Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 13:01:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/04_2023/7mid_23847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/04_2023/7mid_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_23847/04_2023/7mid_23847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/04_2023/7mid_23847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/04_2023/7mid_23847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mid_23847/04_2023/7mid_23847_updated.pdb" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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-1.21rc1-4938/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: 5.65, 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: 4.68 Conformation dependent library (CDL) restraints added in 1.2 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: 3.33 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: 2.97 Time building geometry restraints manager: 4.74 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: 5320 28.46 - 56.92: 482 56.92 - 85.38: 67 85.38 - 113.84: 3 113.84 - 142.30: 2 Dihedral angle restraints: 5874 sinusoidal: 2774 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 5871 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: 1.010 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: 4.340 Check model and map are aligned: 0.140 Set scattering table: 0.070 Process input model: 32.050 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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: 40.760 ------------------------------------------------------------------------------- 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 : 20.243 142.304 3886 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 % 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 *********************** 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 : 1.001 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 outliers start: 52 outliers final: 9 residues processed: 339 average time/residue: 0.3326 time to fit residues: 141.7401 Evaluate side-chains 169 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 160 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2615 time to fit residues: 4.6519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 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 206 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 ASN A 420 ASN 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.062 10123 Z= 0.271 Angle : 0.762 11.515 13946 Z= 0.401 Chirality : 0.046 0.171 1516 Planarity : 0.007 0.067 1618 Dihedral : 19.614 140.880 1792 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.97 % Favored : 93.94 % Rotamer Outliers : 3.31 % 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: -0.98 (0.26), residues: 1072 helix: 0.62 (0.24), residues: 481 sheet: -0.33 (0.48), residues: 135 loop : -2.20 (0.27), residues: 456 *********************** 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 214 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 184 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 14 residues processed: 201 average time/residue: 0.2555 time to fit residues: 69.9819 Evaluate side-chains 161 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 147 time to evaluate : 1.052 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.0968 time to fit residues: 3.9693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 HIS B 342 ASN ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 3 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 10123 Z= 0.267 Angle : 0.677 8.276 13946 Z= 0.359 Chirality : 0.044 0.178 1516 Planarity : 0.006 0.070 1618 Dihedral : 19.442 141.785 1792 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer Outliers : 1.32 % 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: -0.60 (0.26), residues: 1072 helix: 0.99 (0.24), residues: 472 sheet: 0.07 (0.50), residues: 130 loop : -2.07 (0.26), residues: 470 *********************** 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 171 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 6 residues processed: 166 average time/residue: 0.2673 time to fit residues: 60.0830 Evaluate side-chains 137 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 131 time to evaluate : 1.078 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0921 time to fit residues: 2.5601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 0.0670 chunk 102 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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** ** B 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5836 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= 0.196 Angle : 0.635 7.944 13946 Z= 0.331 Chirality : 0.042 0.150 1516 Planarity : 0.004 0.044 1618 Dihedral : 19.368 140.556 1792 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.41 % Favored : 94.50 % Rotamer Outliers : 1.21 % 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: -0.43 (0.26), residues: 1072 helix: 1.19 (0.25), residues: 472 sheet: 0.22 (0.50), residues: 128 loop : -2.06 (0.26), residues: 472 *********************** 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 149 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 144 average time/residue: 0.2333 time to fit residues: 46.9218 Evaluate side-chains 133 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0963 time to fit residues: 2.0292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 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** ** C 91 GLN ** 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: 0.7718 moved from start: 0.7377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.065 10123 Z= 0.390 Angle : 0.767 9.619 13946 Z= 0.403 Chirality : 0.046 0.160 1516 Planarity : 0.006 0.064 1618 Dihedral : 19.637 141.603 1792 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer Outliers : 2.87 % 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: -0.63 (0.25), residues: 