Starting phenix.real_space_refine on Fri Feb 16 01:48:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a5p_15180/02_2024/8a5p_15180_neut_updated.pdb" } resolution = 3.4 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= 0.003 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 81 5.49 5 Mg 3 5.21 5 S 61 5.16 5 C 8565 2.51 5 N 2464 2.21 5 O 2763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G PHE 722": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 731": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 785": "OD1" <-> "OD2" Residue "G GLU 805": "OE1" <-> "OE2" Residue "G GLU 816": "OE1" <-> "OE2" Residue "U ASP 102": "OD1" <-> "OD2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "U GLU 154": "OE1" <-> "OE2" Residue "U ARG 156": "NH1" <-> "NH2" Residue "U TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 194": "OD1" <-> "OD2" Residue "U PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 204": "OE1" <-> "OE2" Residue "U GLU 218": "OE1" <-> "OE2" Residue "U GLU 278": "OE1" <-> "OE2" Residue "U ASP 282": "OD1" <-> "OD2" Residue "U TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 365": "OE1" <-> "OE2" Residue "U GLU 371": "OE1" <-> "OE2" Residue "U TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 704": "OD1" <-> "OD2" Residue "U GLU 705": "OE1" <-> "OE2" Residue "U ASP 723": "OD1" <-> "OD2" Residue "V TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "V GLU 57": "OE1" <-> "OE2" Residue "V ARG 62": "NH1" <-> "NH2" Residue "V TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 100": "OE1" <-> "OE2" Residue "V GLU 107": "OE1" <-> "OE2" Residue "V GLU 167": "OE1" <-> "OE2" Residue "V ASP 179": "OD1" <-> "OD2" Residue "V ARG 196": "NH1" <-> "NH2" 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 270": "OE1" <-> "OE2" Residue "V GLU 361": "OE1" <-> "OE2" Residue "V ARG 372": "NH1" <-> "NH2" Residue "V PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 14": "OD1" <-> "OD2" Residue "W GLU 20": "OE1" <-> "OE2" Residue "W TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 63": "OE1" <-> "OE2" Residue "W TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 84": "OE1" <-> "OE2" Residue "W GLU 143": "OE1" <-> "OE2" Residue "W PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 264": "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 TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 427": "OE1" <-> "OE2" Residue "W GLU 464": "OE1" <-> "OE2" 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-5238/modules/chem_data/mon_lib" Total number of atoms: 13937 Number of models: 1 Model: "" Number of chains: 10 Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 831 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Chain: "K" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 739 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 737 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "U" Number of atoms: 4913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4913 Classifications: {'peptide': 605} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 576} 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: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 413 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "U" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 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, 'ATP': 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, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.19, per 1000 atoms: 0.52 Number of scatterers: 13937 At special positions: 0 Unit cell: (96.48, 112.56, 155.44, 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 61 16.00 P 81 15.00 Mg 3 11.99 O 2763 8.00 N 2464 7.00 C 8565 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: 5.72 Conformation dependent library (CDL) restraints added in 2.2 seconds 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 70 helices and 14 sheets defined 42.6% alpha, 11.7% beta 32 base pairs and 67 stacking pairs defined. Time for finding SS restraints: 6.33 Creating SS restraints... Processing helix chain 'G' and resid 725 through 740 Processing helix chain 'G' and resid 742 through 776 removed outlier: 3.508A pdb=" N LYS G 773 " --> pdb=" O SER G 769 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TRP G 775 " --> pdb=" O GLU G 771 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLN G 776 " --> pdb=" O ALA G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 780 through 805 Processing helix chain 'U' and resid 7 through 12 Processing helix chain 'U' and resid 50 through 67 removed outlier: 3.765A pdb=" N GLN U 55 " --> pdb=" O SER U 51 " (cutoff:3.500A) 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 202 removed outlier: 3.548A pdb=" N PHE U 199 " --> pdb=" O LEU U 195 " (cutoff:3.500A) Processing helix chain 'U' and resid 210 through 212 No H-bonds generated for 'chain 'U' and resid 210 through 212' Processing helix chain 'U' and resid 237 through 241 Processing helix chain 'U' and resid 270 through 287 Processing helix chain 'U' and