Starting phenix.real_space_refine on Fri Feb 16 13:36:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi5_23840/02_2024/7mi5_23840_neut_updated.pdb" } resolution = 3.57 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= 0.049 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 6 7.51 5 Fe 4 7.16 5 P 60 5.49 5 S 87 5.16 5 C 9573 2.51 5 N 2847 2.21 5 O 2892 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 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 146": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 234": "NH1" <-> "NH2" Residue "A GLU 251": "OE1" <-> "OE2" 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 ARG 326": "NH1" <-> "NH2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 365": "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 454": "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 ARG 220": "NH1" <-> "NH2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B GLU 244": "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 386": "NH1" <-> "NH2" 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 GLU 485": "OE1" <-> "OE2" 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 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 220": "NH1" <-> "NH2" Residue "C TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C ARG 413": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 447": "NH1" <-> "NH2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ARG 469": "NH1" <-> "NH2" Residue "C GLU 485": "OE1" <-> "OE2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 513": "OE1" <-> "OE2" Residue "C ARG 514": "NH1" <-> "NH2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 336": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 413": "NH1" <-> "NH2" Residue "D ARG 432": "NH1" <-> "NH2" Residue "D ARG 447": "NH1" <-> "NH2" Residue "D ARG 454": "NH1" <-> "NH2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D ARG 469": "NH1" <-> "NH2" Residue "D GLU 485": "OE1" <-> "OE2" Residue "D ARG 487": "NH1" <-> "NH2" Residue "D ARG 493": "NH1" <-> "NH2" Residue "D ARG 505": "NH1" <-> "NH2" Residue "D ARG 507": "NH1" <-> "NH2" Residue "D ARG 514": "NH1" <-> "NH2" Residue "D GLU 517": "OE1" <-> "OE2" Residue "D ARG 532": "NH1" <-> "NH2" Residue "D ARG 533": "NH1" <-> "NH2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 16": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 60": "OE1" <-> "OE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 16": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F GLU 60": "OE1" <-> "OE2" Residue "F ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15469 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 553, 4347 Classifications: {'peptide': 553} Link IDs: {'PTRANS': 35, 'TRANS': 517} 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: 2887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2887 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 22, 'TRANS': 339} Chain: "D" 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: "E" 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: "F" 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: "G" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 529 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} 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: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" 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} Chain: "H" 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 134 SG CYS A 22 58.998 39.159 120.263 1.00121.43 S ATOM 1460 SG CYS A 196 60.316 44.706 121.026 1.00115.75 S ATOM 1421 SG CYS A 190 56.911 44.316 116.691 1.00122.55 S ATOM 1397 SG CYS A 187 61.613 42.265 116.734 1.00110.23 S Time building chain proxies: 8.55, per 1000 atoms: 0.55 Number of scatterers: 15469 At special positions: 0 Unit cell: (94.71, 105.78, 177.12, 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 6 24.99 S 87 16.00 P 60 15.00 O 2892 8.00 N 2847 7.00 C 9573 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: 7.06 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 601 " pdb="FE1 SF4 A 601 " - pdb=" SG CYS A 22 " pdb="FE4 SF4 A 601 " - pdb=" SG CYS A 187 " pdb="FE2 SF4 A 601 " - pdb=" SG CYS A 196 " pdb="FE3 SF4 A 601 " - pdb=" SG CYS A 190 " Number of angles added : 12 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3282 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 20 sheets defined 46.3% alpha, 11.4% beta 16 base pairs and 33 stacking pairs defined. Time for finding SS restraints: 6.43 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 removed outlier: 3.509A pdb=" N TYR A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 39 through 52 removed outlier: 3.693A pdb=" N ARG A 50 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' 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 270 through 278 Processing helix chain 'A' and resid 305 through 315 Processing helix chain 'A' and resid 317 through 342 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 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' 