Starting phenix.real_space_refine on Thu Mar 14 21:23:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/03_2024/7mid_23847_updated.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 5 7.51 5 Fe 4 7.16 5 P 57 5.49 5 S 55 5.16 5 C 5994 2.51 5 N 1799 2.21 5 O 1875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 14": "NH1" <-> "NH2" Residue "A TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 34": "OE1" <-> "OE2" Residue "A ARG 47": "NH1" <-> "NH2" Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A GLU 485": "OE1" <-> "OE2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 245": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 413": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B ARG 493": "NH1" <-> "NH2" Residue "B ARG 505": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B GLU 513": "OE1" <-> "OE2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B GLU 517": "OE1" <-> "OE2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 16": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 39": "NH1" <-> "NH2" Residue "C ARG 44": "NH1" <-> "NH2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 16": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 39": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9789 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 4355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4355 Classifications: {'peptide': 554} Link IDs: {'PTRANS': 35, 'TRANS': 518} Chain: "B" Number of atoms: 2711 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2711 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 18, 'TRANS': 321} Chain: "C" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 786 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 758 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "E" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 488 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "F" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 678 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 9 Unusual residues: {' MN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 142 SG CYS A 22 67.781 52.551 83.007 1.00 50.21 S ATOM 1468 SG CYS A 196 64.162 56.883 83.234 1.00 54.73 S ATOM 1429 SG CYS A 190 63.083 53.528 78.591 1.00 55.03 S ATOM 1405 SG CYS A 187 67.882 56.088 79.078 1.00 56.92 S Time building chain proxies: 5.71, per 1000 atoms: 0.58 Number of scatterers: 9789 At special positions: 0 Unit cell: (89.8242, 114.062, 135.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Mn 5 24.99 S 55 16.00 P 57 15.00 O 1875 8.00 N 1799 7.00 C 5994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " Number of angles added : 12 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 13 sheets defined 42.7% alpha, 12.3% beta 16 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 4.55 Creating SS restraints... Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.895A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 130 Processing helix chain 'A' and resid 155 through 174 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 193 through 196 No H-bonds generated for 'chain 'A' and resid 193 through 196' Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.681A pdb=" N ARG A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 317 through 341 Processing helix chain 'A' and resid 354 through 368 Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 407 through 409 No H-bonds generated for 'chain 'A' and resid 407 through 409' Processing helix chain 'A' and resid 418 through 441 removed outlier: 4.066A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 441 " --> pdb=" O ALA A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 464 No H-bonds generated for 'chain 'A' and resid 461 through 464' Processing helix chain 'A' and resid 466 through 483 Proline residue: A 470 - end of helix removed outlier: 4.801A pdb=" N ALA A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP A 474 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 475 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN A 482 " --> pdb=" O MET A 479 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASN A 483 " --> pdb=" O ALA A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 490 No H-bonds generated for 'chain 'A' and resid 488 through 490' Processing helix chain 'A' and resid 