Starting phenix.real_space_refine on Fri Mar 15 17:03:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/03_2024/8a5d_15165_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/03_2024/8a5d_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_15165/03_2024/8a5d_15165.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/03_2024/8a5d_15165.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/03_2024/8a5d_15165_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5d_15165/03_2024/8a5d_15165_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.58, per 1000 atoms: 0.54 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: 4.93 Conformation dependent library (CDL) restraints added in 2.4 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: 3.15 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: 5.80 Time building geometry restraints manager: 5.41 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: 6936 17.96 - 35.92: 496 35.92 - 53.88: 95 53.88 - 71.85: 26 71.85 - 89.81: 16 Dihedral angle restraints: 7569 sinusoidal: 3160 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 7566 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 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: 0.910 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: 4.040 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 39.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 : 14.052 89.808 4723 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 % Allowed : 3.07 % Favored : 96.70 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.100 0.016 TRP W 433 HIS 0.033 0.005 HIS V 371 PHE 0.070 0.012 PHE V 132 TYR 0.072 0.014 TYR V 133 ARG 0.029 0.003 ARG V 312 *********************** 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 : 1.146 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7665 (tt0) cc_final: 0.7360 (tt0) REVERT: G 737 ASP cc_start: 0.8185 (m-30) cc_final: 0.7884 (m-30) REVERT: G 777 LEU cc_start: 0.8581 (mp) cc_final: 0.8367 (mp) REVERT: G 778 ARG cc_start: 0.7860 (mtt180) cc_final: 0.7589 (mtt180) REVERT: G 781 LYS cc_start: 0.7069 (tttt) cc_final: 0.6437 (tppt) REVERT: G 784 LYS cc_start: 0.7146 (mttt) cc_final: 0.6784 (mptt) REVERT: U 19 ASP cc_start: 0.7043 (m-30) cc_final: 0.6788 (p0) REVERT: U 36 LYS cc_start: 0.8076 (tttt) cc_final: 0.7456 (mmpt) REVERT: U 47 ASP cc_start: 0.8449 (t0) cc_final: 0.7939 (p0) REVERT: U 56 ASN cc_start: 0.7016 (m-40) cc_final: 0.6583 (m-40) REVERT: U 60 ARG cc_start: 0.7885 (ttt180) cc_final: 0.7549 (mmt180) REVERT: U 146 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7873 (pt0) REVERT: U 159 GLU cc_start: 0.7509 (tt0) cc_final: 0.7052 (pp20) REVERT: U 160 GLN cc_start: 0.7514 (mt0) cc_final: 0.7122 (tm-30) REVERT: U 218 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7888 (pm20) REVERT: U 224 LYS cc_start: 0.7091 (tttt) cc_final: 0.6837 (tmtt) REVERT: U 250 LYS cc_start: 0.8063 (tttt) cc_final: 0.7785 (tttt) REVERT: U 266 ASP cc_start: 0.7969 (m-30) cc_final: 0.7712 (t70) REVERT: U 292 THR cc_start: 0.9020 (m) cc_final: 0.8809 (p) REVERT: U 298 LYS cc_start: 0.7796 (pttt) cc_final: 0.7457 (mttp) REVERT: U 371 GLU cc_start: 0.7954 (tt0) cc_final: 0.7688 (mt-10) REVERT: U 392 MET cc_start: 0.8125 (mtm) cc_final: 0.7585 (mmm) REVERT: U 401 ASP cc_start: 0.8544 (m-30) cc_final: 0.8127 (t0) REVERT: U 415 GLU cc_start: 0.7509 (tt0) cc_final: 0.7126 (tp30) REVERT: U 418 MET cc_start: 0.8379 (mtt) cc_final: 0.8173 (mtm) REVERT: U 437 LEU cc_start: 0.8034 (tp) cc_final: 0.7771 (tt) REVERT: U 653 GLU cc_start: 0.7485 (pt0) cc_final: 0.7019 (pp20) REVERT: U 702 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8782 (mp0) REVERT: V 16 MET cc_start: 0.8745 (mmt) cc_final: 0.8423 (mmt) REVERT: V 57 GLU cc_start: 0.7272 (mt-10) cc_final: 0.7016 (mt-10) REVERT: V 72 GLU cc_start: 0.8370 (tt0) cc_final: 0.7677 (mt-10) REVERT: V 82 MET cc_start: 0.9139 (tpt) cc_final: 0.8910 (tpp) REVERT: V 93 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7856 (mm-30) REVERT: V 118 LYS cc_start: 0.7608 (tptt) cc_final: 0.7079 (ttmt) REVERT: V 191 LYS cc_start: 0.7827 (tttt) cc_final: 0.7574 (ttpt) REVERT: V 195 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7446 (mp0) REVERT: V 241 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8007 (tm-30) REVERT: V 246 GLN cc_start: 0.7925 (pt0) cc_final: 0.6756 (tp40) REVERT: V 288 ASP cc_start: 0.8492 (m-30) cc_final: 0.8156 (p0) REVERT: V 325 MET cc_start: 0.7938 (mmt) cc_final: 0.7736 (mmm) REVERT: V 358 SER cc_start: 0.8483 (t) cc_final: 0.8142 (p) REVERT: V 360 GLN cc_start: 0.7867 (mt0) cc_final: 0.7427 (mp10) REVERT: V 372 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7598 (mtm110) REVERT: W 105 ARG cc_start: 0.7807 (mtt180) cc_final: 0.7344 (mmp80) REVERT: W 143 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8082 (mp0) REVERT: W 167 MET cc_start: 0.8653 (mmt) cc_final: 0.8358 (mmt) REVERT: W 203 THR cc_start: 0.8836 (m) cc_final: 0.8497 (m) REVERT: W 215 LYS cc_start: 0.8366 (mttt) cc_final: 0.7908 (mtpt) REVERT: W 253 ASN cc_start: 0.8066 (m-40) cc_final: 0.7351 (p0) REVERT: W 255 LYS cc_start: 0.8148 (mttt) cc_final: 0.7862 (mmtt) REVERT: W 385 LEU cc_start: 0.8526 (mt) cc_final: 0.8235 (mm) REVERT: X 187 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8417 (mt-10) outliers start: 3 outliers final: 1 residues processed: 244 average time/residue: 1.5288 time to fit residues: 398.5635 Evaluate side-chains 170 