resid 294 through 299 removed outlier: 4.120A 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 395 Processing helix chain 'U' and resid 407 through 420 Processing helix chain 'U' and resid 454 through 463 Proline residue: U 459 - end of helix removed outlier: 4.834A pdb=" N PHE U 462 " --> pdb=" O ALA U 458 " (cutoff:3.500A) removed outlier: 5.123A 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: 3.590A pdb=" N VAL U 508 " --> pdb=" O ILE U 504 " (cutoff:3.500A) Processing helix chain 'U' and resid 621 through 629 Processing helix chain 'U' and resid 637 through 649 removed outlier: 3.518A pdb=" N HIS U 647 " --> pdb=" O THR U 643 " (cutoff:3.500A) Processing helix chain 'U' and resid 653 through 659 Processing helix chain 'U' and resid 668 through 671 Processing helix chain 'U' and resid 675 through 686 Processing helix chain 'U' and resid 688 through 690 No H-bonds generated for 'chain 'U' and resid 688 through 690' Processing helix chain 'U' and resid 708 through 718 Processing helix chain 'U' and resid 728 through 742 removed outlier: 8.420A pdb=" N SER U 736 " --> pdb=" O LYS U 732 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ARG U 737 " --> pdb=" O MET U 733 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N CYS U 738 " --> pdb=" O LEU U 734 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE U 739 " --> pdb=" O GLY U 735 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR U 740 " --> pdb=" O SER U 736 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N MET U 741 " --> pdb=" O ARG U 737 " (cutoff:3.500A) Processing helix chain 'V' and resid 56 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 removed outlier: 4.066A pdb=" N LYS V 84 " --> pdb=" O ASP V 80 " (cutoff:3.500A) 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: 3.515A pdb=" N PHE V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 137 through 145 Processing helix chain 'V' and resid 182 through 196 Processing helix chain 'V' and resid 203 through 216 removed outlier: 4.416A pdb=" N ILE V 208 " --> pdb=" O ALA V 204 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP V 211 " --> pdb=" O GLU V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 223 through 230 Processing helix chain 'V' and resid 252 through 261 removed outlier: 4.362A 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 283 Processing helix chain 'V' and resid 287 through 296 removed outlier: 4.402A pdb=" N LYS V 291 " --> pdb=" O VAL V 287 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP V 292 " --> pdb=" O ASP V 288 " (cutoff:3.500A) Processing helix chain 'V' and resid 302 through 305 Processing helix chain 'V' and resid 309 through 320 Processing helix chain 'V' and resid 338 through 348 Processing helix chain 'V' and resid 350 through 354 removed outlier: 3.544A pdb=" N GLN V 353 " --> pdb=" O SER V 350 " (cutoff:3.500A) Processing helix chain 'V' and resid 359 through 365 removed outlier: 4.052A pdb=" N GLU V 364 " --> pdb=" O GLN V 360 " (cutoff:3.500A) Processing helix chain 'V' and resid 367 through 373 Processing helix chain 'W' and resid 62 through 64 No H-bonds generated for 'chain 'W' and resid 62 through 64' Processing helix chain 'W' and resid 86 through 97 Processing helix chain 'W' and resid 109 through 112 removed outlier: 3.787A pdb=" N ASN W 112 " --> pdb=" O ALA W 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 109 through 112' Processing helix chain 'W' and resid 156 through 169 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 293 removed outlier: 3.822A pdb=" N ARG W 285 " --> pdb=" O PHE W 281 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL W 286 " --> pdb=" O GLU W 282 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 315 removed outlier: 4.612A pdb=" N ASP W 311 " --> pdb=" O PRO W 307 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR W 315 " --> pdb=" O ASP W 311 " (cutoff:3.500A) Processing helix chain 'W' and resid 334 through 342 removed outlier: 4.741A pdb=" N ALA W 339 " --> pdb=" O ARG W 335 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY W 341 " --> pdb=" O ARG W 337 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N MET W 342 " --> pdb=" O VAL W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 347 No H-bonds generated for 'chain 'W' and resid 345 through 347' 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 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 428 through 441 removed outlier: 3.922A pdb=" N GLY W 431 " --> pdb=" O ARG W 428 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N ALA W 432 " --> pdb=" O ARG W 429 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE W 434 " --> pdb=" O GLY W 431 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA W 440 " --> pdb=" O SER W 437 " (cutoff:3.500A) Processing helix chain 'W' and resid 443 through 447 removed outlier: 3.527A pdb=" N HIS W 446 " --> pdb=" O GLY W 443 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN W 447 " --> pdb=" O THR W 444 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 443 through 