.4111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.0030 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 91 optimal weight: 0.0770 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 131 optimal weight: 0.8980 chunk 138 optimal weight: 0.0170 chunk 126 optimal weight: 0.0570 overall best weight: 0.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 232 GLN V 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12501 Z= 0.113 Angle : 0.441 6.794 16947 Z= 0.226 Chirality : 0.040 0.133 1832 Planarity : 0.004 0.040 2185 Dihedral : 5.549 56.831 1695 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1501 helix: 1.64 (0.22), residues: 625 sheet: 0.57 (0.34), residues: 215 loop : 0.92 (0.25), residues: 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 127 time to evaluate : 1.439 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 154 average time/residue: 1.5704 time to fit residues: 260.6583 Evaluate side-chains 141 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.582 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 17 residues processed: 2 average time/residue: 0.9685 time to fit residues: 4.2540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 12501 Z= 0.219 Angle : 0.508 8.682 16947 Z= 0.259 Chirality : 0.042 0.137 1832 Planarity : 0.004 0.042 2185 Dihedral : 5.692 54.725 1695 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1501 helix: 1.57 (0.22), residues: 622 sheet: 0.53 (0.34), residues: 213 loop : 0.85 (0.25), residues: 666 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.577 Fit side-chains outliers start: 26 outliers final: 19 residues processed: 144 average time/residue: 1.6617 time to fit residues: 257.7731 Evaluate side-chains 140 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 121 time to evaluate : 1.686 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 1.6998 time to fit residues: 5.9661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 0.0000 chunk 36 optimal weight: 0.9980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 161 HIS V 246 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 12501 Z= 0.145 Angle : 0.475 8.934 16947 Z= 0.242 Chirality : 0.041 0.133 1832 Planarity : 0.004 0.042 2185 Dihedral : 5.635 56.373 1695 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1501 helix: 1.62 (0.22), residues: 626 sheet: 0.55 (0.34), residues: 213 loop : 0.84 (0.25), residues: 662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3002 Ramachandran restraints generated. 1501 Oldfield, 0 Emsley, 1501 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.727 Fit side-chains outliers start: 23 outliers final: 19 residues processed: 142 average time/residue: 1.5476 time to fit residues: 237.0510 Evaluate side-chains 139 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 120 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 2 average time/residue: 0.9996 time to fit residues: 4.3325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.0370 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 246 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114785 restraints weight = 15041.018| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.75 r_work: 0.3289 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12501 Z= 0.217 Angle : 0.509 8.953 16947 Z= 0.259 Chirality : 0.043 0.136 1832 Planarity : 0.004 0.044 2185 Dihedral : 5.743 54.887 1695 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1501 helix: 1.52 (0.21), residues: 627 sheet: 0.44 (0.34), residues: 213 loop : 0.78 (0.25), residues: 661 =============================================================================== Job complete usr+sys time: 4853.33 seconds wall clock time: 87 minutes 29.87 seconds (5249.87 seconds total)