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 169 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 451 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.1980 chunk 113 optimal weight: 0.0170 chunk 63 optimal weight: 0.9980 chunk 38 optimal weight: 0.0170 chunk 76 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 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 : 0.002 0.039 12501 Z= 0.161 Angle : 0.578 8.417 16947 Z= 0.306 Chirality : 0.044 0.139 1832 Planarity : 0.004 0.038 2185 Dihedral : 7.302 58.439 1729 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.38 % Allowed : 9.74 % Favored : 88.88 % 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: 1.20 (0.22), residues: 1501 helix: 1.09 (0.21), residues: 625 sheet: 0.61 (0.35), residues: 198 loop : 0.78 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 735 HIS 0.005 0.001 HIS V 235 PHE 0.016 0.001 PHE U 397 TYR 0.020 0.001 TYR V 69 ARG 0.003 0.000 ARG U 475 *********************** 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 203 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7105 (tt0) cc_final: 0.6808 (tt0) REVERT: G 737 ASP cc_start: 0.8187 (m-30) cc_final: 0.7791 (m-30) REVERT: G 745 LYS cc_start: 0.6788 (mttt) cc_final: 0.6003 (tptp) REVERT: G 777 LEU cc_start: 0.8499 (mp) cc_final: 0.8269 (mp) REVERT: G 778 ARG cc_start: 0.7900 (mtt180) cc_final: 0.7645 (mtt180) REVERT: G 784 LYS cc_start: 0.6837 (mttt) cc_final: 0.6554 (mmpt) REVERT: U 19 ASP cc_start: 0.7328 (m-30) cc_final: 0.7095 (p0) REVERT: U 36 LYS cc_start: 0.8209 (tttt) cc_final: 0.7581 (mmtt) REVERT: U 47 ASP cc_start: 0.8384 (t0) cc_final: 0.7848 (p0) REVERT: U 56 ASN cc_start: 0.6989 (m-40) cc_final: 0.6645 (m-40) REVERT: U 60 ARG cc_start: 0.7849 (ttt180) cc_final: 0.7497 (mmt180) REVERT: U 127 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7706 (mtmt) REVERT: U 146 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7661 (pt0) REVERT: U 159 GLU cc_start: 0.7019 (tt0) cc_final: 0.6685 (tm-30) REVERT: U 160 GLN cc_start: 0.7658 (mt0) cc_final: 0.7307 (tm-30) REVERT: U 218 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7830 (pm20) REVERT: U 224 LYS cc_start: 0.7019 (tttt) cc_final: 0.6775 (tmtt) REVERT: U 266 ASP cc_start: 0.7835 (m-30) cc_final: 0.7597 (t0) REVERT: U 292 THR cc_start: 0.8866 (m) cc_final: 0.8626 (p) REVERT: U 296 ASP cc_start: 0.7475 (m-30) cc_final: 0.7184 (p0) REVERT: U 298 LYS cc_start: 0.7731 (pttt) cc_final: 0.7392 (mttp) REVERT: U 392 MET cc_start: 0.7941 (mtm) cc_final: 0.7453 (mmm) REVERT: U 401 ASP cc_start: 0.8386 (m-30) cc_final: 0.7934 (t0) REVERT: U 415 GLU cc_start: 0.7234 (tt0) cc_final: 0.6910 (tp30) REVERT: U 437 LEU cc_start: 0.7943 (tp) cc_final: 0.7684 (tt) REVERT: U 653 GLU cc_start: 0.7032 (pt0) cc_final: 0.6639 (pp20) REVERT: U 702 GLU cc_start: 0.8948 (mt-10) cc_final: 0.8605 (mp0) REVERT: V 57 GLU cc_start: 0.7155 (mt-10) cc_final: 0.6930 (mt-10) REVERT: V 72 GLU cc_start: 0.8319 (tt0) cc_final: 0.7964 (mt-10) REVERT: V 82 MET cc_start: 0.8870 (tpt) cc_final: 0.8652 (tpp) REVERT: V 191 LYS cc_start: 0.7597 (tttt) cc_final: 0.7374 (ttpp) REVERT: V 195 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7175 (mm-30) REVERT: V 210 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7727 (ttp-110) REVERT: V 211 ASP cc_start: 0.7836 (m-30) cc_final: 0.7635 (t0) REVERT: V 241 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7938 (tm-30) REVERT: V 246 GLN cc_start: 0.7915 (pt0) cc_final: 0.6859 (tp40) REVERT: V 270 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7137 (mt-10) REVERT: V 288 ASP cc_start: 0.8366 (m-30) cc_final: 0.8071 (p0) REVERT: V 325 MET cc_start: 0.7932 (mmt) cc_final: 0.7682 (mmm) REVERT: V 360 GLN cc_start: 0.7316 (mt0) cc_final: 0.7033 (mp10) REVERT: W 63 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6373 (mp0) REVERT: W 77 MET cc_start: 0.8305 (mmt) cc_final: 0.8064 (mmt) REVERT: W 94 GLU cc_start: 0.8475 (tp30) cc_final: 0.7639 (mt-10) REVERT: W 105 ARG cc_start: 0.7712 (mtt180) cc_final: 0.7266 (mpt-90) REVERT: W 167 MET cc_start: 0.8551 (mmt) cc_final: 0.8313 (mmt) REVERT: W 203 THR cc_start: 0.8737 (m) cc_final: 0.8436 (m) REVERT: W 215 LYS cc_start: 0.8212 (mttt) cc_final: 0.7782 (mtpt) REVERT: W 253 ASN cc_start: 0.7795 (m-40) cc_final: 0.7160 (p0) REVERT: W 264 ASP cc_start: 0.8328 (m-30) cc_final: 0.7890 (t70) outliers start: 18 outliers final: 5 residues processed: 196 average time/residue: 1.5017 time to fit residues: 315.2700 Evaluate side-chains 158 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 150 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 320 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 121 optimal weight: 0.0470 chunk 135 optimal weight: 0.6980 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 overall best weight: 1.3484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 73 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12501 Z= 0.260 Angle : 0.551 9.040 16947 Z= 0.287 Chirality : 0.045 0.153 1832 Planarity : 0.005 0.041 2185 Dihedral : 6.749 62.660 1728 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.99 % Allowed : 10.51 % Favored : 86.50 % 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: 1.36 (0.22), residues: 1501 helix: 1.50 (0.22), residues: 615 sheet: 0.51 (0.33), residues: 207 loop : 0.65 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 735 HIS 0.005 0.001 HIS V 161 PHE 0.023 0.002 PHE U 397 TYR 