502 through 516 removed outlier: 3.512A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 546 removed outlier: 3.551A pdb=" N GLU A 536 " --> pdb=" O ARG A 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 279 Processing helix chain 'B' and resid 301 through 314 removed outlier: 3.725A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 342 Processing helix chain 'B' and resid 354 through 368 Processing helix chain 'B' and resid 373 through 394 removed outlier: 3.921A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ARG B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET B 394 " --> pdb=" O HIS B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 418 through 440 Processing helix chain 'B' and resid 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 469 through 472 No H-bonds generated for 'chain 'B' and resid 469 through 472' Processing helix chain 'B' and resid 474 through 482 Processing helix chain 'B' and resid 488 through 490 No H-bonds generated for 'chain 'B' and resid 488 through 490' Processing helix chain 'B' and resid 502 through 516 Processing helix chain 'B' and resid 531 through 545 removed outlier: 4.196A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 25 Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.738A pdb=" N ASN C 53 " --> pdb=" O GLU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'D' and resid 14 through 25 Processing helix chain 'D' and resid 42 through 53 removed outlier: 3.738A pdb=" N ASN D 53 " --> pdb=" O GLU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing sheet with id= A, first strand: chain 'A' and resid 67 through 71 Processing sheet with id= B, first strand: chain 'A' and resid 73 through 77 Processing sheet with id= C, first strand: chain 'A' and resid 98 through 102 removed outlier: 4.324A pdb=" N PHE A 142 " --> pdb=" O GLU A 147 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A 147 " --> pdb=" O PHE A 142 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 224 through 226 removed outlier: 7.863A pdb=" N LEU A 262 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N THR A 284 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 231 through 236 removed outlier: 3.574A pdb=" N ASP A 236 " --> pdb=" O CYS A 239 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N CYS A 239 " --> pdb=" O ASP A 236 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 491 through 493 Processing sheet with id= G, first strand: chain 'A' and resid 519 through 521 Processing sheet with id= H, first strand: chain 'B' and resid 224 through 226 Processing sheet with id= I, first strand: chain 'B' and resid 232 through 236 removed outlier: 3.815A pdb=" N ALA B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 491 through 493 Processing sheet with id= K, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.507A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 62 through 69 removed outlier: 6.763A pdb=" N LEU C 4 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N GLN C 37 " --> pdb=" O TRP C 30 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TRP C 30 " --> pdb=" O GLN C 37 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 62 through 69 removed outlier: 6.764A pdb=" N LEU D 4 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLN D 37 " --> pdb=" O TRP D 30 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N TRP D 30 " --> pdb=" O GLN D 37 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 3.29 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.42: 4387 1.42 - 1.64: 5639 1.64 - 1.85: 85 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 10123 Sorted by residual: bond pdb=" C1' DG F 23 " pdb=" N9 DG F 23 " ideal model delta sigma weight residual 1.460 1.357 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1' DA F 21 " pdb=" N9 DA F 21 " ideal model delta sigma weight residual 1.460 1.377 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O3' DC E 1 " pdb=" P DA E 2 " ideal model delta sigma weight residual 1.607 1.657 -0.050 1.50e-02 4.44e+03 1.09e+01 bond pdb=" CA HIS B 301 " pdb=" C HIS B 301 " ideal model delta sigma weight residual 1.523 1.467 0.056 1.80e-02 3.09e+03 9.70e+00 bond pdb=" O3' DT E 21 " pdb=" P DA E 22 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.50e-02 4.44e+03 9.07e+00 ... (remaining 10118 not shown) Histogram