Starting phenix.real_space_refine on Sat Aug 23 23:54:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8x_39850/08_2025/8z8x_39850.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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 Anisotropic ADP refinement not supported. Converting 1345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 36 5.49 5 S 82 5.16 5 C 9238 2.51 5 N 2559 2.21 5 O 2853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14768 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5014 Classifications: {'peptide': 620} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 588} Chain: "B" Number of atoms: 5710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5710 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 39, 'TRANS': 670} Chain: "C" Number of atoms: 3273 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 400, 3253 Classifications: {'peptide': 400} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 3317 Chain: "D" Number of atoms: 388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 388 Classifications: {'RNA': 18} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 10, 'rna3p_pyr': 5} Link IDs: {'rna2p': 3, 'rna3p': 14} Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'RNA': 17} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 2, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 9} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AILE C 330 " occ=0.68 ... (14 atoms not shown) pdb=" CD1BILE C 330 " occ=0.32 residue: pdb=" N ASER C 336 " occ=0.72 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.28 residue: pdb=" N ASER C 384 " occ=0.56 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.44 Time building chain proxies: 4.52, per 1000 atoms: 0.31 Number of scatterers: 14768 At special positions: 0 Unit cell: (108.714, 105.12, 138.363, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 36 15.00 O 2853 8.00 N 2559 7.00 C 9238 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 755.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3308 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 21 sheets defined 46.5% alpha, 11.8% beta 8 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 Processing helix chain 'A' and resid 27 through 45 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 155 removed outlier: 3.529A pdb=" N TRP A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 removed outlier: 3.830A pdb=" N VAL A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 removed outlier: 3.515A pdb=" N LEU A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 246 through 257 removed outlier: 3.722A pdb=" N TRP A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.542A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 302 Processing helix chain 'A' and resid 304 through 316 removed outlier: 3.693A pdb=" N GLU A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 344 removed outlier: 4.354A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.368A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 400 removed outlier: 3.686A pdb=" N THR A 398 " --> pdb=" O ALA A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 removed outlier: 3.651A pdb=" N ASN A 493 " --> pdb=" O TYR A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 Processing helix chain 'A' and resid 498 through 517 Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.465A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.502A pdb=" N GLU A 599 " --> pdb=" O ASP A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'B' and resid 11 through 20 removed outlier: 4.310A pdb=" N GLU B 17 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 20 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 47 Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 110 through 113 Processing helix chain 'B' and resid 114 through 121 removed outlier: 3.552A pdb=" N GLY B 121 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.737A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 250 through 266 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.873A pdb=" N GLU B 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 removed outlier: 3.933A pdb=" N LYS B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 326 removed outlier: 3.920A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 336 removed outlier: 3.682A pdb=" N MET B 332 " --> pdb=" O PRO B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 Processing helix chain 'B' and resid 374 through 378 removed outlier: 3.701A pdb=" N VAL B 377 " --> pdb=" O ASP B 374 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG B 378 " --> pdb=" O ASP B 375 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 374 through 378' Processing