0.015 0.002 TYR V 69 ARG 0.007 0.001 ARG V 372 *********************** 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 199 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 160 time to evaluate : 1.347 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7078 (tt0) cc_final: 0.6756 (tt0) REVERT: G 737 ASP cc_start: 0.8246 (m-30) cc_final: 0.7811 (m-30) REVERT: G 778 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7690 (mtt180) REVERT: G 795 ARG cc_start: 0.7313 (mtt180) cc_final: 0.6987 (mtm110) REVERT: U 17 ARG cc_start: 0.6775 (ptt180) cc_final: 0.6515 (ptm160) REVERT: U 36 LYS cc_start: 0.8127 (tttt) cc_final: 0.7478 (mmpt) REVERT: U 56 ASN cc_start: 0.6857 (m-40) cc_final: 0.6535 (m-40) REVERT: U 60 ARG cc_start: 0.7887 (ttt180) cc_final: 0.7507 (mmt180) REVERT: U 127 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7617 (mtmt) REVERT: U 146 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7642 (pt0) REVERT: U 159 GLU cc_start: 0.6973 (tt0) cc_final: 0.6632 (tm-30) REVERT: U 160 GLN cc_start: 0.7774 (mt0) cc_final: 0.7420 (tm-30) REVERT: U 193 LYS cc_start: 0.5855 (tppt) cc_final: 0.5641 (mmpt) REVERT: U 218 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7813 (pm20) REVERT: U 224 LYS cc_start: 0.7051 (tttt) cc_final: 0.6785 (tttt) REVERT: U 266 ASP cc_start: 0.7823 (m-30) cc_final: 0.7579 (t0) REVERT: U 292 THR cc_start: 0.8951 (m) cc_final: 0.8727 (p) REVERT: U 296 ASP cc_start: 0.7397 (m-30) cc_final: 0.7048 (p0) REVERT: U 298 LYS cc_start: 0.7877 (pttt) cc_final: 0.7550 (mttp) REVERT: U 392 MET cc_start: 0.8058 (mtm) cc_final: 0.7591 (mmm) REVERT: U 401 ASP cc_start: 0.8448 (m-30) cc_final: 0.7971 (t0) REVERT: U 415 GLU cc_start: 0.7079 (tt0) cc_final: 0.6784 (tp30) REVERT: U 437 LEU cc_start: 0.7903 (tp) cc_final: 0.7650 (tt) REVERT: U 702 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8576 (mp0) REVERT: V 57 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6963 (mt-10) REVERT: V 72 GLU cc_start: 0.8298 (tt0) cc_final: 0.7948 (mt-10) REVERT: V 111 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7954 (p0) REVERT: V 191 LYS cc_start: 0.7499 (tttt) cc_final: 0.7285 (ttpp) REVERT: V 210 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7737 (ttp-110) REVERT: V 241 GLU cc_start: 0.8547 (mt-10) cc_final: 0.8118 (tm-30) REVERT: V 246 GLN cc_start: 0.7899 (pt0) cc_final: 0.6855 (tp40) REVERT: V 288 ASP cc_start: 0.8494 (m-30) cc_final: 0.8188 (p0) REVERT: V 358 SER cc_start: 0.8552 (t) cc_final: 0.8249 (p) REVERT: V 360 GLN cc_start: 0.7510 (mt0) cc_final: 0.7171 (mp10) REVERT: W 63 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6390 (mp0) REVERT: W 94 GLU cc_start: 0.8481 (tp30) cc_final: 0.8120 (tm-30) REVERT: W 105 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7347 (mpt-90) REVERT: W 167 MET cc_start: 0.8490 (mmt) cc_final: 0.8272 (mmt) REVERT: W 203 THR cc_start: 0.8744 (m) cc_final: 0.8456 (m) REVERT: W 215 LYS cc_start: 0.8334 (mttt) cc_final: 0.7878 (mtpt) REVERT: W 253 ASN cc_start: 0.7931 (m-40) cc_final: 0.7134 (p0) REVERT: W 264 ASP cc_start: 0.8169 (m-30) cc_final: 0.7726 (t70) REVERT: W 266 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6650 (ptt90) REVERT: W 310 GLU cc_start: 0.8031 (tt0) cc_final: 0.7823 (tt0) REVERT: W 312 PHE cc_start: 0.7453 (t80) cc_final: 0.7199 (t80) REVERT: X 187 GLU cc_start: 0.8539 (mt-10) cc_final: 0.8200 (mm-30) outliers start: 39 outliers final: 16 residues processed: 185 average time/residue: 1.5264 time to fit residues: 302.6627 Evaluate side-chains 168 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 235 HIS Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 266 ARG Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 91 optimal weight: 0.4980 chunk 136 optimal weight: 0.0040 chunk 144 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 776 GLN V 78 ASN W 253 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12501 Z= 0.157 Angle : 0.482 7.483 16947 Z= 0.249 Chirality : 0.042 0.142 1832 Planarity : 0.004 0.041 2185 Dihedral : 6.392 56.463 1728 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.61 % Allowed : 11.96 % Favored : 85.43 % 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: 1.49 (0.22), residues: 1501 helix: 1.62 (0.22), residues: 621 sheet: 0.58 (0.34), residues: 207 loop : 0.69 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 735 HIS 0.003 0.001 HIS V 235 PHE 0.015 0.001 PHE U 397 TYR 0.013 0.001 TYR V 69 ARG 0.004 0.000 ARG V 372 *********************** 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 185 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7065 (tt0) cc_final: 0.6746 (tt0) REVERT: G 737 ASP cc_start: 0.8319 (m-30) cc_final: 0.7876 (m-30) REVERT: G 778 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7721 (mtt180) REVERT: G 795 ARG cc_start: 0.7299 (mtt180) cc_final: 0.6980 (mtm110) REVERT: U 36 LYS cc_start: 0.8087 (tttt) cc_final: 0.7425 (mmtt) REVERT: U 56 ASN cc_start: 0.6828 (m-40) cc_final: 0.6506 (m-40) REVERT: U 60 ARG cc_start: 0.7863 (ttt180) cc_final: 0.7465 (mmt180) REVERT: U 146 GLU cc_start: 0.7907 (mt-10) cc_final: 0.7650 (pt0) REVERT: U 159 GLU cc_start: 0.6881 (tt0) cc_final: 0.6541 (tm-30) REVERT: U 160 GLN cc_start: 0.7906 (mt0) cc_final: 0.7485 (tm-30) REVERT: U 193 LYS cc_start: 0.5771 (tppt) cc_final: 0.5401 (mmmt) REVERT: U 218 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7800 (pm20) REVERT: U 224 LYS cc_start: 0.7036 (tttt) cc_final: 