of bond angle deviations from ideal: 73.55 - 86.49: 12 86.49 - 99.44: 5 99.44 - 112.38: 5596 112.38 - 125.32: 7996 125.32 - 138.27: 337 Bond angle restraints: 13946 Sorted by residual: angle pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " ideal model delta sigma weight residual 124.40 138.27 -13.87 1.40e+00 5.10e-01 9.81e+01 angle pdb=" CG ARG B 386 " pdb=" CD ARG B 386 " pdb=" NE ARG B 386 " ideal model delta sigma weight residual 112.00 130.89 -18.89 2.20e+00 2.07e-01 7.37e+01 angle pdb=" C4' DA E 22 " pdb=" O4' DA E 22 " pdb=" C1' DA E 22 " ideal model delta sigma weight residual 109.70 97.14 12.56 1.50e+00 4.44e-01 7.01e+01 angle pdb=" CA LYS C 22 " pdb=" CB LYS C 22 " pdb=" CG LYS C 22 " ideal model delta sigma weight residual 114.10 129.60 -15.50 2.00e+00 2.50e-01 6.01e+01 angle pdb=" CA LYS D 22 " pdb=" CB LYS D 22 " pdb=" CG LYS D 22 " ideal model delta sigma weight residual 114.10 129.55 -15.45 2.00e+00 2.50e-01 5.97e+01 ... (remaining 13941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.46: 5346 28.46 - 56.92: 504 56.92 - 85.38: 67 85.38 - 113.84: 3 113.84 - 142.30: 2 Dihedral angle restraints: 5922 sinusoidal: 2822 harmonic: 3100 Sorted by residual: dihedral pdb=" CD ARG A 146 " pdb=" NE ARG A 146 " pdb=" CZ ARG A 146 " pdb=" NH1 ARG A 146 " ideal model delta sinusoidal sigma weight residual 0.00 -57.87 57.87 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CA ARG A 412 " pdb=" C ARG A 412 " pdb=" N ARG A 413 " pdb=" CA ARG A 413 " ideal model delta harmonic sigma weight residual -180.00 -147.79 -32.21 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ARG A 393 " pdb=" C ARG A 393 " pdb=" N MET A 394 " pdb=" CA MET A 394 " ideal model delta harmonic sigma weight residual -180.00 -150.33 -29.67 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 5919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1353 0.088 - 0.176: 155 0.176 - 0.265: 5 0.265 - 0.353: 1 0.353 - 0.441: 2 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C3' DA E 22 " pdb=" C4' DA E 22 " pdb=" O3' DA E 22 " pdb=" C2' DA E 22 " both_signs ideal model delta sigma weight residual False -2.66 -2.22 -0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" C4' DA E 22 " pdb=" C5' DA E 22 " pdb=" O4' DA E 22 " pdb=" C3' DA E 22 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ARG A 146 " pdb=" N ARG A 146 " pdb=" C ARG A 146 " pdb=" CB ARG A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 1513 not shown) Planarity restraints: 1618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 146 " -0.412 9.50e-02 1.11e+02 1.97e-01 7.98e+01 pdb=" NE ARG A 146 " 0.072 2.00e-02 2.50e+03 pdb=" CZ ARG A 146 " -0.128 2.00e-02 2.50e+03 pdb=" NH1 ARG A 146 " 0.044 2.00e-02 2.50e+03 pdb=" NH2 ARG A 146 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA E 22 " 0.031 2.00e-02 2.50e+03 1.64e-02 7.43e+00 pdb=" N9 DA E 22 " -0.044 2.00e-02 2.50e+03 pdb=" C8 DA E 22 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA E 22 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA E 22 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DA E 22 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA E 22 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA E 22 " 0.000 2.00e-02 2.50e+03 pdb=" C2 DA E 22 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA E 22 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DA E 22 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 316 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PRO B 317 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 317 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 317 " 0.036 5.00e-02 4.00e+02 ... (remaining 1615 not shown) Histogram of nonbonded interaction distances: 0.92 - 1.71: 8 1.71 - 2.51: 119 2.51 - 3.31: 11367 3.31 - 4.10: 24587 4.10 - 4.90: 45344 Warning: very small nonbonded interaction distances. Nonbonded interactions: 81425 Sorted by model distance: nonbonded pdb=" N3 DC E 23 " pdb=" O6 DG F 4 " model vdw 0.918 2.496 nonbonded pdb=" N1 DG E 24 " pdb=" N4 DC F 3 " model vdw 0.939 2.560 nonbonded pdb=" N2 DG E 24 " pdb=" N3 DC F 3 " model vdw 1.029 2.560 nonbonded pdb=" CD2 TYR B 232 " pdb=" N1 DA E 2 " model vdw 1.049 3.420 nonbonded pdb=" CG TYR B 232 " pdb=" C2 DA E 2 " model vdw 1.295 3.560 ... (remaining 81420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 1 through 91 or resid 101)) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.070 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 34.600 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 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 : 0.010 0.103 10123 Z= 0.617 Angle : 1.018 18.887 13946 Z= 0.573 Chirality : 0.057 0.441 1516 Planarity : 0.008 0.197 1618 Dihedral : 20.373 142.304 3934 Min Nonbonded Distance : 0.918 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.58 % Favored : 91.32 % Rotamer: Outliers : 5.73 % Allowed : 1.98 % Favored : 92.