helix chain 'B' and resid 397 through 409 Processing helix chain 'B' and resid 432 through 450 removed outlier: 3.568A pdb=" N VAL B 450 " --> pdb=" O THR B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.904A pdb=" N CYS B 459 " --> pdb=" O PRO B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 490 Proline residue: B 488 - end of helix Processing helix chain 'B' and resid 496 through 514 Processing helix chain 'B' and resid 518 through 537 Processing helix chain 'B' and resid 543 through 551 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 572 removed outlier: 4.005A pdb=" N MET B 572 " --> pdb=" O PHE B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 587 through 595 removed outlier: 3.599A pdb=" N ARG B 593 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 645 No H-bonds generated for 'chain 'B' and resid 643 through 645' Processing helix chain 'B' and resid 646 through 662 removed outlier: 4.205A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 695 Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 33 through 36 removed outlier: 6.284A pdb=" N THR C 36 " --> pdb=" O LYS C 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 33 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 52 through 55 removed outlier: 3.840A pdb=" N MET C 55 " --> pdb=" O ALA C 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 52 through 55' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 102 through 110 removed outlier: 3.871A pdb=" N LYS C 109 " --> pdb=" O ASP C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 208 through 221 removed outlier: 3.932A pdb=" N HIS C 214 " --> pdb=" O GLU C 210 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 245 removed outlier: 3.755A pdb=" N CYS C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 413 removed outlier: 3.591A pdb=" N LEU C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 Processing helix chain 'C' and resid 447 through 455 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.670A pdb=" N PHE A 119 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 210 through 211 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 7.674A pdb=" N TRP A 426 " --> pdb=" O ILE A 450 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU A 475 " --> pdb=" O MET A 451 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 240 through 242 removed outlier: 5.566A pdb=" N PHE A 425 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR A 416 " --> pdb=" O PHE A 425 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLY A 427 " --> pdb=" O ILE A 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.954A pdb=" N LEU B 360 " --> pdb=" O LYS B 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 527 through 530 Processing sheet with id=AA9, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AB1, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB2, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AB3, first strand: chain 'B' and resid 188 through 191 removed outlier: 4.894A pdb=" N GLN B 188 " --> pdb=" O VAL B 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.450A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 467 through 470 removed outlier: 4.418A pdb=" N PHE B 474 " --> pdb=" O VAL B 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 608 through 611 removed outlier: 3.701A pdb=" N MET B 609 " --> pdb=" O MET B 621 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 67 through 69 removed outlier: 5.041A pdb=" N ARG C 98 " --> pdb=" O ASP C 86 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AB9, first strand: chain 'C' and resid 141 through 143 Processing sheet with id=AC1, first strand: chain 'C' and resid 149 through 154 Processing sheet with id=AC2, first strand: chain 'C' and resid 339 through 340 removed outlier: 3.539A pdb=" N ASN C 339 " --> pdb=" O LYS C 371 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS C 394 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU C 392 " --> pdb=" O ASER C 384 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THR C 386 " --> pdb=" O ILE C 390 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ILE C 390 " --> pdb=" O THR C 386 " (cutoff:3.500A) removed outlier: 8.684A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 345 through 352 625 hydrogen bonds defined for protein. 