0.6789 (tttm) REVERT: U 266 ASP cc_start: 0.7856 (m-30) cc_final: 0.7607 (t0) REVERT: U 275 ASP cc_start: 0.7602 (m-30) cc_final: 0.7328 (m-30) REVERT: U 292 THR cc_start: 0.8911 (m) cc_final: 0.8706 (p) REVERT: U 296 ASP cc_start: 0.7361 (m-30) cc_final: 0.7030 (p0) REVERT: U 298 LYS cc_start: 0.7898 (pttt) cc_final: 0.7534 (mttp) REVERT: U 392 MET cc_start: 0.8036 (mtm) cc_final: 0.7645 (mmm) REVERT: U 401 ASP cc_start: 0.8388 (m-30) cc_final: 0.7862 (t0) REVERT: U 415 GLU cc_start: 0.7167 (tt0) cc_final: 0.6860 (tp30) REVERT: U 446 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7287 (tmmm) REVERT: U 702 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8604 (mp0) REVERT: V 57 GLU cc_start: 0.7274 (mt-10) cc_final: 0.6986 (mt-10) REVERT: V 72 GLU cc_start: 0.8267 (tt0) cc_final: 0.7734 (mt-10) REVERT: V 210 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7738 (ttp-110) REVERT: V 241 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8105 (tm-30) REVERT: V 246 GLN cc_start: 0.8054 (pt0) cc_final: 0.6951 (tp40) REVERT: V 270 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7089 (mt-10) REVERT: V 288 ASP cc_start: 0.8401 (m-30) cc_final: 0.8145 (p0) REVERT: V 358 SER cc_start: 0.8488 (t) cc_final: 0.8170 (p) REVERT: V 360 GLN cc_start: 0.7445 (mt0) cc_final: 0.7136 (mp10) REVERT: W 63 GLU cc_start: 0.6974 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: W 94 GLU cc_start: 0.8512 (tp30) cc_final: 0.8121 (tm-30) REVERT: W 105 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7291 (mpt-90) REVERT: W 215 LYS cc_start: 0.8317 (mttt) cc_final: 0.7875 (mtpt) REVERT: W 253 ASN cc_start: 0.7908 (m110) cc_final: 0.7376 (p0) REVERT: W 264 ASP cc_start: 0.8152 (m-30) cc_final: 0.7388 (p0) REVERT: W 312 PHE cc_start: 0.7479 (t80) cc_final: 0.7253 (t80) REVERT: X 187 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8146 (mm-30) outliers start: 34 outliers final: 14 residues processed: 169 average time/residue: 1.5049 time to fit residues: 272.8015 Evaluate side-chains 157 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 235 HIS Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 107 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 100 optimal weight: 0.2980 chunk 0 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 320 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12501 Z= 0.178 Angle : 0.476 7.284 16947 Z= 0.245 Chirality : 0.042 0.144 1832 Planarity : 0.004 0.043 2185 Dihedral : 6.271 54.285 1728 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.84 % Allowed : 12.27 % Favored : 84.89 % 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: 1.50 (0.22), residues: 1501 helix: 1.64 (0.22), residues: 621 sheet: 0.44 (0.34), residues: 213 loop : 0.73 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP X 186 HIS 0.003 0.001 HIS V 87 PHE 0.016 0.001 PHE U 397 TYR 0.011 0.001 TYR V 69 ARG 0.004 0.000 ARG V 372 *********************** 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 188 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.588 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7094 (tt0) cc_final: 0.6824 (tt0) REVERT: G 737 ASP cc_start: 0.8278 (m-30) cc_final: 0.7841 (m-30) REVERT: G 795 ARG cc_start: 0.7310 (mtt180) cc_final: 0.6947 (mtm110) REVERT: U 36 LYS cc_start: 0.8081 (tttt) cc_final: 0.7424 (mmpt) REVERT: U 56 ASN cc_start: 0.6827 (m-40) cc_final: 0.6507 (m-40) REVERT: U 60 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7454 (mmt180) REVERT: U 146 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7643 (pt0) REVERT: U 159 GLU cc_start: 0.6890 (tt0) cc_final: 0.6567 (tm-30) REVERT: U 160 GLN cc_start: 0.7948 (mt0) cc_final: 0.7450 (tm-30) REVERT: U 193 LYS cc_start: 0.5813 (tppt) cc_final: 0.5453 (mmmt) REVERT: U 224 LYS cc_start: 0.7065 (tttt) cc_final: 0.6820 (tttm) REVERT: U 266 ASP cc_start: 0.7849 (m-30) cc_final: 0.7632 (t0) REVERT: U 292 THR cc_start: 0.8952 (m) cc_final: 0.8724 (p) REVERT: U 296 ASP cc_start: 0.7318 (m-30) cc_final: 0.6979 (p0) REVERT: U 298 LYS cc_start: 0.7907 (pttt) cc_final: 0.7545 (mttp) REVERT: U 392 MET cc_start: 0.7963 (mtm) cc_final: 0.7670 (mmm) REVERT: U 401 ASP cc_start: 0.8390 (m-30) cc_final: 0.7864 (t0) REVERT: U 415 GLU cc_start: 0.7140 (tt0) cc_final: 0.6822 (tp30) REVERT: U 446 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7310 (tmmm) REVERT: U 702 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8595 (mp0) REVERT: V 57 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6959 (mt-10) REVERT: V 72 GLU cc_start: 0.8271 (tt0) cc_final: 0.7830 (mt-10) REVERT: V 210 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7758 (ttp-110) REVERT: V 241 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8117 (tm-30) REVERT: V 246 GLN cc_start: 0.8048 (pt0) cc_final: 0.6954 (tp40) REVERT: V 288 ASP cc_start: 0.8383 (m-30) cc_final: 0.8141 (p0) REVERT: V 358 SER cc_start: 0.8546 (t) cc_final: 0.8242 (p) REVERT: V 360 GLN cc_start: 0.7518 (mt0) cc_final: 0.7205 (mp10) REVERT: W 63 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: W 94 GLU cc_start: 0.8578 (tp30) cc_final: 0.8182 (tm-30) REVERT: W 105 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7219 (mpt-90) REVERT: W 215 LYS cc_start: 0.8459 (mttt) cc_final: 0.8031 (mtpt) REVERT: W 253 ASN cc_start: 0.7965 (m110) cc_final: 0.7405 (p0) REVERT: W 264 ASP cc_start: 0.8169 (m-30) cc_final: 0.7386 (p0) REVERT: W 312 PHE cc_start: 0.7544 (t80) cc_final: 0.7324 (t80) REVERT: X 187 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8162 (mm-30) outliers start: 37 outliers final: 19 residues processed: 176 average time/residue: 1.4437 time to fit residues: 273.0257 Evaluate side-chains 163 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 685 ILE Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 227 ILE Chi-restraints excluded: chain V residue 235 HIS Chi-restraints excluded: chain V residue 300 SER Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 335 ARG Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain X residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 67 optimal weight: 0.0470 chunk 12 optimal weight: 0.0470 chunk 76 optimal weight: 0.1980 chunk 139 optimal weight: 0.7980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 733 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12501 Z= 0.117 Angle : 0.442 6.382 16947 Z= 0.226 Chirality : 0.040 0.134 1832 Planarity : 0.004 0.040 2185 Dihedral : 6.002 51.778 1728 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.38 % Allowed : 13.19 % Favored : 84.43 % 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: 1.66 (0.22), residues: 1501 helix: 1.77 (0.22), residues: 625 sheet: 0.55 (0.34), residues: 213 loop : 0.82 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 254 HIS 0.003 0.001 HIS V 87 PHE 0.010 0.001 PHE W 249 TYR 0.010 0.001 TYR V 69 ARG 0.003 0.000 ARG U 701 *********************** 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 183 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 152 time to evaluate : 1.438 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7115 (tt0) cc_final: 0.6841 (tt0) REVERT: G 737 ASP cc_start: 0.8304 (m-30) cc_final: 0.7847 (m-30) REVERT: G 795 ARG cc_start: 0.7318 (mtt180) cc_final: 0.6944 (mtm110) REVERT: U 36 LYS cc_start: 0.8074 (tttt) cc_final: 0.7420 (mmpt) REVERT: U 56 ASN cc_start: 0.6661 (m-40) cc_final: 0.6331 (m-40) REVERT: U 60 ARG cc_start: 0.7821 (ttt180) cc_final: 0.7453 (mmt180) REVERT: U 101 MET cc_start: 0.5808 (OUTLIER) cc_final: 0.5489 (mtt) REVERT: U 146 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7647 (pt0) REVERT: U 159 GLU cc_start: 0.6866 (tt0) cc_final: 0.6569 (tm-30) REVERT: U 160 GLN cc_start: 0.8008 (mt0) cc_final: 0.7517 (tm-30) REVERT: U 224 LYS cc_start: 0.7079 (tttt) cc_final: 0.6844 (tttm) REVERT: U 266 ASP cc_start: 0.7827 (m-30) cc_final: 0.7583 (t0) REVERT: U 292 THR cc_start: 0.8904 (m) cc_final: 0.8673 (p) REVERT: U 296 ASP cc_start: 0.7336 (m-30) cc_final: 0.7008 (p0) REVERT: U 298 LYS cc_start: 0.7887 (pttt) cc_final: 0.7530 (mttp) REVERT: U 401 ASP cc_start: 0.8357 (m-30) cc_final: 0.7852 (t0) REVERT: U 415 GLU cc_start: 0.7154 (tt0) cc_final: 0.6839 (tp30) REVERT: U 446 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7277 (tmmm) REVERT: U 702 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8525 (mp0) REVERT: V 57 GLU cc_start: 0.7357 (mt-10) cc_final: 0.6723 (tp30) REVERT: V 72 GLU cc_start: 0.8164 (tt0) cc_final: 0.7759 (mt-10) REVERT: V 111 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7606 (p0) REVERT: V 210 ARG cc_start: 0.8075 (OUTLIER) cc_final: 0.7856 (ttp-170) REVERT: V 241 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8080 (tm-30) REVERT: V 246 GLN cc_start: 0.8115 (pt0) cc_final: 0.6859 (tp40) REVERT: V 288 ASP cc_start: 0.8386 (m-30) cc_final: 0.8141 (p0) REVERT: V 358 SER cc_start: 0.8494 (t) cc_final: 0.8164 (p) REVERT: V 360 GLN cc_start: 0.7373 (mt0) cc_final: 0.7088 (mp10) REVERT: W 63 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: W 94 GLU cc_start: 0.8580 (tp30) cc_final: 0.8172 (tm-30) REVERT: W 105 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7242 (mmp80) REVERT: W 215 LYS cc_start: 0.8422 (mttt) cc_final: 0.8003 (mtpt) REVERT: W 253 ASN cc_start: 0.8019 (m110) cc_final: 0.7449 (p0) REVERT: W 264 ASP cc_start: 0.8222 (m-30) cc_final: 0.7414 (p0) REVERT: X 187 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8127 (mm-30) outliers start: 31 outliers final: 14 residues processed: 171 average time/residue: 1.4069 time to fit residues: 258.0412 Evaluate side-chains 161 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 650 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12501 Z= 0.208 Angle : 0.483 6.809 16947 Z= 0.246 Chirality : 0.042 0.139 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.098 55.109 1728 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.76 % Allowed : 13.50 % Favored : 83.74 % 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: 627 sheet: 0.48 (0.34), residues: 213 loop : 0.79 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.016 0.001 PHE U 397 TYR 0.011 0.001 TYR U 379 ARG 0.007 0.000 ARG U 475 *********************** 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 184 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 1.559 Fit side-chains revert: symmetry clash REVERT: G 733 GLN cc_start: 0.7118 (tt0) cc_final: 0.6856 (tt0) REVERT: G 737 ASP cc_start: 0.8211 (m-30) cc_final: 0.7718 (m-30) REVERT: G 795 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6963 (mtm110) REVERT: U 19 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6667 (p0) REVERT: U 36 LYS cc_start: 0.8080 (tttt) cc_final: 0.7424 (mmpt) REVERT: U 56 ASN cc_start: 0.6822 (m-40) cc_final: 0.6494 (m-40) REVERT: U 60 ARG cc_start: 0.7861 (ttt180) cc_final: 0.7472 (mmt180) REVERT: U 101 MET cc_start: 0.5773 (OUTLIER) cc_final: 0.5504 (mtt) REVERT: U 146 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7632 (pt0) REVERT: U 159 GLU cc_start: 0.6886 (tt0) cc_final: 0.6562 (tm-30) REVERT: U 160 GLN cc_start: 0.7975 (mt0) cc_final: 0.7474 (tm-30) REVERT: U 193 LYS cc_start: 0.5908 (OUTLIER) cc_final: 0.5681 (mmmt) REVERT: U 232 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7213 (mt0) REVERT: U 266 ASP cc_start: 0.7842 (m-30) cc_final: 0.7598 (t0) REVERT: U 292 THR cc_start: 0.8912 (m) cc_final: 0.8700 (p) REVERT: U 296 ASP cc_start: 0.7339 (m-30) cc_final: 0.7005 (p0) REVERT: U 298 LYS cc_start: 0.7910 (pttt) cc_final: 0.7551 (mttp) REVERT: U 401 ASP cc_start: 0.8397 (m-30) cc_final: 0.7862 (t0) REVERT: U 415 GLU cc_start: 0.7153 (tt0) cc_final: 0.6841 (tp30) REVERT: U 446 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7350 (tmmm) REVERT: U 702 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8611 (mp0) REVERT: V 57 GLU cc_start: 0.7353 (mt-10) cc_final: 0.6996 (mt-10) REVERT: V 72 GLU cc_start: 0.8191 (tt0) cc_final: 0.7781 (mt-10) REVERT: V 111 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7697 (p0) REVERT: V 210 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7860 (ttp-110) REVERT: V 241 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8130 (tm-30) REVERT: V 246 GLN cc_start: 0.8110 (pt0) cc_final: 0.6935 (tp40) REVERT: V 288 ASP cc_start: 0.8402 (m-30) cc_final: 0.8167 (p0) REVERT: V 358 SER cc_start: 0.8569 (t) cc_final: 0.8257 (p) REVERT: V 360 GLN cc_start: 0.7516 (mt0) cc_final: 0.7201 (mp10) REVERT: W 63 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: W 94 GLU cc_start: 0.8581 (tp30) cc_final: 0.8170 (tm-30) REVERT: W 105 ARG cc_start: 0.7685 (mtt180) cc_final: 0.7250 (mmp80) REVERT: W 215 LYS cc_start: 0.8444 (mttt) cc_final: 0.8035 (mtpt) REVERT: W 253 ASN cc_start: 0.7956 (m110) cc_final: 0.7366 (p0) REVERT: W 264 ASP cc_start: 0.8223 (m-30) cc_final: 0.7416 (p0) REVERT: X 187 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8077 (mm-30) outliers start: 36 outliers final: 20 residues processed: 174 average time/residue: 1.4915 time to fit residues: 278.5886 Evaluate side-chains 171 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 650 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 195 GLU Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 126 optimal weight: 0.0010 overall best weight: 0.9190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12501 Z= 0.184 Angle : 0.477 7.165 16947 Z= 0.243 Chirality : 0.042 0.134 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.103 55.599 1728 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.84 % Allowed : 13.73 % Favored : 83.44 % 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: 1.58 (0.22), residues: 1501 helix: 1.69 (0.22), residues: 627 sheet: 0.47 (0.34), residues: 215 loop : 0.80 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 186 HIS 0.004 0.001 HIS V 235 PHE 0.013 0.001 PHE U 397 TYR 0.010 0.001 TYR U 379 ARG 0.006 0.000 ARG V 372 *********************** 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 182 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.529 Fit side-chains REVERT: G 733 GLN cc_start: 0.7112 (tt0) cc_final: 0.6859 (tt0) REVERT: G 737 ASP cc_start: 0.8213 (m-30) cc_final: 0.7718 (m-30) REVERT: G 795 ARG cc_start: 0.7336 (mtt180) cc_final: 0.6947 (mtm110) REVERT: U 19 ASP cc_start: 0.7120 (OUTLIER) cc_final: 0.6637 (p0) REVERT: U 36 LYS cc_start: 0.8079 (tttt) cc_final: 0.7421 (mmpt) REVERT: U 56 ASN cc_start: 0.6663 (m-40) cc_final: 0.6337 (m-40) REVERT: U 60 ARG cc_start: 0.7930 (ttt180) cc_final: 0.7552 (mmt180) REVERT: U 146 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7619 (pt0) REVERT: U 159 GLU cc_start: 0.6905 (tt0) cc_final: 0.6575 (tm-30) REVERT: U 160 GLN cc_start: 0.8011 (mt0) cc_final: 0.7625 (tm-30) REVERT: U 193 LYS cc_start: 0.5818 (OUTLIER) cc_final: 0.5554 (mmmt) REVERT: U 232 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7200 (mt0) REVERT: U 266 ASP cc_start: 0.7861 (m-30) cc_final: 0.7621 (t0) REVERT: U 292 THR cc_start: 0.8907 (m) cc_final: 0.8703 (p) REVERT: U 296 ASP cc_start: 0.7287 (m-30) cc_final: 0.6967 (p0) REVERT: U 298 LYS cc_start: 0.7914 (pttt) cc_final: 0.7560 (mttp) REVERT: U 401 ASP cc_start: 0.8438 (m-30) cc_final: 0.7869 (t0) REVERT: U 415 GLU cc_start: 0.7225 (tt0) cc_final: 0.6915 (tp30) REVERT: U 446 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7366 (tmmm) REVERT: U 702 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8642 (mp0) REVERT: V 57 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6994 (mt-10) REVERT: V 72 GLU cc_start: 0.8175 (tt0) cc_final: 0.7788 (mt-10) REVERT: V 111 ASN cc_start: 0.7883 (OUTLIER) cc_final: 0.7616 (p0) REVERT: V 210 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7789 (ttp-170) REVERT: V 241 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8129 (tm-30) REVERT: V 246 GLN cc_start: 0.8083 (pt0) cc_final: 0.6936 (tp40) REVERT: V 288 ASP cc_start: 0.8402 (m-30) cc_final: 0.8167 (p0) REVERT: V 358 SER cc_start: 0.8564 (t) cc_final: 0.8257 (p) REVERT: V 360 GLN cc_start: 0.7410 (mt0) cc_final: 0.7107 (mp10) REVERT: W 63 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6364 (mp0) REVERT: W 94 GLU cc_start: 0.8581 (tp30) cc_final: 0.8171 (tm-30) REVERT: W 105 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7252 (mmp80) REVERT: W 215 LYS cc_start: 0.8460 (mttt) cc_final: 