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.26), residues: 1072 helix: 0.17 (0.23), residues: 493 sheet: -0.70 (0.47), residues: 138 loop : -2.10 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 30 HIS 0.011 0.002 HIS B 522 PHE 0.022 0.002 PHE B 425 TYR 0.019 0.002 TYR B 545 ARG 0.133 0.002 ARG A 146 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 312 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 VAL cc_start: 0.8896 (t) cc_final: 0.8614 (t) REVERT: A 335 CYS cc_start: 0.4388 (m) cc_final: 0.4112 (m) REVERT: A 516 MET cc_start: 0.8354 (mmm) cc_final: 0.8127 (mmm) REVERT: B 432 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7453 (mtt180) REVERT: B 479 MET cc_start: 0.7090 (mmp) cc_final: 0.6644 (mmt) REVERT: B 509 ILE cc_start: 0.8087 (mt) cc_final: 0.7715 (mm) outliers start: 52 outliers final: 9 residues processed: 339 average time/residue: 0.3179 time to fit residues: 135.0522 Evaluate side-chains 173 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 164 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 407 PHE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain C residue 94 ILE Chi-restraints excluded: chain D residue 22 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 0.0870 chunk 53 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 GLN B 274 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 HIS ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 10123 Z= 0.263 Angle : 0.732 10.208 13946 Z= 0.387 Chirality : 0.045 0.153 1516 Planarity : 0.006 0.076 1618 Dihedral : 20.038 140.412 1862 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.69 % Favored : 94.22 % Rotamer: Outliers : 3.75 % Allowed : 14.44 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.26), residues: 1072 helix: 0.70 (0.24), residues: 484 sheet: -0.41 (0.47), residues: 140 loop : -2.18 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 30 HIS 0.011 0.001 HIS B 390 PHE 0.018 0.002 PHE D 36 TYR 0.026 0.002 TYR A 527 ARG 0.010 0.001 ARG B 386 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7371 (mm-30) REVERT: A 224 LEU cc_start: 0.8430 (tp) cc_final: 0.8129 (tp) REVERT: A 230 LYS cc_start: 0.7718 (pttp) cc_final: 0.7359 (pttp) REVERT: A 235 LYS cc_start: 0.8778 (tttp) cc_final: 0.7523 (tttt) REVERT: A 328 ILE cc_start: 0.7746 (OUTLIER) cc_final: 0.7516 (pt) REVERT: A 373 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 516 MET cc_start: 0.8293 (mmm) cc_final: 0.7885 (mmm) REVERT: B 224 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7389 (tp) REVERT: B 364 MET cc_start: 0.5134 (mtm) cc_final: 0.4851 (mtt) REVERT: B 429 MET cc_start: 0.7067 (ptp) cc_final: 0.6781 (ptm) REVERT: B 432 ARG cc_start: 0.7724 (ttt90) cc_final: 0.7450 (mtt180) REVERT: B 464 MET cc_start: 0.8062 (tpp) cc_final: 0.7833 (tpp) REVERT: B 479 MET cc_start: 0.6680 (mmp) cc_final: 0.6160 (mmt) REVERT: D 10 ASP cc_start: 0.6287 (m-30) cc_final: 0.5958 (m-30) REVERT: D 25 HIS cc_start: 0.7190 (t70) cc_final: 0.6972 (t-170) REVERT: D 67 ASP cc_start: 0.6818 (t0) cc_final: 0.6616 (t0) outliers start: 34 outliers final: 16 residues processed: 204 average time/residue: 0.2461 time to fit residues: 67.0096 Evaluate side-chains 168 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 392 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 258 SER Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 365 ARG Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 10123 Z= 0.402 Angle : 0.796 9.005 13946 Z= 0.427 Chirality : 0.049 0.241 1516 Planarity : 0.007 0.057 1618 Dihedral : 20.033 142.286 1843 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.42 % Rotamer: Outliers : 3.64 % Allowed : 16.87 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.25), residues: 