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 440 removed outlier: 3.867A pdb=" N GLU A 433 " --> pdb=" O MET A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 482 removed outlier: 3.968A pdb=" N GLU A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Proline residue: A 467 - end of helix Proline residue: A 470 - end of helix removed outlier: 4.450A pdb=" N SER A 475 " --> pdb=" O LEU A 471 " (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 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 301 through 315 removed outlier: 3.654A pdb=" N GLU B 305 " --> pdb=" O HIS B 301 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.815A pdb=" N HIS B 390 " --> pdb=" O ARG B 386 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.731A 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 459 through 482 removed outlier: 3.689A pdb=" N GLU B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) Proline residue: B 467 - end of helix Proline residue: B 470 - end of helix removed outlier: 3.626A pdb=" N ASP B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) 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 517 Processing helix chain 'B' and resid 531 through 548 removed outlier: 3.628A pdb=" N GLU B 536 " --> pdb=" O ARG B 532 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N SER B 547 " --> pdb=" O THR B 543 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY B 548 " --> pdb=" O ARG B 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 204 Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 305 through 315 Processing helix chain 'C' and resid 317 through 342 Processing helix chain 'C' and resid 354 through 368 Processing helix chain 'C' and resid 373 through 389 Processing helix chain 'C' and resid 391 through 393 No H-bonds generated for 'chain 'C' and resid 391 through 393' Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 418 through 440 removed outlier: 3.867A pdb=" N GLU C 433 " --> pdb=" O MET C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 482 removed outlier: 3.967A pdb=" N GLU C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) Proline residue: C 467 - end of helix Proline residue: C 470 - end of helix removed outlier: 4.449A pdb=" N SER C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 490 No H-bonds generated for 'chain 'C' and resid 488 through 490' Processing helix chain 'C' and resid 502 through 516 Processing helix chain 'C' and resid 531 through 547 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 301 through 315 removed outlier: 3.653A pdb=" N GLU D 305 " --> pdb=" O HIS D 301 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 342 Processing helix chain 'D' and resid 354 through 368 Processing helix chain 'D' and resid 373 through 394 removed outlier: 3.814A pdb=" N HIS D 390 " --> pdb=" O ARG D 386 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG D 393 " --> pdb=" O GLN D 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N MET D 394 " --> pdb=" O HIS D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 418 through 440 Processing helix chain 'D' and resid 459 through 482 removed outlier: 3.688A pdb=" N GLU D 466 " --> pdb=" O LEU D 462 " (cutoff:3.500A) Proline residue: D 467 - end of helix Proline residue: D 470 - end of helix removed outlier: 3.626A pdb=" N ASP D 474 " --> pdb=" O PRO D 470 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 490 No H-bonds generated for 'chain 'D' and resid 488 through 490' Processing helix chain 'D' and resid 502 through 517 Processing helix chain 'D' and resid 531 through 548 removed outlier: 3.629A pdb=" N GLU D 536 " --> pdb=" O ARG D 532 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N SER D 547 " --> pdb=" O THR D 543 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLY D 548 " --> pdb=" O ARG D 544 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 25 Processing helix chain 'E' and resid 42 through 53 removed outlier: 3.598A pdb=" N ASN E 53 " --> pdb=" O GLU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'F' and resid 14 through 25 Processing helix chain 'F' and resid 42 through 53 removed outlier: 3.599A pdb=" N ASN F 53 " --> pdb=" O GLU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing sheet with id= A, first strand: chain 'A' and resid 67 through 70 removed outlier: 7.666A pdb=" N GLY A 137 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ASP A 100 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ALA A 139 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LYS A 102 " --> pdb=" O ALA A 139 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N TYR A 141 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 73 through 77 removed outlier: 3.699A pdb=" N VAL A 73 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 231 through 236 removed outlier: 6.519A pdb=" N GLU A 244 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG A 248 " --> pdb=" O GLU A 244 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.835A pdb=" N LEU A 224 " --> pdb=" O