1723 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 2.97 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4723 1.34 - 1.47: 3681 1.47 - 1.60: 6603 1.60 - 1.72: 36 1.72 - 1.85: 135 Bond restraints: 15178 Sorted by residual: bond pdb=" N GLY C 455 " pdb=" CA GLY C 455 " ideal model delta sigma weight residual 1.449 1.471 -0.021 1.45e-02 4.76e+03 2.20e+00 bond pdb=" C3' A E 2 " pdb=" O3' A E 2 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.34e+00 bond pdb=" CG1 ILE A 393 " pdb=" CD1 ILE A 393 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.27e+00 bond pdb=" CB PRO B 644 " pdb=" CG PRO B 644 " ideal model delta sigma weight residual 1.492 1.545 -0.053 5.00e-02 4.00e+02 1.12e+00 bond pdb=" CB GLU B 263 " pdb=" CG GLU B 263 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.10e+00 ... (remaining 15173 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 20288 1.88 - 3.75: 386 3.75 - 5.63: 38 5.63 - 7.51: 8 7.51 - 9.38: 2 Bond angle restraints: 20722 Sorted by residual: angle pdb=" C ARG C 62 " pdb=" N LYS C 63 " pdb=" CA LYS C 63 " ideal model delta sigma weight residual 120.49 129.87 -9.38 1.42e+00 4.96e-01 4.37e+01 angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 113.53 107.59 5.94 9.80e-01 1.04e+00 3.68e+01 angle pdb=" C VAL C 102 " pdb=" N VAL C 103 " pdb=" CA VAL C 103 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sigma weight residual 120.20 125.12 -4.92 1.50e+00 4.44e-01 1.07e+01 angle pdb=" N VAL A 597 " pdb=" CA VAL A 597 " pdb=" C VAL A 597 " ideal model delta sigma weight residual 111.81 109.14 2.67 8.60e-01 1.35e+00 9.67e+00 ... (remaining 20717 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.81: 9066 33.81 - 67.61: 229 67.61 - 101.42: 26 101.42 - 135.22: 1 135.22 - 169.03: 2 Dihedral angle restraints: 9324 sinusoidal: 4228 harmonic: 5096 Sorted by residual: dihedral pdb=" CA GLU A 456 " pdb=" C GLU A 456 " pdb=" N GLU A 457 " pdb=" CA GLU A 457 " ideal model delta harmonic sigma weight residual 180.00 158.83 21.17 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" C4' A E 2 " pdb=" C3' A E 2 " pdb=" O3' A E 2 " pdb=" P C E 3 " ideal model delta sinusoidal sigma weight residual -110.00 59.03 -169.03 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' C E 7 " pdb=" C3' C E 7 " pdb=" O3' C E 7 " pdb=" P U E 8 " ideal model delta sinusoidal sigma weight residual 220.00 69.54 150.46 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 9321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1611 0.037 - 0.074: 496 0.074 - 0.111: 167 0.111 - 0.148: 37 0.148 - 0.185: 2 Chirality restraints: 2313 Sorted by residual: chirality pdb=" C3' A E 2 " pdb=" C4' A E 2 " pdb=" O3' A E 2 " pdb=" C2' A E 2 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.18 2.00e-01 2.50e+01 8.55e-01 chirality pdb=" CA GLU B 263 " pdb=" N GLU B 263 " pdb=" C GLU B 263 " pdb=" CB GLU B 263 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA ILE C 395 " pdb=" N ILE C 395 " pdb=" C ILE C 395 " pdb=" CB ILE C 395 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.31e-01 ... (remaining 2310 not shown) Planarity restraints: 2532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 643 " 0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 644 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 644 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 644 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 463 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 464 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 464 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 464 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 354 " -0.040 5.00e-02 4.00e+02 6.10e-02 5.94e+00 pdb=" N PRO C 355 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 355 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C 355 " -0.034 5.00e-02 4.00e+02 ... (remaining 2529 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 427 2.70 - 3.25: 14967 3.25 - 3.80: 23895 3.80 - 4.35: 32670 4.35 - 4.90: 52933 Nonbonded interactions: 124892 Sorted by model distance: nonbonded pdb=" OE1 GLU A 126 " pdb=" OG SER A 128 " model vdw 2.148 3.040 nonbonded pdb=" OG1 THR C 229 " pdb=" O VAL C 231 " model vdw 2.158 3.040 nonbonded pdb=" OD2 ASP B 500 " pdb=" OH TYR B 537 " model vdw 2.184 3.040 nonbonded pdb=" OE1 GLU C 10 " pdb=" OG1 THR C 12 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASN B 132 " pdb=" ND2 ASN B 227 " model vdw 2.264 3.120 ... (remaining 124887 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.28 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: 0.