1072 helix: 0.53 (0.23), residues: 477 sheet: 0.13 (0.51), residues: 118 loop : -2.13 (0.26), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 30 HIS 0.013 0.002 HIS B 390 PHE 0.046 0.003 PHE B 407 TYR 0.023 0.002 TYR A 527 ARG 0.009 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 157 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7582 (pttt) REVERT: B 341 ARG cc_start: 0.5330 (OUTLIER) cc_final: 0.5013 (mmp80) REVERT: B 479 MET cc_start: 0.7419 (mmp) cc_final: 0.7053 (mmt) REVERT: D 39 ARG cc_start: 0.7147 (OUTLIER) cc_final: 0.6583 (ptm-80) outliers start: 33 outliers final: 18 residues processed: 183 average time/residue: 0.2683 time to fit residues: 64.9962 Evaluate side-chains 142 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 121 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 472 ILE Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 39 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 48 optimal weight: 0.0370 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10123 Z= 0.193 Angle : 0.639 7.959 13946 Z= 0.338 Chirality : 0.043 0.167 1516 Planarity : 0.005 0.043 1618 Dihedral : 19.595 140.096 1841 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.20 % Allowed : 19.29 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.26), residues: 1072 helix: 1.20 (0.24), residues: 473 sheet: 0.03 (0.48), residues: 127 loop : -1.97 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 30 HIS 0.003 0.001 HIS B 295 PHE 0.011 0.001 PHE D 85 TYR 0.019 0.001 TYR A 527 ARG 0.004 0.000 ARG A 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.8357 (mmm) cc_final: 0.8063 (mmm) REVERT: B 232 TYR cc_start: 0.7022 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: B 341 ARG cc_start: 0.5626 (OUTLIER) cc_final: 0.5138 (mmp80) REVERT: B 403 MET cc_start: 0.5972 (mpp) cc_final: 0.5275 (mpp) REVERT: B 479 MET cc_start: 0.7302 (mmp) cc_final: 0.7037 (mmt) REVERT: B 492 VAL cc_start: 0.8675 (t) cc_final: 0.8431 (m) REVERT: D 67 ASP cc_start: 0.7048 (t0) cc_final: 0.6570 (m-30) outliers start: 29 outliers final: 14 residues processed: 161 average time/residue: 0.2582 time to fit residues: 55.9144 Evaluate side-chains 137 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 232 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 0.0980 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.3980 chunk 97 optimal weight: 0.2980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 HIS ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.7155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10123 Z= 0.179 Angle : 0.627 9.669 13946 Z= 0.323 Chirality : 0.041 0.146 1516 Planarity : 0.004 0.041 1618 Dihedral : 19.454 139.224 1840 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.98 % Allowed : 20.51 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1072 helix: 1.52 (0.25), residues: 469 sheet: 0.22 (0.48), residues: 128 loop : -1.91 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 291 HIS 0.003 0.001 HIS C 25 PHE 0.028 0.001 PHE A 407 TYR 0.021 0.001 TYR B 527 ARG 0.006 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 MET cc_start: 0.8456 (mmm) cc_final: 0.8200 (mmm) REVERT: A 394 MET cc_start: 0.6090 (mtm) cc_final: 0.5811 (mtt) REVERT: B 341 ARG cc_start: 0.5524 (OUTLIER) cc_final: 0.5136 (mmp80) REVERT: B 403 MET cc_start: 0.5724 (mpp) cc_final: 0.5137 (mpp) REVERT: B 479 MET cc_start: 0.7408 (mmp) cc_final: 0.7100 (mmt) REVERT: C 3 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7186 (m170) REVERT: D 67 ASP cc_start: 0.7121 (t0) cc_final: 0.6504 (m-30) outliers start: 18 outliers final: 11 residues processed: 148 average time/residue: 0.2763 time to fit residues: 54.1602 Evaluate side-chains 134 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.0670 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 108 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.7463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10123 Z= 0.189 Angle : 0.624 10.889 13946 Z= 0.320 Chirality : 0.041 0.151 1516 Planarity : 0.004 0.042 1618 Dihedral : 19.450 139.263 1840 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.65 % Allowed : 21.61 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1072 helix: 1.72 (0.25), residues: 464 sheet: 0.05 (0.46), residues: 136 loop : -1.96 