0.8051 (mtpt) REVERT: W 253 ASN cc_start: 0.7998 (m110) cc_final: 0.7363 (p0) REVERT: W 264 ASP cc_start: 0.8198 (m-30) cc_final: 0.7428 (p0) REVERT: X 187 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8082 (mm-30) outliers start: 37 outliers final: 21 residues processed: 171 average time/residue: 1.4295 time to fit residues: 263.0321 Evaluate side-chains 171 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 650 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.0980 chunk 127 optimal weight: 0.0980 chunk 88 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12501 Z= 0.203 Angle : 0.493 7.983 16947 Z= 0.249 Chirality : 0.042 0.136 1832 Planarity : 0.004 0.044 2185 Dihedral : 6.154 55.761 1728 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.76 % Allowed : 14.19 % Favored : 83.05 % 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: 1.51 (0.22), residues: 1501 helix: 1.64 (0.21), residues: 632 sheet: 0.43 (0.34), residues: 215 loop : 0.75 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.024 0.001 PHE W 312 TYR 0.011 0.001 TYR U 379 ARG 0.005 0.000 ARG V 372 *********************** 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 179 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.438 Fit side-chains REVERT: G 733 GLN cc_start: 0.7122 (tt0) cc_final: 0.6380 (tp-100) REVERT: G 737 ASP cc_start: 0.8214 (m-30) cc_final: 0.7522 (m-30) REVERT: G 795 ARG cc_start: 0.7302 (mtt180) cc_final: 0.6912 (mtm110) REVERT: U 19 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6690 (p0) REVERT: U 36 LYS cc_start: 0.8073 (tttt) cc_final: 0.7416 (mmpt) REVERT: U 56 ASN cc_start: 0.6661 (m-40) cc_final: 0.6339 (m-40) REVERT: U 60 ARG cc_start: 0.7928 (ttt180) cc_final: 0.7542 (mmt180) REVERT: U 101 MET cc_start: 0.5394 (OUTLIER) cc_final: 0.5028 (mtm) REVERT: U 127 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7429 (mtmt) REVERT: U 146 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7602 (pt0) REVERT: U 159 GLU cc_start: 0.6931 (tt0) cc_final: 0.6655 (tm-30) REVERT: U 160 GLN cc_start: 0.8044 (mt0) cc_final: 0.7649 (tm-30) REVERT: U 193 LYS cc_start: 0.6001 (mmtm) cc_final: 0.5744 (mmmt) REVERT: U 232 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7198 (mt0) REVERT: U 266 ASP cc_start: 0.7848 (m-30) cc_final: 0.7636 (t0) REVERT: U 278 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7612 (tm-30) REVERT: U 292 THR cc_start: 0.8912 (m) cc_final: 0.8710 (p) REVERT: U 296 ASP cc_start: 0.7284 (m-30) cc_final: 0.6967 (p0) REVERT: U 298 LYS cc_start: 0.7905 (pttt) cc_final: 0.7563 (mttp) REVERT: U 401 ASP cc_start: 0.8487 (m-30) cc_final: 0.7910 (t0) REVERT: U 415 GLU cc_start: 0.7230 (tt0) cc_final: 0.6918 (tp30) REVERT: U 446 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7389 (tmmm) REVERT: U 702 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8684 (mp0) REVERT: V 57 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6999 (mt-10) REVERT: V 72 GLU cc_start: 0.8190 (tt0) cc_final: 0.7790 (mt-10) REVERT: V 111 ASN cc_start: 0.7849 (OUTLIER) cc_final: 0.7592 (p0) REVERT: V 210 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7769 (ttp-170) REVERT: V 241 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8195 (tm-30) REVERT: V 246 GLN cc_start: 0.7962 (pt0) cc_final: 0.6834 (tp40) REVERT: V 288 ASP cc_start: 0.8366 (m-30) cc_final: 0.8131 (p0) REVERT: V 358 SER cc_start: 0.8598 (t) cc_final: 0.8298 (p) REVERT: V 360 GLN cc_start: 0.7443 (mt0) cc_final: 0.7119 (mp10) REVERT: W 63 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: W 94 GLU cc_start: 0.8576 (tp30) cc_final: 0.8163 (tm-30) REVERT: W 105 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7299 (mmp80) REVERT: W 253 ASN cc_start: 0.8002 (m110) cc_final: 0.7358 (p0) REVERT: W 264 ASP cc_start: 0.8290 (m-30) cc_final: 0.7501 (p0) REVERT: X 187 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8093 (mm-30) outliers start: 36 outliers final: 24 residues processed: 168 average time/residue: 1.4474 time to fit residues: 261.4565 Evaluate side-chains 173 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 127 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 494 ASP Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain U residue 733 MET Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain V residue 179 ASP Chi-restraints excluded: chain V residue 208 ILE Chi-restraints excluded: chain V residue 210 ARG Chi-restraints excluded: chain V residue 269 LEU Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 246 VAL Chi-restraints excluded: chain W residue 276 ASP Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 411 MET Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 149 optimal weight: 0.0050 chunk 137 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 72 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 126 optimal weight: 0.1980 chunk 36 optimal weight: 0.6980 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 12501 Z= 0.129 Angle : 0.457 8.711 16947 Z= 0.230 Chirality : 0.040 0.132 1832 Planarity : 0.004 0.043 2185 Dihedral : 5.936 52.190 1728 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.38 % Allowed : 14.72 % Favored : 82.90 % 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: 1.65 (0.22), residues: 1501 helix: 1.73 (0.21), residues: 637 sheet: 0.54 (0.34), residues: 213 loop : 0.83 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 735 HIS 0.004 0.001 HIS V 235 