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.790 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 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 : 0.003 0.053 15178 Z= 0.124 Angle : 0.610 9.385 20722 Z= 0.328 Chirality : 0.041 0.185 2313 Planarity : 0.006 0.083 2532 Dihedral : 14.960 169.029 6016 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1729 helix: 0.66 (0.20), residues: 715 sheet: -0.83 (0.37), residues: 207 loop : -1.33 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 264 TYR 0.010 0.001 TYR B 533 PHE 0.024 0.002 PHE C 335 TRP 0.016 0.001 TRP B 185 HIS 0.003 0.001 HIS C 242 Details of bonding type rmsd covalent geometry : bond 0.00268 (15178) covalent geometry : angle 0.61026 (20722) hydrogen bonds : bond 0.18644 ( 642) hydrogen bonds : angle 7.08157 ( 1765) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.8841 (m-30) cc_final: 0.8636 (m-30) REVERT: A 150 GLU cc_start: 0.8924 (mp0) cc_final: 0.8692 (pm20) REVERT: B 259 ASP cc_start: 0.8364 (m-30) cc_final: 0.8147 (m-30) REVERT: C 380 GLN cc_start: 0.8244 (pm20) cc_final: 0.7997 (pm20) REVERT: C 383 PHE cc_start: 0.8549 (p90) cc_final: 0.8223 (p90) REVERT: C 410 ILE cc_start: 0.8952 (mt) cc_final: 0.8511 (mt) REVERT: C 421 PHE cc_start: 0.7675 (m-80) cc_final: 0.7413 (m-80) REVERT: C 433 ARG cc_start: 0.8001 (tpp-160) cc_final: 0.7538 (tpp80) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1571 time to fit residues: 53.7179 Evaluate side-chains 199 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 358 ASN ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 123 GLN B 148 GLN C 233 HIS C 254 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.122055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.089116 restraints weight = 58008.725| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.55 r_work: 0.2877 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15178 Z= 0.131 Angle : 0.594 6.834 20722 Z= 0.305 Chirality : 0.042 0.170 2313 Planarity : 0.005 0.062 2532 Dihedral : 13.470 164.157 2463 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 7.24 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.20), residues: 1729 helix: 0.96 (0.20), residues: 724 sheet: -0.90 (0.36), residues: 215 loop : -1.24 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 65 TYR 0.035 0.001 TYR C 382 PHE 0.029 0.002 PHE C 41 TRP 0.011 0.001 TRP A 253 HIS 0.011 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00298 (15178) covalent geometry : angle 0.59418 (20722) hydrogen bonds : bond 0.04010 ( 642) hydrogen bonds : angle 5.05623 ( 1765) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 212 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: A 595 ASP cc_start: 0.8358 (m-30) cc_final: 0.8090 (m-30) REVERT: B 151 ARG cc_start: 0.8780 (mtm-85) cc_final: 0.8456 (mmt90) REVERT: B 259 ASP cc_start: 0.8895 (m-30) cc_final: 0.8589 (m-30) REVERT: B 393 MET cc_start: 0.8253 (ppp) cc_final: 0.8017 (ptm) REVERT: B 473 LYS cc_start: 0.8241 (mmmt) cc_final: 0.7786 (mtmm) REVERT: C 110 TYR cc_start: 0.8441 (m-80) cc_final: 0.8174 (m-80) REVERT: C 346 GLU cc_start: 0.9095 (tt0) cc_final: 0.8350 (tm-30) REVERT: C 380 GLN cc_start: 0.8479 (pm20) cc_final: 0.8194 (pm20) REVERT: C 423 GLN cc_start: 0.8153 (pm20) cc_final: 0.7895 (pm20) REVERT: C 433 ARG cc_start: 0.8085 (tpp-160) cc_final: 0.7610 (tpp80) outliers start: 17 outliers final: 9 residues processed: 220 average time/residue: 0.1587 time to fit residues: 48.7318 Evaluate side-chains 205 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 196 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 642 ASP Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 156 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 227 ASN C 39 ASN ** C 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 254 ASN C 375 GLN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.116523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.080585 restraints weight = 66156.590| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 3.72 r_work: 0.2750 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2761 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15178 Z= 0.228 Angle : 0.628 7.511 20722 Z= 0.324 Chirality : 0.045 0.195 2313 Planarity : 0.005 0.058 2532 Dihedral : 13.443 164.664 2463 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.28 % Allowed : 9.55 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1729 helix: 0.86 (0.20), residues: 730 sheet: -1.02 (0.34), residues: 227 loop : -1.35 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 701 TYR 0.021 0.002 TYR B 537 PHE 0.026 0.002 PHE C 41 TRP 0.013 0.001 TRP C 470 HIS 0.012 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00539 (15178) covalent geometry : angle 0.62845 (20722) hydrogen bonds : bond 0.04391 ( 642) hydrogen bonds : angle 4.86737 ( 1765) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 0.363 Fit side-chains REVERT: A 159 GLN cc_start: 0.9006 (tp40) cc_final: 0.8693 (tp-100) REVERT: A 569 MET cc_start: 0.9168 (tpp) cc_final: 0.8927 (tpt) REVERT: A 607 VAL cc_start: 0.9317 (OUTLIER) cc_final: 0.9094 (t) REVERT: B 185 TRP cc_start: 0.9027 (p-90) cc_final: 0.8812 (p-90) REVERT: B 255 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8584 (tttp) REVERT: B 259 ASP cc_start: 0.8872 (m-30) cc_final: 0.8523 (m-30) REVERT: C 110 TYR cc_start: 0.8544 (m-80) cc_final: 0.8327 (m-80) REVERT: C 346 GLU cc_start: 0.9120 (tt0) cc_final: 0.8402 (tm-30) REVERT: C 380 GLN cc_start: 0.8514 (pm20) cc_final: 0.8194 (pm20) REVERT: C 416 PHE cc_start: 0.8102 (m-80) cc_final: 0.7729 (m-10) REVERT: C 423 GLN cc_start: 0.8185 (pm20) cc_final: 0.7905 (pm20) REVERT: C 433 ARG cc_start: 0.8072 (tpp-160) cc_final: 0.7606 (tpp80) outliers start: 20 outliers final: 11 residues processed: 207 average time/residue: 0.1450 time to fit residues: 42.5153 Evaluate side-chains 197 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN C 233 HIS C 254 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.117852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.083474 restraints weight = 48529.500| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.36 r_work: 0.2803 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15178 Z= 0.153 Angle : 0.575 7.503 20722 Z= 0.294 Chirality : 0.042 0.184 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.366 163.745 2463 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.73 % Allowed : 10.32 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.20), residues: 1729 helix: 1.01 (0.20), residues: 725 sheet: -0.99 (0.34), residues: 228 loop : -1.26 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 701 TYR 0.015 0.001 TYR B 533 PHE 0.026 0.002 PHE C 41 TRP 0.013 0.001 TRP A 253 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00356 (15178) covalent geometry : angle 0.57495 (20722) hydrogen bonds : bond 0.03769 ( 642) hydrogen bonds : angle 4.68596 ( 1765) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 0.445 Fit side-chains REVERT: A 159 GLN cc_start: 0.8989 (tp40) cc_final: 0.8657 (tp-100) REVERT: A 569 MET cc_start: 0.9118 (tpp) cc_final: 0.8885 (tpt) REVERT: A 607 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9082 (t) REVERT: B 186 ASP cc_start: 0.8851 (t70) cc_final: 0.8520 (t0) REVERT: B 255 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8519 (tttp) REVERT: B 259 ASP cc_start: 0.8828 (m-30) cc_final: 0.8533 (m-30) REVERT: B 473 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7785 (mtmm) REVERT: C 110 TYR cc_start: 0.8499 (m-80) cc_final: 0.8264 (m-80) REVERT: C 346 GLU cc_start: 0.9092 (tt0) cc_final: 0.8453 (tm-30) REVERT: C 380 GLN cc_start: 0.8511 (pm20) cc_final: 0.8172 (pm20) REVERT: C 416 PHE cc_start: 0.8155 (m-80) cc_final: 0.7772 (m-10) REVERT: C 423 GLN cc_start: 0.8253 (pm20) cc_final: 0.7967 (pm20) REVERT: C 433 ARG cc_start: 0.8067 (tpp-160) cc_final: 0.7599 (tpp80) outliers start: 27 outliers final: 19 residues processed: 214 average time/residue: 0.1483 time to fit residues: 44.8784 Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Chi-restraints excluded: chain C residue 393 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 97 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 173 optimal weight: 7.9990 chunk 149 optimal weight: 1.9990 chunk 108 optimal weight: 8.9990 chunk 11 optimal weight: 9.9990 chunk 161 optimal weight: 40.0000 chunk 33 optimal weight: 1.9990 chunk 110 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 650 ASN C 233 HIS C 254 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087139 restraints weight = 61819.072| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.53 r_work: 0.2843 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15178 Z= 0.113 Angle : 0.546 7.143 20722 Z= 0.279 Chirality : 0.041 0.176 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.264 163.044 2463 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.41 % Allowed : 11.15 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1729 helix: 1.11 (0.20), residues: 723 sheet: -0.95 (0.34), residues: 228 loop : -1.18 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 708 TYR 0.015 0.001 TYR B 533 PHE 0.025 0.001 PHE C 41 TRP 0.012 0.001 TRP A 253 HIS 0.008 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00252 (15178) covalent geometry : angle 0.54644 (20722) hydrogen bonds : bond 0.03413 ( 642) hydrogen bonds : angle 4.51513 ( 1765) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 GLN cc_start: 0.8939 (tp40) cc_final: 0.8608 (tp-100) REVERT: A 607 VAL cc_start: 0.9281 (OUTLIER) cc_final: 0.9073 (t) REVERT: B 259 ASP cc_start: 0.8775 (m-30) cc_final: 0.8568 (m-30) REVERT: B 473 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7888 (mtmm) REVERT: C 29 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8860 (ttpp) REVERT: C 110 TYR cc_start: 0.8474 (m-80) cc_final: 0.8248 (m-80) REVERT: C 160 GLU cc_start: 0.8216 (tp30) cc_final: 0.7996 (tp30) REVERT: C 346 GLU cc_start: 0.9076 (tt0) cc_final: 0.8479 (tm-30) REVERT: C 380 GLN cc_start: 0.8532 (pm20) cc_final: 0.8169 (pm20) REVERT: C 423 GLN cc_start: 0.8372 (pm20) cc_final: 0.8072 (pm20) REVERT: C 433 ARG cc_start: 0.8094 (tpp-160) cc_final: 0.7627 (tpp80) outliers start: 22 outliers final: 14 residues processed: 219 average time/residue: 0.1536 time to fit residues: 47.9276 Evaluate side-chains 205 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 190 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 68 optimal weight: 8.9990 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 chunk 127 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.116606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.081682 restraints weight = 77421.777| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.86 r_work: 0.2741 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 15178 Z= 0.259 Angle : 0.637 7.582 20722 Z= 0.328 Chirality : 0.045 0.200 2313 Planarity : 0.005 0.054 2532 Dihedral : 13.406 164.327 2463 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.86 % Allowed : 11.15 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.20), residues: 1729 helix: 0.97 (0.20), residues: 726 sheet: -0.95 (0.34), residues: 227 loop : -1.26 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 708 TYR 0.018 0.002 TYR B 537 PHE 0.027 0.002 PHE C 41 TRP 0.013 0.001 TRP C 470 HIS 0.007 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00614 (15178) covalent geometry : angle 0.63692 (20722) hydrogen bonds : bond 0.04181 ( 642) hydrogen bonds : angle 4.67325 ( 1765) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 194 time to evaluate : 0.614 Fit side-chains REVERT: A 159 GLN cc_start: 0.8978 (tp40) cc_final: 0.8638 (tp-100) REVERT: A 569 MET cc_start: 0.9210 (tpp) cc_final: 0.8983 (tpt) REVERT: A 607 VAL cc_start: 0.9311 (OUTLIER) cc_final: 0.9062 (t) REVERT: B 186 ASP cc_start: 0.8911 (t70) cc_final: 0.8499 (t0) REVERT: B 255 LYS cc_start: 0.9112 (ttmm) cc_final: 0.8590 (tttp) REVERT: B 259 ASP cc_start: 0.8859 (m-30) cc_final: 0.8639 (m-30) REVERT: B 473 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7927 (mtmm) REVERT: C 29 LYS cc_start: 0.9210 (mtmt) cc_final: 0.8865 (ttpp) REVERT: C 110 TYR cc_start: 0.8609 (m-80) cc_final: 0.8373 (m-80) REVERT: C 346 GLU cc_start: 0.9063 (tt0) cc_final: 0.8507 (tm-30) REVERT: C 380 GLN cc_start: 0.8558 (pm20) cc_final: 0.8197 (pm20) REVERT: C 423 GLN cc_start: 0.8419 (pm20) cc_final: 0.8077 (pm20) REVERT: C 437 ASP cc_start: 0.8789 (m-30) cc_final: 0.8493 (m-30) outliers start: 29 outliers final: 19 residues processed: 214 average time/residue: 0.1567 time to fit residues: 46.9623 Evaluate side-chains 204 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 184 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 601 VAL Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 376 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 27 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.118477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.084146 restraints weight = 56141.570| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.38 r_work: 0.2796 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15178 Z= 0.167 Angle : 0.602 9.369 20722 Z= 0.307 Chirality : 0.043 0.257 2313 Planarity : 0.005 0.053 2532 Dihedral : 13.349 163.795 2463 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.60 % Allowed : 12.12 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1729 helix: 1.02 (0.20), residues: 726 sheet: -0.87 (0.34), residues: 227 loop : -1.21 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 708 TYR 0.016 0.001 TYR B 533 PHE 0.026 0.002 PHE C 41 TRP 0.011 0.001 TRP A 253 HIS 0.006 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00393 (15178) covalent geometry : angle 0.60229 (20722) hydrogen bonds : bond 0.03744 ( 642) hydrogen bonds : angle 4.58410 ( 1765) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 192 time to evaluate : 0.638 Fit side-chains REVERT: A 159 GLN cc_start: 0.8951 (tp40) cc_final: 0.8625 (tp-100) REVERT: A 607 VAL cc_start: 0.9302 (OUTLIER) cc_final: 0.9067 (t) REVERT: B 120 LYS cc_start: 0.9222 (mtmt) cc_final: 0.9006 (mtmt) REVERT: B 167 ASP cc_start: 0.8212 (m-30) cc_final: 0.7949 (m-30) REVERT: B 248 MET cc_start: 0.9165 (tpp) cc_final: 0.8919 (tpt) REVERT: B 255 LYS cc_start: 0.9075 (ttmm) cc_final: 0.8554 (tttp) REVERT: B 259 ASP cc_start: 0.8816 (m-30) cc_final: 0.8572 (m-30) REVERT: B 473 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7883 (mtmm) REVERT: B 701 ARG cc_start: 0.9234 (mtp85) cc_final: 0.9023 (mtp85) REVERT: C 29 LYS cc_start: 0.9190 (mtmt) cc_final: 0.8850 (ttpp) REVERT: C 110 TYR cc_start: 0.8563 (m-80) cc_final: 0.8344 (m-80) REVERT: C 346 