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 327 HIS 0.003 0.001 HIS B 451 PHE 0.028 0.001 PHE A 407 TYR 0.015 0.001 TYR A 527 ARG 0.005 0.000 ARG A 515 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7850 (pttt) cc_final: 0.7643 (pttp) REVERT: A 358 MET cc_start: 0.8420 (mmm) cc_final: 0.8112 (mmm) REVERT: A 383 SER cc_start: 0.8706 (OUTLIER) cc_final: 0.8385 (p) REVERT: A 394 MET cc_start: 0.6099 (mtm) cc_final: 0.5809 (mtm) REVERT: A 516 MET cc_start: 0.8359 (mmm) cc_final: 0.7580 (mmm) REVERT: B 341 ARG cc_start: 0.5176 (OUTLIER) cc_final: 0.4772 (mmp80) REVERT: B 394 MET cc_start: 0.7944 (mmp) cc_final: 0.7698 (mmp) REVERT: B 403 MET cc_start: 0.5695 (mpp) cc_final: 0.5345 (mpp) REVERT: B 479 MET cc_start: 0.7449 (mmp) cc_final: 0.7195 (mmt) outliers start: 15 outliers final: 12 residues processed: 142 average time/residue: 0.2786 time to fit residues: 52.8538 Evaluate side-chains 136 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 366 HIS Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 0.0970 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10123 Z= 0.191 Angle : 0.617 9.866 13946 Z= 0.317 Chirality : 0.041 0.154 1516 Planarity : 0.004 0.038 1618 Dihedral : 19.446 139.151 1840 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.21 % Allowed : 21.39 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 1072 helix: 1.80 (0.26), residues: 467 sheet: 0.05 (0.46), residues: 135 loop : -1.85 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 327 HIS 0.002 0.001 HIS B 451 PHE 0.025 0.001 PHE A 407 TYR 0.015 0.001 TYR A 288 ARG 0.009 0.000 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 MET cc_start: 0.8921 (mmm) cc_final: 0.8647 (mpp) REVERT: A 230 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7569 (pttp) REVERT: A 358 MET cc_start: 0.8456 (mmm) cc_final: 0.8122 (mmm) REVERT: A 365 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8073 (ptp-170) REVERT: A 383 SER cc_start: 0.8756 (OUTLIER) cc_final: 0.8444 (p) REVERT: A 394 MET cc_start: 0.6019 (mtm) cc_final: 0.5753 (mtm) REVERT: A 516 MET cc_start: 0.7783 (mmm) cc_final: 0.7574 (mmt) REVERT: B 341 ARG cc_start: 0.5609 (OUTLIER) cc_final: 0.5172 (mmp80) REVERT: B 364 MET cc_start: 0.6204 (mtt) cc_final: 0.5810 (mmm) REVERT: B 394 MET cc_start: 0.7965 (mmp) cc_final: 0.7739 (mmp) REVERT: B 403 MET cc_start: 0.5845 (mpp) cc_final: 0.5480 (mpp) REVERT: B 479 MET cc_start: 0.7565 (mmp) cc_final: 0.7190 (mmm) REVERT: C 3 HIS cc_start: 0.7458 (OUTLIER) cc_final: 0.7159 (m170) outliers start: 20 outliers final: 12 residues processed: 139 average time/residue: 0.2514 time to fit residues: 47.3667 Evaluate side-chains 135 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 73 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 98 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 522 HIS C 3 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.8190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10123 Z= 0.209 Angle : 0.628 8.945 13946 Z= 0.321 Chirality : 0.042 0.172 1516 Planarity : 0.004 0.043 1618 Dihedral : 19.469 139.289 1840 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.09 % Allowed : 21.61 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1072 helix: 1.90 (0.25), residues: 463 sheet: 0.00 (0.45), residues: 135 loop : -1.87 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 327 HIS 0.008 0.001 HIS B 451 PHE 0.023 0.001 PHE A 407 TYR 0.015 0.001 TYR B 527 ARG 0.006 0.000 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7547 (pttp) REVERT: A 341 ARG cc_start: 0.6450 (mpt180) cc_final: 0.6179 (tpp-160) REVERT: A 365 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.7733 (ttm-80) REVERT: A 383 SER cc_start: 0.8869 (OUTLIER) cc_final: 0.8584 (p) REVERT: A 394 MET cc_start: 0.5958 (mtm) cc_final: 0.5742 (mtm) REVERT: B 341 ARG cc_start: 0.5791 (OUTLIER) cc_final: 0.5234 (mmp80) REVERT: B 387 TYR cc_start: 0.7929 (t80) cc_final: 0.7225 (t80) REVERT: B 391 PHE cc_start: 0.8348 (t80) cc_final: 0.8033 (t80) REVERT: B 394 MET cc_start: 0.7968 (mmp) cc_final: 0.7766 (mmp) REVERT: B 403 MET cc_start: 0.6353 (mpp) cc_final: 0.5969 (mpp) outliers start: 19 outliers final: 13 residues processed: 147 average time/residue: 0.2606 time to fit residues: 50.8404 Evaluate side-chains 136 