447' Processing helix chain 'W' and resid 452 through 458 Processing helix chain 'W' and resid 461 through 464 No H-bonds generated for 'chain 'W' and resid 461 through 464' Processing helix chain 'X' and resid 156 through 160 Processing sheet with id= A, first strand: chain 'U' and resid 127 through 130 removed outlier: 6.449A pdb=" N SER U 301 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ILE U 109 " --> pdb=" O SER U 301 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL U 303 " --> pdb=" O ILE U 109 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG U 330 " --> pdb=" O CYS U 302 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE U 304 " --> pdb=" O ARG U 330 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ALA U 332 " --> pdb=" O ILE U 304 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE U 306 " --> pdb=" O ALA U 332 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE U 334 " --> pdb=" O ILE U 306 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'U' and resid 132 through 136 Processing sheet with id= C, first strand: chain 'U' and resid 206 through 208 removed outlier: 3.578A pdb=" N ARG U 445 " --> pdb=" O LEU U 437 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'U' and resid 696 through 698 removed outlier: 6.467A pdb=" N ILE U 663 " --> pdb=" O SER U 697 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N MET U 664 " --> pdb=" O GLN U 348 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N CYS U 350 " --> pdb=" O MET U 664 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N VAL U 666 " --> pdb=" O CYS U 350 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N VAL U 352 " --> pdb=" O VAL U 666 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'V' and resid 132 through 136 removed outlier: 6.478A pdb=" N VAL V 103 " --> pdb=" O TYR V 133 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N SER V 135 " --> pdb=" O VAL V 103 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU V 105 " --> pdb=" O SER V 135 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N LEU V 8 " --> pdb=" O LEU V 104 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N THR V 106 " --> pdb=" O LEU V 8 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE V 10 " --> pdb=" O THR V 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'V' and resid 65 through 69 Processing sheet with id= G, first strand: chain 'V' and resid 297 through 300 removed outlier: 6.025A pdb=" N ILE V 151 " --> pdb=" O VAL V 298 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N SER V 300 " --> pdb=" O ILE V 151 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU V 153 " --> pdb=" O SER V 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'V' and resid 239 through 241 Processing sheet with id= I, first strand: chain 'W' and resid 175 through 179 removed outlier: 6.629A pdb=" N LEU W 146 " --> pdb=" O TRP W 176 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N SER W 178 " --> pdb=" O LEU W 146 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N MET W 148 " --> pdb=" O SER W 178 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU W 24 " --> pdb=" O LEU W 147 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N THR W 149 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 7.346A 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: 6.475A pdb=" N VAL W 388 " --> pdb=" O HIS W 420 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU W 194 " --> pdb=" O VAL W 389 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR W 391 " --> pdb=" O LEU W 194 " (cutoff:3.500A) removed outlier: 6.370A 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: 6.916A 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 179 452 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 160 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 67 stacking parallelities Total time for adding SS restraints: 5.06 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 3373 1.34 - 1.49: 5000 1.49 - 1.64: 5914 1.64 - 1.79: 14 1.79 - 1.93: 94 Bond restraints: 14395 Sorted by residual: bond pdb=" CE1 HIS V 371 " pdb=" NE2 HIS V 371 " ideal model delta sigma weight residual 1.321 1.395 -0.074 1.00e-02 1.00e+04 5.44e+01 bond pdb=" CE1 HIS U 320 " pdb=" NE2 HIS U 320 " ideal model delta sigma weight residual 1.321 1.391 -0.070 1.00e-02 1.00e+04 4.92e+01 bond pdb=" CE1 HIS U 746 " pdb=" NE2 HIS U 746 " ideal model delta sigma weight residual 1.321 1.379 -0.058 1.00e-02 1.00e+04 3.40e+01 bond pdb=" CE1 HIS U 408 " pdb=" NE2 HIS U 408 " ideal model delta sigma weight residual 1.321 1.376 -0.055 1.00e-02 1.00e+04 2.99e+01 bond pdb=" CG MET V 355 " pdb=" SD MET V 355 " ideal model delta sigma weight residual 1.803 1.934 -0.131 2.50e-02 1.60e+03 2.75e+01 ... (remaining 14390 not shown) Histogram of bond angle deviations from ideal: 89.48 - 98.67: 19 98.67 - 107.86: 1528 107.86 - 117.05: 8879 117.05 - 126.23: 8993 126.23 - 135.42: 395 Bond angle restraints: 19814 Sorted by residual: angle pdb=" PB ATP U 900 " pdb=" O3B ATP U 900 " pdb=" PG ATP U 900 " ideal model delta sigma weight residual 139.87 118.06 21.81 1.00e+00 1.00e+00 4.76e+02 angle pdb=" PA ATP V 500 " pdb=" O3A ATP V 500 " pdb=" PB ATP V 500 " ideal model delta sigma weight residual 136.83 117.10 19.73 1.00e+00 1.00e+00 3.89e+02 angle pdb=" PA ATP U 900 " pdb=" O3A ATP U 900 " pdb=" PB ATP U 900 " ideal model delta sigma weight residual 136.83 117.99 18.84 1.00e+00 1.00e+00 3.55e+02 angle pdb=" PB ATP V 500 " pdb=" O3B ATP V 500 " pdb=" PG ATP V 500 " ideal model delta sigma weight residual 139.87 122.61 17.26 1.00e+00 1.00e+00 2.98e+02 angle pdb=" PA ATP W 500 " pdb=" O3A ATP W 500 " pdb=" PB ATP W 500 " ideal model delta sigma weight residual 136.83 119.62 17.21 1.00e+00 1.00e+00 2.96e+02 ... (remaining 19809 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7307 17.13 - 34.25: 792 34.25 - 51.38: 295 51.38 - 68.50: 126 68.50 - 85.62: 24 Dihedral angle restraints: 8544 sinusoidal: 4046 harmonic: 4498 Sorted by residual: dihedral pdb=" CA ARG V 372 " pdb=" C ARG V 372 " pdb=" N LYS V 373 " pdb=" CA LYS V 373 " ideal model delta harmonic sigma weight residual -180.00 -149.23 -30.77 0 5.00e+00 4.00e-02 3.79e+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 180.00 153.15 26.85 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA LEU V 65 " pdb=" C LEU V 65 " pdb=" N THR V 66 " pdb=" CA THR V 66 " ideal model delta harmonic sigma weight residual 180.00 153.90 26.10 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 1780 0.130 - 0.260: 309 0.260 - 0.389: 59 0.389 - 0.519: 0 0.519 - 0.649: 2 Chirality restraints: 2150 Sorted by residual: chirality pdb=" P DC K 75 " pdb=" OP1 DC K 75 " pdb=" OP2 DC K 75 " pdb=" O5' DC K 75 " both_signs ideal model delta sigma weight residual True 2.35 -2.99 -0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" P DC L-110 " pdb=" OP1 DC L-110 " pdb=" OP2 DC L-110 " pdb=" O5' DC L-110 " both_signs ideal model delta sigma weight residual True 2.35 -2.94 -0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" P DC K 89 " pdb=" OP1 DC K 89 " pdb=" OP2 DC K 89 " pdb=" O5' DC K 89 " both_signs ideal model delta sigma weight residual True 2.35 -2.69 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 2147 not shown) Planarity restraints: 2299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT K 82 " -0.105 2.00e-02 2.50e+03 4.84e-02 5.86e+01 pdb=" N1 DT K 82 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DT K 82 " 0.034 2.00e-02 2.50e+03 pdb=" O2 DT K 82 " 0.042 2.00e-02 2.50e+03 pdb=" N3 DT K 82 " 0.007 2.00e-02 2.50e+03 pdb=" C4 DT K 82 " -0.019 2.00e-02 2.50e+03 pdb=" O4 DT K 82 " -0.075 2.00e-02 2.50e+03 pdb=" C5 DT K 82 " 0.030 2.00e-02 2.50e+03 pdb=" C7 DT K 82 " 0.024 2.00e-02 2.50e+03 pdb=" C6 DT K 82 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 340 " 0.093 2.00e-02 2.50e+03 4.40e-02 4.83e+01 pdb=" CG TRP V 340 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP V 340 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP V 340 " -0.036 2.00e-02 2.50e+03 pdb=" NE1 TRP V 340 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP V 340 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP V 340 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 340 " 0.039 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 340 " -0.030 2.00e-02 2.50e+03 pdb=" CH2 TRP V 340 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT L -76 " -0.091 2.00e-02 2.50e+03 4.39e-02 4.82e+01 pdb=" N1 DT L -76 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT L -76 " 0.032 2.00e-02 2.50e+03 pdb=" O2 DT L -76 " 0.047 2.00e-02 2.50e+03 pdb=" N3 DT L -76 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT L -76 " -0.020 2.00e-02 2.50e+03 pdb=" O4 DT L -76 " -0.066 2.00e-02 2.50e+03 pdb=" C5 DT L -76 " 0.016 2.00e-02 2.50e+03 pdb=" C7 DT L -76 " 0.044 2.00e-02 2.50e+03 pdb=" C6 DT L -76 " 0.010 2.00e-02 2.50e+03 ... (remaining 2296 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 12 2.43 - 3.05: 8448 3.05 - 3.67: 20780 3.67 - 4.28: 33332 4.28 - 4.90: 52771 Nonbonded interactions: 115343 Sorted by model distance: nonbonded pdb=" O1B ATP W 500 " pdb="MG MG W 501 " model vdw 1.816 2.170 nonbonded pdb=" O2B ATP V 500 " pdb="MG MG V 501 " model vdw 1.851 2.170 nonbonded pdb=" O2G ATP W 500 " pdb="MG MG W 501 " model vdw 1.943 2.170 nonbonded pdb=" O2G ATP V 500 " pdb="MG MG V 501 " model vdw 2.048 2.170 nonbonded pdb=" O1B ATP U 900 " pdb="MG MG U 901 " model vdw 2.048 2.170 ... (remaining 115338 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: 0.370 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: 2.310 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 43.190 Find NCS groups from input model: 0.340 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 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 : 0.011 0.131 14395 Z= 0.721 Angle : 1.651 21.811 19814 Z= 1.110 Chirality : 0.101 0.649 2150 Planarity : 0.022 0.239 2299 Dihedral : 17.868 85.625 5640 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.26 % Favored : 96.61 % Rotamer: Outliers : 0.90 % Allowed : 3.47 % Favored : 95.63 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.12 (0.20), residues: 1532 helix: -1.25 (0.18), residues: 634 sheet: 0.38 (0.36), residues: 195 loop : -0.38 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.093 0.017 TRP V 340 HIS 0.020 0.005 HIS U 320 PHE 0.073 0.012 PHE U 716 TYR 0.079 0.016 TYR U 314 ARG 0.028 0.004 ARG U 17 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 797 MET cc_start: 0.9492 (tmm) cc_final: 0.9213 (tmm) REVERT: U 43 MET cc_start: 0.9378 (mtp) cc_final: 0.9163 (mtp) REVERT: U 144 MET cc_start: 0.9687 (mtp) cc_final: 0.9477 (mtm) REVERT: U 182 ARG cc_start: 0.9595 (mtt180) cc_final: 0.9222 (mmp-170) REVERT: U 194 ASP cc_start: 0.9414 (m-30) cc_final: 0.9179 (t70) REVERT: U 396 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.7962 (t0) REVERT: U 397 PHE cc_start: 0.9421 (t80) cc_final: 0.9178 (t80) REVERT: V 132 PHE cc_start: 0.9226 (OUTLIER) cc_final: 0.8768 (t80) REVERT: W 77 MET cc_start: 0.9327 (mmm) cc_final: 0.8702 (mmm) REVERT: W 82 MET cc_start: 0.9081 (mtm) cc_final: 0.8541 (mtm) REVERT: W 250 MET cc_start: 0.9480 (mtp) cc_final: 0.9271 (mtp) REVERT: W 448 MET cc_start: 0.8713 (mmm) cc_final: 0.8414 (mmt) REVERT: W 466 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7394 (mmt-90) outliers start: 12 outliers final: 1 residues processed: 135 average time/residue: 0.3100 time to fit residues: 58.9682 Evaluate side-chains 78 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 390 VAL Chi-restraints excluded: chain W residue 466 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 64 optimal weight: 10.0000 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.0980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 161 GLN U 184 ASN U 425 GLN V 275 HIS W 458 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 14395 Z= 0.182 Angle : 0.629 9.171 19814 Z= 0.339 Chirality : 0.042 0.152 2150 Planarity : 0.004 0.037 2299 Dihedral : 18.849 79.044 2588 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.28 % Favored : 97.65 % Rotamer: Outliers : 0.90 % Allowed : 6.78 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.65 (0.21), residues: 1532 helix: 0.40 (0.20), residues: 639 sheet: 1.08 (0.38), residues: 191 loop : 0.48 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP V 340 HIS 0.006 0.001 HIS V 235 PHE 0.014 0.001 PHE V 255 TYR 0.017 0.002 TYR U 463 ARG 0.008 0.001 ARG U 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9705 (m-30) cc_final: 0.9439 (t0) REVERT: G 797 MET cc_start: 0.9471 (tmm) cc_final: 0.9021 (tmm) REVERT: U 144 MET cc_start: 0.9633 (mtp) cc_final: 0.9400 (mtm) REVERT: U 182 ARG cc_start: 0.9536 (mtt180) cc_final: 0.9247 (mmt180) REVERT: U 392 MET cc_start: 0.9491 (OUTLIER) cc_final: 0.9127 (ttm) REVERT: U 396 ASN cc_start: 0.8265 (OUTLIER) cc_final: 0.7473 (t0) REVERT: U 425 GLN cc_start: 0.9166 (tt0) cc_final: 0.8838 (tt0) REVERT: U 507 MET cc_start: 0.9516 (mmm) cc_final: 0.9255 (mpp) REVERT: W 77 MET cc_start: 0.9271 (mmm) cc_final: 0.8686 (mmm) outliers start: 12 outliers final: 5 residues processed: 98 average time/residue: 0.2611 time to fit residues: 39.2718 Evaluate side-chains 78 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 329 SER Chi-restraints excluded: chain U residue 392 MET Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 120 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 144 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 128 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 116 optimal weight: 0.0030 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS U 299 GLN U 396 ASN ** X 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14395 Z= 0.145 Angle : 0.538 9.143 19814 Z= 0.289 Chirality : 0.040 0.148 2150 Planarity : 0.004 0.039 2299 Dihedral : 18.736 83.301 2583 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.22 % Favored : 97.72 % Rotamer: Outliers : 0.83 % Allowed : 8.06 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.16 (0.22), residues: 1532 helix: 0.97 (0.21), residues: 643 sheet: 1.02 (0.37), residues: 209 loop : 0.70 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 186 HIS 0.010 0.001 HIS V 235 PHE 0.013 0.001 PHE U 235 TYR 0.014 0.001 TYR G 754 ARG 0.004 0.000 ARG U 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 81 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9717 (m-30) cc_final: 0.9368 (t0) REVERT: G 797 MET cc_start: 0.9513 (tmm) cc_final: 0.9015 (tmm) REVERT: G 805 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9054 (mm-30) REVERT: U 182 ARG cc_start: 0.9569 (mtt180) cc_final: 0.9362 (mmt180) REVERT: U 396 ASN cc_start: 0.7697 (OUTLIER) cc_final: 0.7015 (t0) REVERT: U 507 MET cc_start: 0.9533 (mmm) cc_final: 0.9282 (mpp) REVERT: W 77 MET cc_start: 0.9207 (mmm) cc_final: 0.8751 (mmm) REVERT: W 148 MET cc_start: 0.8932 (tpp) cc_final: 0.8658 (tpp) REVERT: W 448 MET cc_start: 0.8548 (mmm) cc_final: 0.8328 (mmt) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 0.2653 time to fit residues: 35.7163 Evaluate side-chains 76 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 132 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 69 optimal weight: 0.2980 chunk 97 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 41 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 14395 Z= 0.460 Angle : 0.671 8.608 19814 Z= 0.350 Chirality : 0.043 0.150 2150 Planarity : 0.005 0.043 2299 Dihedral : 18.911 84.387 2583 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.94 % Favored : 97.00 % Rotamer: Outliers : 1.81 % Allowed : 7.91 % Favored : 90.