GLU cc_start: 0.9044 (tt0) cc_final: 0.8503 (tm-30) REVERT: C 380 GLN cc_start: 0.8566 (pm20) cc_final: 0.8194 (pm20) REVERT: C 423 GLN cc_start: 0.8428 (pm20) cc_final: 0.8092 (pm20) REVERT: C 433 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7894 (ptm160) outliers start: 25 outliers final: 20 residues processed: 209 average time/residue: 0.1623 time to fit residues: 47.1566 Evaluate side-chains 206 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 28 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 139 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 153 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 156 optimal weight: 10.0000 chunk 77 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 376 ASN ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086870 restraints weight = 66759.280| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.68 r_work: 0.2836 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15178 Z= 0.111 Angle : 0.576 12.410 20722 Z= 0.291 Chirality : 0.041 0.209 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.238 162.816 2463 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.28 % Allowed : 12.95 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1729 helix: 1.16 (0.20), residues: 718 sheet: -0.82 (0.34), residues: 225 loop : -1.18 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 708 TYR 0.016 0.001 TYR B 533 PHE 0.027 0.001 PHE C 383 TRP 0.012 0.001 TRP A 253 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00251 (15178) covalent geometry : angle 0.57635 (20722) hydrogen bonds : bond 0.03295 ( 642) hydrogen bonds : angle 4.43762 ( 1765) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 159 GLN cc_start: 0.8956 (tp40) cc_final: 0.8621 (tp-100) REVERT: A 607 VAL cc_start: 0.9275 (OUTLIER) cc_final: 0.9056 (t) REVERT: B 248 MET cc_start: 0.9071 (tpp) cc_final: 0.8848 (tpt) REVERT: B 259 ASP cc_start: 0.8847 (m-30) cc_final: 0.8629 (m-30) REVERT: B 473 LYS cc_start: 0.8333 (mmmt) cc_final: 0.7905 (mtmm) REVERT: C 29 LYS cc_start: 0.9201 (mtmt) cc_final: 0.8867 (ttpp) REVERT: C 110 TYR cc_start: 0.8531 (m-80) cc_final: 0.8318 (m-80) REVERT: C 346 GLU cc_start: 0.9045 (tt0) cc_final: 0.8509 (tm-30) REVERT: C 380 GLN cc_start: 0.8564 (pm20) cc_final: 0.8189 (pm20) REVERT: C 423 GLN cc_start: 0.8358 (pm20) cc_final: 0.8048 (pm20) outliers start: 20 outliers final: 17 residues processed: 209 average time/residue: 0.1578 time to fit residues: 46.1645 Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 190 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 40 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 108 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 97 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 173 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 171 optimal weight: 0.0370 chunk 146 optimal weight: 9.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 663 ASN C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.118332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.084623 restraints weight = 56712.910| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.76 r_work: 0.2789 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15178 Z= 0.138 Angle : 0.583 11.968 20722 Z= 0.295 Chirality : 0.042 0.173 2313 Planarity : 0.005 0.055 2532 Dihedral : 13.246 163.039 2463 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 1.60 % Allowed : 12.88 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1729 helix: 1.16 (0.20), residues: 724 sheet: -0.79 (0.34), residues: 225 loop : -1.15 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 708 TYR 0.024 0.001 TYR B 632 PHE 0.025 0.002 PHE C 383 TRP 0.011 0.001 TRP A 253 HIS 0.010 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00323 (15178) covalent geometry : angle 0.58335 (20722) hydrogen bonds : bond 0.03427 ( 642) hydrogen bonds : angle 4.44922 ( 1765) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 196 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8661 (p0) cc_final: 0.8404 (p0) REVERT: A 159 GLN cc_start: 0.9028 (tp40) cc_final: 0.8673 (tp-100) REVERT: A 607 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9086 (t) REVERT: B 186 ASP cc_start: 0.8880 (t70) cc_final: 0.8557 (t0) REVERT: B 259 ASP cc_start: 0.8942 (m-30) cc_final: 0.8676 (m-30) REVERT: B 473 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7792 (mtmm) REVERT: C 29 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8844 (ttpp) REVERT: C 95 LYS cc_start: 0.8478 (mtmm) cc_final: 0.7890 (ptmm) REVERT: C 110 TYR cc_start: 0.8591 (m-80) cc_final: 0.8334 (m-80) REVERT: C 346 GLU cc_start: 0.9073 (tt0) cc_final: 0.8466 (tm-30) REVERT: C 380 GLN cc_start: 0.8562 (pm20) cc_final: 0.8195 (pm20) REVERT: C 423 GLN cc_start: 0.8282 (pm20) cc_final: 0.7973 (pm20) outliers start: 25 outliers final: 19 residues processed: 211 average time/residue: 0.1549 time to fit residues: 45.6938 Evaluate side-chains 208 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 663 ASN Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 13 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 19 optimal weight: 0.5980 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 chunk 128 optimal weight: 0.0970 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 155 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.120732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.085278 restraints weight = 67967.541| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.80 r_work: 0.2836 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2843 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2843 r_free = 0.2843 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2843 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15178 Z= 0.105 Angle : 0.575 12.510 20722 Z= 0.288 Chirality : 0.041 0.173 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.192 162.377 2463 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.47 % Allowed : 12.69 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.20), residues: 1729 helix: 1.27 (0.20), residues: 718 sheet: -0.66 (0.35), residues: 223 loop : -1.08 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 708 TYR 0.016 0.001 TYR B 533 PHE 0.024 0.001 PHE C 41 TRP 0.020 0.001 TRP B 185 HIS 0.005 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00236 (15178) covalent geometry : angle 0.57450 (20722) hydrogen bonds : bond 0.03158 ( 642) hydrogen bonds : angle 4.37229 ( 1765) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3458 Ramachandran restraints generated. 1729 Oldfield, 0 Emsley, 1729 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 196 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: A 120 ASN cc_start: 0.8645 (p0) cc_final: 0.8370 (p0) REVERT: A 159 GLN cc_start: 0.8955 (tp40) cc_final: 0.8478 (tp-100) REVERT: A 607 VAL cc_start: 0.9285 (OUTLIER) cc_final: 0.9078 (t) REVERT: B 259 ASP cc_start: 0.8923 (m-30) cc_final: 0.8659 (m-30) REVERT: B 473 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7806 (mtmm) REVERT: C 29 LYS cc_start: 0.9198 (mtmt) cc_final: 0.8868 (ttpp) REVERT: C 95 LYS cc_start: 0.8464 (mtmm) cc_final: 0.7892 (ptmm) REVERT: C 110 TYR cc_start: 0.8537 (m-80) cc_final: 0.8287 (m-80) REVERT: C 346 GLU cc_start: 0.9055 (tt0) cc_final: 0.8447 (tm-30) REVERT: C 380 GLN cc_start: 0.8564 (pm20) cc_final: 0.8176 (pm20) outliers start: 23 outliers final: 20 residues processed: 209 average time/residue: 0.1588 time to fit residues: 46.4344 Evaluate side-chains 207 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 HIS Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 584 GLN Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 229 MET Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 423 ASP Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain C residue 24 CYS Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 183 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 335 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 115 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 150 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 157 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 HIS ** C 453 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.084112 restraints weight = 59729.959| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 3.56 r_work: 0.2819 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2828 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2828 r_free = 0.2828 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2828 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15178 Z= 0.128 Angle : 0.581 16.104 20722 Z= 0.292 Chirality : 0.041 0.172 2313 Planarity : 0.005 0.056 2532 Dihedral : 13.199 162.670 2463 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.54 % Allowed : 12.82 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.20), residues: 1729 helix: 1.28 (0.20), residues: 718 sheet: -0.58 (0.35), residues: 223 loop : -1.08 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 708 TYR 0.016 0.001 TYR B 632 PHE 0.025 0.001 PHE C 383 TRP 0.020 0.001 TRP B 185 HIS 0.012 0.001 HIS C 233 Details of bonding type rmsd covalent geometry : bond 0.00299 (15178) covalent geometry : angle 0.58147 (20722) hydrogen bonds : bond 0.03335 ( 642) hydrogen bonds : angle 4.36062 ( 1765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3961.69 seconds wall clock time: 68 minutes 47.34 seconds (4127.34 seconds total)