1072 helix: 0.98 (0.24), residues: 462 sheet: 0.10 (0.50), residues: 118 loop : -2.00 (0.26), residues: 492 *********************** 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 155 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 147 average time/residue: 0.2669 time to fit residues: 52.7226 Evaluate side-chains 121 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0920 time to fit residues: 3.6417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 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 ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 10123 Z= 0.311 Angle : 0.696 9.577 13946 Z= 0.366 Chirality : 0.045 0.169 1516 Planarity : 0.005 0.040 1618 Dihedral : 19.605 140.760 1792 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer Outliers : 1.32 % 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: -0.60 (0.26), residues: 1072 helix: 1.13 (0.25), residues: 462 sheet: -0.54 (0.48), residues: 123 loop : -1.94 (0.26), residues: 487 *********************** 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 138 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 134 average time/residue: 0.2675 time to fit residues: 48.3128 Evaluate side-chains 117 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 1.071 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0943 time to fit residues: 2.3095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.8516 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= 0.193 Angle : 0.655 10.594 13946 Z= 0.337 Chirality : 0.042 0.146 1516 Planarity : 0.004 0.042 1618 Dihedral : 19.535 141.075 1792 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.88 % 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: -0.34 (0.26), residues: 1072 helix: 1.36 (0.25), residues: 466 sheet: -0.14 (0.48), residues: 123 loop : -1.93 (0.26), residues: 483 *********************** 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 137 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 136 average time/residue: 0.2738 time to fit residues: 50.4487 Evaluate side-chains 119 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 115 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2957 time to fit residues: 3.0266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 84 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 GLN ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.8780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10123 Z= 0.201 Angle : 0.642 9.613 13946 Z= 0.327 Chirality : 0.042 0.150 1516 Planarity : 0.004 0.045 1618 Dihedral : 19.458 140.590 1792 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer Outliers : 0.66 % 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: -0.21 (0.26), residues: 1072 helix: 1.50 (0.25), residues: 462 sheet: 0.13 (0.49), residues: 118 loop : -1.92 (0.26), residues: 492 *********************** 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 134 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.2842 time to fit residues: 49.5926 Evaluate side-chains 121 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 1.111 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1141 time to fit residues: 1.8666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.0770 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.8997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 10123 Z= 0.207 Angle : 0.664 12.016 13946 Z= 0.339 Chirality : 0.043 0.228 1516 Planarity : 0.004 0.045 1618 Dihedral : 19.415 140.231 1792 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer Outliers : 0.11 % 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: 1.54 (0.26), residues: 464 sheet: 0.41 (0.51), residues: 109 loop : -1.88 (0.25), residues: 499 *********************** 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 122 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 122 average time/residue: 0.2611 time to fit residues: 43.5502 Evaluate side-chains 117 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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** ** 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: 0.7728 moved from start: 0.9160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 10123 Z= 0.190 Angle : 0.665 12.513 13946 Z= 0.340 Chirality : 0.042 0.249 1516 Planarity : 0.004 0.049 1618 Dihedral : 19.338 139.823 1792 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer Outliers : 0.00 % 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: -0.04 (0.26), residues: 1072 helix: 1.60 (0.26), residues: 465 sheet: 0.45 (0.51), residues: 110 loop : -1.83 (0.25), residues: 497 ********************** 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 126 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2559 time to fit residues: 44.8106 Evaluate side-chains 122 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 13 optimal weight: 0.2980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.0170 overall best weight: 0.6018 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.080707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.066635 restraints weight = 36987.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.068630 restraints weight = 20158.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.069961 restraints weight = 13539.498| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.9267 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= 0.184 Angle : 0.651 11.088 13946 Z= 0.330 Chirality : 0.042 0.221 1516 Planarity : 0.004 0.048 1618 Dihedral : 19.257 140.123 1792 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer Outliers : 0.11 % 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: -0.00 (0.26), residues: 1072 helix: 1.65 (0.26), residues: 464 sheet: 0.27 (0.49), residues: 120 loop : -1.81 (0.26), residues: 488 =============================================================================== Job complete usr+sys time: 1961.87 seconds wall clock time: 36 minutes 23.78 seconds (2183.78 seconds total)