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.8353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10123 Z= 0.199 Angle : 0.642 12.433 13946 Z= 0.324 Chirality : 0.041 0.146 1516 Planarity : 0.004 0.042 1618 Dihedral : 19.439 139.001 1840 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.09 % Allowed : 22.27 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.27), residues: 1072 helix: 1.88 (0.26), residues: 466 sheet: 0.13 (0.46), residues: 135 loop : -1.83 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 327 HIS 0.012 0.001 HIS C 3 PHE 0.022 0.001 PHE A 407 TYR 0.017 0.001 TYR B 450 ARG 0.006 0.000 ARG A 533 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7515 (pttp) REVERT: A 341 ARG cc_start: 0.6417 (mpt180) cc_final: 0.6166 (tpp-160) REVERT: A 383 SER cc_start: 0.8867 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 341 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.5502 (mmp80) REVERT: B 403 MET cc_start: 0.6369 (mpp) cc_final: 0.5980 (mpp) outliers start: 19 outliers final: 15 residues processed: 140 average time/residue: 0.2762 time to fit residues: 51.5005 Evaluate side-chains 140 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 61 GLU Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.4980 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 54 optimal weight: 0.0670 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.0060 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.8478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10123 Z= 0.186 Angle : 0.667 13.033 13946 Z= 0.335 Chirality : 0.042 0.236 1516 Planarity : 0.004 0.048 1618 Dihedral : 19.389 138.685 1840 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.09 % Allowed : 22.38 % Favored : 75.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1072 helix: 1.84 (0.26), residues: 463 sheet: 0.06 (0.47), residues: 124 loop : -1.85 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 285 HIS 0.016 0.001 HIS C 3 PHE 0.022 0.001 PHE A 407 TYR 0.018 0.001 TYR B 450 ARG 0.006 0.000 ARG A 533 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7459 (pttp) REVERT: A 341 ARG cc_start: 0.6386 (mpt180) cc_final: 0.6134 (tpp-160) REVERT: A 383 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 394 MET cc_start: 0.6320 (mtm) cc_final: 0.5942 (mmm) REVERT: B 259 GLN cc_start: 0.8591 (pt0) cc_final: 0.8359 (pt0) REVERT: B 288 TYR cc_start: 0.6063 (t80) cc_final: 0.5813 (t80) REVERT: B 341 ARG cc_start: 0.6029 (OUTLIER) cc_final: 0.5481 (mmp80) REVERT: B 506 LYS cc_start: 0.8827 (ptpt) cc_final: 0.8621 (mtmm) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 0.2544 time to fit residues: 48.5171 Evaluate side-chains 144 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 230 LYS Chi-restraints excluded: chain A residue 365 ARG Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 434 TRP Chi-restraints excluded: chain A residue 483 ASN Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 328 ILE Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 429 MET Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 509 ILE Chi-restraints excluded: chain C residue 3 HIS Chi-restraints excluded: chain C residue 7 VAL Chi-restraints excluded: chain C residue 25 HIS Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 65 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.081991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.067631 restraints weight = 37145.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.069639 restraints weight = 20533.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071016 restraints weight = 13861.765| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.8675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10123 Z= 0.220 Angle : 0.662 12.322 13946 Z= 0.334 Chirality : 0.042 0.188 1516 Planarity : 0.004 0.047 1618 Dihedral : 19.372 139.101 1840 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.09 % Allowed : 22.60 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1072 helix: 1.87 (0.26), residues: 463 sheet: 0.08 (0.46), residues: 129 loop : -1.84 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 285 HIS 0.017 0.001 HIS C 3 PHE 0.021 0.001 PHE A 407 TYR 0.017 0.001 TYR B 450 ARG 0.006 0.000 ARG A 533 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2116.09 seconds wall clock time: 38 minutes 44.86 seconds (2324.86 seconds total)