PHE 0.010 0.001 PHE W 249 TYR 0.009 0.001 TYR V 69 ARG 0.005 0.000 ARG V 372 ********************** 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 172 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.449 Fit side-chains revert: symmetry clash REVERT: G 737 ASP cc_start: 0.8225 (m-30) cc_final: 0.7712 (m-30) REVERT: G 795 ARG cc_start: 0.7315 (mtt180) cc_final: 0.6915 (mtm110) REVERT: U 19 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6496 (p0) REVERT: U 36 LYS cc_start: 0.8074 (tttt) cc_final: 0.7438 (mmpt) REVERT: U 56 ASN cc_start: 0.6615 (m-40) cc_final: 0.6292 (m-40) REVERT: U 60 ARG cc_start: 0.7959 (ttt180) cc_final: 0.7590 (mmp80) REVERT: U 101 MET cc_start: 0.5360 (OUTLIER) cc_final: 0.4994 (mtm) REVERT: U 146 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7613 (pt0) REVERT: U 159 GLU cc_start: 0.6925 (tt0) cc_final: 0.6657 (tm-30) REVERT: U 160 GLN cc_start: 0.8079 (mt0) cc_final: 0.7604 (tm-30) REVERT: U 181 MET cc_start: 0.7225 (ttm) cc_final: 0.6980 (mtm) REVERT: U 191 ASN cc_start: 0.5474 (p0) cc_final: 0.5140 (t0) REVERT: U 193 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5669 (mmmt) REVERT: U 232 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7192 (mt0) REVERT: U 266 ASP cc_start: 0.7831 (m-30) cc_final: 0.7598 (t0) REVERT: U 278 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7426 (tm-30) REVERT: U 292 THR cc_start: 0.8890 (m) cc_final: 0.8673 (p) REVERT: U 296 ASP cc_start: 0.7273 (m-30) cc_final: 0.6986 (p0) REVERT: U 298 LYS cc_start: 0.7971 (pttt) cc_final: 0.7642 (mttp) REVERT: U 324 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: U 401 ASP cc_start: 0.8453 (m-30) cc_final: 0.7893 (t0) REVERT: U 415 GLU cc_start: 0.7243 (tt0) cc_final: 0.6904 (tp30) REVERT: U 446 LYS cc_start: 0.7832 (OUTLIER) cc_final: 0.7356 (tmmm) REVERT: U 702 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8649 (mp0) REVERT: V 57 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6999 (mt-10) REVERT: V 72 GLU cc_start: 0.8161 (tt0) cc_final: 0.7797 (mt-10) REVERT: V 111 ASN cc_start: 0.7861 (OUTLIER) cc_final: 0.7616 (p0) REVERT: V 241 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8157 (tm-30) REVERT: V 246 GLN cc_start: 0.8058 (pt0) cc_final: 0.6886 (tp40) REVERT: V 270 GLU cc_start: 0.7239 (mt-10) cc_final: 0.6905 (mt-10) REVERT: V 288 ASP cc_start: 0.8341 (m-30) cc_final: 0.8128 (p0) REVERT: V 358 SER cc_start: 0.8528 (t) cc_final: 0.8215 (p) REVERT: V 360 GLN cc_start: 0.7394 (mt0) cc_final: 0.7089 (mp10) REVERT: W 63 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: W 94 GLU cc_start: 0.8574 (tp30) cc_final: 0.8220 (tm-30) REVERT: W 105 ARG cc_start: 0.7725 (mtt180) cc_final: 0.7287 (mmp80) REVERT: W 253 ASN cc_start: 0.7791 (m110) cc_final: 0.7164 (p0) REVERT: W 264 ASP cc_start: 0.8288 (m-30) cc_final: 0.7515 (p0) REVERT: W 322 GLU cc_start: 0.8516 (mt-10) cc_final: 0.8079 (tt0) REVERT: X 187 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8140 (mm-30) outliers start: 31 outliers final: 17 residues processed: 163 average time/residue: 1.4473 time to fit residues: 253.6138 Evaluate side-chains 164 residues out of total 1304 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 759 SER Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 19 ASP Chi-restraints excluded: chain U residue 101 MET Chi-restraints excluded: chain U residue 193 LYS Chi-restraints excluded: chain U residue 206 GLU Chi-restraints excluded: chain U residue 232 GLN Chi-restraints excluded: chain U residue 324 GLU Chi-restraints excluded: chain U residue 386 GLU Chi-restraints excluded: chain U residue 446 LYS Chi-restraints excluded: chain U residue 650 LYS Chi-restraints excluded: chain U residue 660 VAL Chi-restraints excluded: chain U residue 695 LEU Chi-restraints excluded: chain U residue 699 SER Chi-restraints excluded: chain V residue 56 ASP Chi-restraints excluded: chain V residue 111 ASN Chi-restraints excluded: chain V residue 123 VAL Chi-restraints excluded: chain W residue 22 SER Chi-restraints excluded: chain W residue 63 GLU Chi-restraints excluded: chain W residue 245 VAL Chi-restraints excluded: chain W residue 320 VAL Chi-restraints excluded: chain W residue 426 SER Chi-restraints excluded: chain W residue 451 SER Chi-restraints excluded: chain X residue 172 THR Chi-restraints excluded: chain X residue 175 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 49 optimal weight: 0.0870 chunk 122 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.139690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.116718 restraints weight = 14913.670| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.63 r_work: 0.3325 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3057 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= 0.160 Angle : 0.472 8.885 16947 Z= 0.236 Chirality : 0.041 0.135 1832 Planarity : 0.004 0.043 2185 Dihedral : 5.941 53.961 1728 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 14.80 % Favored : 82.82 % 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: 1.69 (0.22), residues: 1501 helix: 1.81 (0.21), residues: 630 sheet: 0.53 (0.34), residues: 213 loop : 0.81 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 340 HIS 0.004 0.001 HIS V 235 PHE 0.028 0.001 PHE W 312 TYR 0.009 0.001 TYR U 379 ARG 0.005 0.000 ARG V 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.59 seconds wall clock time: 87 minutes 7.12 seconds (5227.12 seconds total)