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.12 (0.22), residues: 1532 helix: 1.11 (0.21), residues: 627 sheet: 0.70 (0.37), residues: 212 loop : 0.59 (0.25), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP W 449 HIS 0.008 0.002 HIS V 235 PHE 0.017 0.002 PHE U 235 TYR 0.020 0.002 TYR G 754 ARG 0.008 0.001 ARG G 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 68 time to evaluate : 1.656 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9756 (m-30) cc_final: 0.9423 (t0) REVERT: G 797 MET cc_start: 0.9467 (tmm) cc_final: 0.8960 (tmm) REVERT: G 805 GLU cc_start: 0.9426 (mt-10) cc_final: 0.9016 (mm-30) REVERT: U 216 GLN cc_start: 0.9081 (OUTLIER) cc_final: 0.8777 (pm20) REVERT: U 396 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7194 (m110) REVERT: U 442 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.9194 (mp10) REVERT: U 507 MET cc_start: 0.9523 (mmm) cc_final: 0.9227 (mmm) REVERT: W 77 MET cc_start: 0.9364 (mmm) cc_final: 0.9005 (mmm) REVERT: W 148 MET cc_start: 0.9134 (tpp) cc_final: 0.8801 (tpp) REVERT: W 411 MET cc_start: 0.9391 (ptm) cc_final: 0.9191 (ptp) REVERT: W 425 THR cc_start: 0.9371 (OUTLIER) cc_final: 0.9102 (p) REVERT: X 178 MET cc_start: 0.8451 (mmm) cc_final: 0.8209 (mmm) outliers start: 24 outliers final: 12 residues processed: 89 average time/residue: 0.2514 time to fit residues: 34.9405 Evaluate side-chains 79 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 241 LEU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 664 MET Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 42 MET Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 87 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 106 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9022 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14395 Z= 0.146 Angle : 0.535 8.557 19814 Z= 0.279 Chirality : 0.039 0.140 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.741 86.359 2583 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.35 % Favored : 97.58 % Rotamer: Outliers : 1.06 % Allowed : 8.74 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.46 (0.22), residues: 1532 helix: 1.50 (0.22), residues: 621 sheet: 0.68 (0.37), residues: 210 loop : 0.75 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.011 0.001 PHE U 235 TYR 0.013 0.001 TYR U 42 ARG 0.006 0.000 ARG U 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 71 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9721 (m-30) cc_final: 0.9372 (t0) REVERT: G 797 MET cc_start: 0.9485 (tmm) cc_final: 0.8912 (tmm) REVERT: G 798 MET cc_start: 0.9442 (mmm) cc_final: 0.9200 (mmp) REVERT: G 805 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9051 (mm-30) REVERT: U 396 ASN cc_start: 0.7346 (OUTLIER) cc_final: 0.6895 (m110) REVERT: U 664 MET cc_start: 0.8669 (ttm) cc_final: 0.8449 (ptm) REVERT: W 77 MET cc_start: 0.9202 (mmm) cc_final: 0.8945 (mmm) REVERT: W 82 MET cc_start: 0.8909 (mtm) cc_final: 0.8421 (mtp) REVERT: W 148 MET cc_start: 0.9073 (tpp) cc_final: 0.8780 (tpp) REVERT: W 197 ASP cc_start: 0.9320 (t0) cc_final: 0.9064 (p0) REVERT: W 448 MET cc_start: 0.8636 (mmm) cc_final: 0.8422 (mmt) outliers start: 14 outliers final: 9 residues processed: 83 average time/residue: 0.2440 time to fit residues: 32.1953 Evaluate side-chains 78 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14395 Z= 0.241 Angle : 0.553 7.703 19814 Z= 0.286 Chirality : 0.039 0.154 2150 Planarity : 0.004 0.047 2299 Dihedral : 18.641 83.488 2583 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.74 % Favored : 97.19 % Rotamer: Outliers : 1.43 % Allowed : 9.19 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.22), residues: 1532 helix: 1.55 (0.22), residues: 623 sheet: 0.52 (0.37), residues: 211 loop : 0.78 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 449 HIS 0.005 0.001 HIS V 235 PHE 0.011 0.001 PHE U 235 TYR 0.014 0.001 TYR G 754 ARG 0.005 0.000 ARG U 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9726 (m-30) cc_final: 0.9367 (t0) REVERT: G 797 MET cc_start: 0.9474 (tmm) cc_final: 0.8951 (tmm) REVERT: G 798 MET cc_start: 0.9432 (mmm) cc_final: 0.9177 (mmt) REVERT: G 805 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9052 (mm-30) REVERT: U 181 MET cc_start: 0.9593 (ptm) cc_final: 0.9372 (ptt) REVERT: U 216 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8740 (pm20) REVERT: U 396 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6921 (m110) REVERT: U 507 MET cc_start: 0.9392 (mpp) cc_final: 0.9117 (mpp) REVERT: V 202 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8830 (p) REVERT: W 77 MET cc_start: 0.9286 (mmm) cc_final: 0.8924 (mmm) REVERT: W 82 MET cc_start: 0.8961 (mtm) cc_final: 0.8413 (mtp) REVERT: W 148 MET cc_start: 0.9115 (tpp) cc_final: 0.8881 (tpp) REVERT: W 197 ASP cc_start: 0.9332 (t0) cc_final: 0.9075 (p0) REVERT: W 411 MET cc_start: 0.9353 (ptm) cc_final: 0.9121 (ptp) REVERT: W 425 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.9081 (p) REVERT: W 448 MET cc_start: 0.8635 (mmm) cc_final: 0.8404 (mmt) outliers start: 19 outliers final: 11 residues processed: 86 average time/residue: 0.2929 time to fit residues: 41.1111 Evaluate side-chains 82 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 24 GLN ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14395 Z= 0.221 Angle : 0.551 8.258 19814 Z= 0.284 Chirality : 0.039 0.149 2150 Planarity : 0.004 0.073 2299 Dihedral : 18.603 82.001 2583 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.58 % Allowed : 9.34 % Favored : 89.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.52 (0.22), residues: 1532 helix: 1.60 (0.22), residues: 623 sheet: 0.46 (0.37), residues: 211 loop : 0.83 (0.25), residues: 698 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 0.010 0.001 PHE U 235 TYR 0.013 0.001 TYR G 754 ARG 0.006 0.000 ARG U 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 71 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9723 (m-30) cc_final: 0.9383 (t0) REVERT: G 797 MET cc_start: 0.9468 (tmm) cc_final: 0.8950 (tmm) REVERT: G 798 MET cc_start: 0.9434 (mmm) cc_final: 0.9213 (mmt) REVERT: G 805 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9032 (mm-30) REVERT: U 216 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8725 (pm20) REVERT: U 396 ASN cc_start: 0.7281 (OUTLIER) cc_final: 0.6883 (m110) REVERT: U 507 MET cc_start: 0.9348 (mpp) cc_final: 0.9057 (mpp) REVERT: W 77 MET cc_start: 0.9246 (mmm) cc_final: 0.8900 (mmm) REVERT: W 82 MET cc_start: 0.9038 (mtm) cc_final: 0.8515 (mtm) REVERT: W 197 ASP cc_start: 0.9321 (t0) cc_final: 0.9051 (p0) REVERT: W 411 MET cc_start: 0.9338 (ptm) cc_final: 0.9095 (ptp) REVERT: W 425 THR cc_start: 0.9301 (OUTLIER) cc_final: 0.9082 (p) REVERT: W 448 MET cc_start: 0.8524 (mmm) cc_final: 0.8305 (mmt) outliers start: 21 outliers final: 15 residues processed: 89 average time/residue: 0.2224 time to fit residues: 31.9565 Evaluate side-chains 84 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 66 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 146 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9074 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14395 Z= 0.341 Angle : 0.613 10.296 19814 Z= 0.315 Chirality : 0.040 0.160 2150 Planarity : 0.004 0.050 2299 Dihedral : 18.732 79.974 2583 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.34 % Rotamer: Outliers : 1.66 % Allowed : 10.25 % Favored : 88.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.22), residues: 1532 helix: 1.47 (0.22), residues: 622 sheet: 0.39 (0.36), residues: 211 loop : 0.78 (0.25), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP W 93 HIS 0.006 0.001 HIS V 235 PHE 0.013 0.001 PHE U 235 TYR 0.016 0.001 TYR G 754 ARG 0.006 0.000 ARG U 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 62 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9734 (m-30) cc_final: 0.9363 (t0) REVERT: G 797 MET cc_start: 0.9488 (tmm) cc_final: 0.9030 (tmm) REVERT: G 798 MET cc_start: 0.9435 (mmm) cc_final: 0.9183 (mmt) REVERT: G 805 GLU cc_start: 0.9420 (mt-10) cc_final: 0.9020 (mm-30) REVERT: U 216 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: U 396 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6859 (m110) REVERT: U 460 MET cc_start: 0.9585 (mtm) cc_final: 0.9266 (mpp) REVERT: U 507 MET cc_start: 0.9314 (mpp) cc_final: 0.8934 (mtm) REVERT: V 202 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8846 (p) REVERT: W 77 MET cc_start: 0.9231 (mmm) cc_final: 0.8855 (mmm) REVERT: W 82 MET cc_start: 0.9080 (mtm) cc_final: 0.8443 (mtp) REVERT: W 411 MET cc_start: 0.9344 (ptm) cc_final: 0.9101 (ptp) REVERT: W 425 THR cc_start: 0.9369 (OUTLIER) cc_final: 0.9124 (p) REVERT: W 448 MET cc_start: 0.8613 (mmm) cc_final: 0.8388 (mmt) outliers start: 22 outliers final: 17 residues processed: 83 average time/residue: 0.2236 time to fit residues: 30.2657 Evaluate side-chains 82 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 61 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 396 ASN Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 402 ASP Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 146 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 93 optimal weight: 4.9990 chunk 151 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14395 Z= 0.212 Angle : 0.547 7.865 19814 Z= 0.283 Chirality : 0.039 0.152 2150 Planarity : 0.004 0.051 2299 Dihedral : 18.660 79.767 2583 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.00 % Favored : 96.93 % Rotamer: Outliers : 1.66 % Allowed : 10.17 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1532 helix: 1.62 (0.22), residues: 623 sheet: 0.23 (0.35), residues: 223 loop : 0.87 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.010 0.001 PHE U 388 TYR 0.013 0.001 TYR G 754 ARG 0.005 0.000 ARG W 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 67 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9720 (m-30) cc_final: 0.9378 (t0) REVERT: G 797 MET cc_start: 0.9485 (tmm) cc_final: 0.9013 (tmm) REVERT: G 798 MET cc_start: 0.9414 (mmm) cc_final: 0.9202 (mmt) REVERT: G 805 GLU cc_start: 0.9456 (mt-10) cc_final: 0.9188 (mp0) REVERT: U 216 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8795 (pm20) REVERT: U 460 MET cc_start: 0.9596 (mtm) cc_final: 0.9261 (mpp) REVERT: V 202 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8860 (p) REVERT: W 77 MET cc_start: 0.9171 (mmm) cc_final: 0.8828 (mmm) REVERT: W 82 MET cc_start: 0.9030 (mtm) cc_final: 0.8475 (mtp) REVERT: W 411 MET cc_start: 0.9332 (ptm) cc_final: 0.9079 (ptp) REVERT: W 425 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9114 (p) outliers start: 22 outliers final: 16 residues processed: 87 average time/residue: 0.2297 time to fit residues: 32.2377 Evaluate side-chains 85 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 730 ILE Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 216 GLN Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 364 VAL Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain U residue 441 ASN Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 189 LEU Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 425 THR Chi-restraints excluded: chain W residue 438 ILE Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 92 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 104 optimal weight: 0.8980 chunk 158 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 13 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 396 ASN V 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9016 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14395 Z= 0.139 Angle : 0.531 8.236 19814 Z= 0.274 Chirality : 0.039 0.309 2150 Planarity : 0.004 0.049 2299 Dihedral : 18.421 78.180 2581 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 1.13 % Allowed : 10.55 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1532 helix: 1.66 (0.22), residues: 626 sheet: 0.28 (0.35), residues: 222 loop : 0.90 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.010 0.001 PHE V 375 TYR 0.011 0.001 TYR V 306 ARG 0.003 0.000 ARG U 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 2.790 Fit side-chains revert: symmetry clash REVERT: G 732 ASP cc_start: 0.9702 (m-30) cc_final: 0.9295 (t0) REVERT: G 797 MET cc_start: 0.9478 (tmm) cc_final: 0.9011 (tmm) REVERT: G 805 GLU cc_start: 0.9428 (mt-10) cc_final: 0.9120 (mm-30) REVERT: U 460 MET cc_start: 0.9573 (mtm) cc_final: 0.9357 (mpp) REVERT: V 202 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8929 (p) REVERT: W 77 MET cc_start: 0.9120 (mmm) cc_final: 0.8867 (mmm) REVERT: W 82 MET cc_start: 0.8884 (mtm) cc_final: 0.8415 (mtt) REVERT: W 411 MET cc_start: 0.9334 (ptm) cc_final: 0.9082 (ptp) outliers start: 15 outliers final: 12 residues processed: 89 average time/residue: 0.2449 time to fit residues: 34.3006 Evaluate side-chains 82 residues out of total 1327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 771 GLU Chi-restraints excluded: chain U residue 298 LYS Chi-restraints excluded: chain U residue 401 ASP Chi-restraints excluded: chain U residue 442 GLN Chi-restraints excluded: chain U residue 665 VAL Chi-restraints excluded: chain V residue 66 THR Chi-restraints excluded: chain V residue 132 PHE Chi-restraints excluded: chain V residue 134 VAL Chi-restraints excluded: chain V residue 202 THR Chi-restraints excluded: chain W residue 116 VAL Chi-restraints excluded: chain W residue 265 CYS Chi-restraints excluded: chain W residue 402 ASP Chi-restraints excluded: chain X residue 158 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 52 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** V 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 446 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.054529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.037382 restraints weight = 62293.764| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 3.41 r_work: 0.2618 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14395 Z= 0.154 Angle : 0.542 9.642 19814 Z= 0.275 Chirality : 0.039 0.280 2150 Planarity : 0.004 0.045 2299 Dihedral : 18.358 76.692 2581 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.68 % Favored : 97.26 % Rotamer: Outliers : 1.13 % Allowed : 10.70 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.61 (0.22), residues: 1532 helix: 1.66 (0.22), residues: 626 sheet: 0.33 (0.35), residues: 222 loop : 0.98 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 340 HIS 0.005 0.001 HIS V 235 PHE 0.008 0.001 PHE V 375 TYR 0.011 0.001 TYR G 754 ARG 0.005 0.000 ARG W 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2244.32 seconds wall clock time: 42 minutes 20.58 seconds (2540.58 seconds total)