SER A 258 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 260 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL A 226 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU A 262 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N LEU A 262 " --> pdb=" O PRO A 282 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR A 284 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 491 through 493 Processing sheet with id= F, first strand: chain 'A' and resid 519 through 521 Processing sheet with id= G, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.799A pdb=" N VAL B 226 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 232 through 236 Processing sheet with id= I, first strand: chain 'B' and resid 491 through 493 Processing sheet with id= J, first strand: chain 'B' and resid 283 through 286 removed outlier: 3.550A pdb=" N GLY B 294 " --> pdb=" O TRP B 285 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 231 through 236 removed outlier: 6.519A pdb=" N GLU C 244 " --> pdb=" O ARG C 248 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ARG C 248 " --> pdb=" O GLU C 244 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 222 through 226 removed outlier: 6.836A pdb=" N LEU C 224 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL C 260 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL C 226 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU C 262 " --> pdb=" O VAL C 226 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N LEU C 262 " --> pdb=" O PRO C 282 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR C 284 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 491 through 493 Processing sheet with id= N, first strand: chain 'C' and resid 519 through 521 Processing sheet with id= O, first strand: chain 'D' and resid 224 through 226 removed outlier: 3.797A pdb=" N VAL D 226 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 232 through 236 Processing sheet with id= Q, first strand: chain 'D' and resid 491 through 493 Processing sheet with id= R, first strand: chain 'D' and resid 283 through 286 removed outlier: 3.549A pdb=" N GLY D 294 " --> pdb=" O TRP D 285 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 62 through 69 removed outlier: 6.719A pdb=" N LEU E 4 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN E 37 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP E 30 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 62 through 69 removed outlier: 6.719A pdb=" N LEU F 4 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN F 37 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N TRP F 30 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 642 hydrogen bonds defined for protein. 1872 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 37 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 16 basepair parallelities 33 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 7.48 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: 6894 1.42 - 1.63: 8898 1.63 - 1.85: 137 1.85 - 2.06: 0 2.06 - 2.28: 12 Bond restraints: 15941 Sorted by residual: bond pdb=" C1' DG H 20 " pdb=" N9 DG H 20 " ideal model delta sigma weight residual 1.460 1.360 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" C1' DA H 21 " pdb=" N9 DA H 21 " ideal model delta sigma weight residual 1.460 1.368 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" SD MET D 364 " pdb=" CE MET D 364 " ideal model delta sigma weight residual 1.791 1.695 0.096 2.50e-02 1.60e+03 1.46e+01 bond pdb=" SD MET B 364 " pdb=" CE MET B 364 " ideal model delta sigma weight residual 1.791 1.696 0.095 2.50e-02 1.60e+03 1.44e+01 bond pdb=" C LEU A 197 " pdb=" O LEU A 197 " ideal model delta sigma weight residual 1.233 1.250 -0.017 4.80e-03 4.34e+04 1.29e+01 ... (remaining 15936 not shown) Histogram of bond angle deviations from ideal: 73.34 - 87.61: 12 87.61 - 101.88: 96 101.88 - 116.15: 10586 116.15 - 130.42: 11044 130.42 - 144.70: 97 Bond angle restraints: 21835 Sorted by residual: angle pdb=" CA MET D 364 " pdb=" CB MET D 364 " pdb=" CG MET D 364 " ideal model delta sigma weight residual 114.10 139.65 -25.55 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET B 364 " pdb=" CB MET B 364 " pdb=" CG MET B 364 " ideal model delta sigma weight residual 114.10 139.62 -25.52 2.00e+00 2.50e-01 1.63e+02 angle pdb=" CA MET D 479 " pdb=" CB MET D 479 " pdb=" CG MET D 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CA MET B 479 " pdb=" CB MET B 479 " pdb=" CG MET B 479 " ideal model delta sigma weight residual 114.10 137.14 -23.04 2.00e+00 2.50e-01 1.33e+02 angle pdb=" CB MET B 479 " pdb=" CG MET B 479 " pdb=" SD MET B 479 " ideal model delta sigma weight residual 112.70 144.70 -32.00 3.00e+00 1.11e-01 1.14e+02 ... (remaining 21830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.22: 8506 29.22 - 58.43: 797 58.43 - 87.65: 103 87.65 - 116.87: 4 116.87 - 146.08: 2 Dihedral angle restraints: 9412 sinusoidal: 4289 harmonic: 5123 Sorted by residual: dihedral pdb=" CA ARG B 412 " pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta harmonic sigma weight residual -180.00 -145.33 -34.67 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA ARG D 412 " pdb=" C ARG D 412 " pdb=" N ARG D 413 " pdb=" CA ARG D 413 " ideal model delta harmonic sigma weight residual -180.00 -145.36 -34.64 0 5.00e+00 4.00e-02 4.80e+01 dihedral pdb=" CA GLN C 312 " pdb=" C GLN C 312 " pdb=" N ARG C 313 " pdb=" CA ARG C 313 " ideal model delta harmonic sigma weight residual 180.00 149.32 30.68 0 5.00e+00 4.00e-02 3.76e+01 ... (remaining 9409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2013 0.084 - 0.169: 293 0.169 - 0.253: 47 0.253 - 0.338: 6 0.338 - 0.422: 2 Chirality restraints: 2361 Sorted by residual: chirality pdb=" CA MET B 364 " pdb=" N MET B 364 " pdb=" C MET B 364 " pdb=" CB MET B 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CA MET D 364 " pdb=" N MET D 364 " pdb=" C MET D 364 " pdb=" CB MET D 364 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" CA TYR A 232 " pdb=" N TYR A 232 " pdb=" C TYR A 232 " pdb=" CB TYR A 232 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2358 not shown) Planarity restraints: 2644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 327 " 0.029 2.00e-02 2.50e+03 2.96e-02 2.20e+01 pdb=" CG TRP D 327 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP D 327 " 0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP D 327 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 327 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP D 327 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 327 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 327 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 327 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP D 327 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 327 " -0.029 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP B 327 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP B 327 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TRP B 327 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 327 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 327 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 327 " -0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 327 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 327 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 327 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 340 " 0.061 9.50e-02 1.11e+02 3.44e-02 5.96e+00 pdb=" NE ARG B 340 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG B 340 " 0.040 2.00e-02 2.50e+03 pdb=" NH1 ARG B 340 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG B 340 " -0.012 2.00e-02 2.50e+03 ... (remaining 2641 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 125 2.31 - 2.96: 8864 2.96 - 3.60: 25609 3.60 - 4.25: 38400 4.25 - 4.90: 60996 Nonbonded interactions: 133994 Sorted by model distance: nonbonded pdb=" N2 DG G 8 " pdb=" N3 DG H 20 " model vdw 1.662 2.600 nonbonded pdb=" OP1 DG H 32 " pdb="MN MN H 801 " model vdw 1.716 2.320 nonbonded pdb=" N GLY A 237 " pdb=" OP1 DT G 6 " model vdw 1.916 2.520 nonbonded pdb=" NE2 HIS A 48 " pdb="MN MN H 801 " model vdw 1.916 2.400 nonbonded pdb=" C2 DG G 8 " pdb=" C2 DG H 20 " model vdw 1.925 3.480 ... (remaining 133989 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 'B' and resid 219 through 558) selection = (chain 'C' and resid 219 through 558) selection = (chain 'D' and resid 219 through 558) } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 0.440 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: 3.130 Check model and map are aligned: 0.220 Set scattering table: 0.160 Process input model: 49.360 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 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 0.100 15941 Z= 0.632 Angle : 1.468 31.996 21835 Z= 0.787 Chirality : 0.063 0.422 2361 Planarity : 0.006 0.045 2644 Dihedral : 21.219 146.085 6130 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 35.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.42 % Favored : 90.47 % Rotamer: Outliers : 11.95 % Allowed : 2.28 % Favored : 85.77 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -2.45 (0.18), residues: 1773 helix: -1.06 (0.16), residues: 822 sheet: -0.81 (0.46), residues: 124 loop : -2.33 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.004 TRP D 327 HIS 0.017 0.002 HIS C 206 PHE 0.021 0.003 PHE D 491 TYR 0.026 0.003 TYR C 311 ARG 0.041 0.003 ARG B 340 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 483 time to evaluate : 1.706 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 HIS cc_start: 0.7512 (t70) cc_final: 0.7238 (t70) REVERT: A 143 VAL cc_start: 0.8024 (t) cc_final: 0.6933 (t) REVERT: A 154 ASP cc_start: 0.5798 (OUTLIER) cc_final: 0.5556 (t70) REVERT: A 256 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7269 (tt0) REVERT: A 358 MET cc_start: 0.6460 (OUTLIER) cc_final: 0.5847 (ppp) REVERT: A 420 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6280 (m-40) REVERT: A 557 VAL cc_start: 0.8015 (t) cc_final: 0.7710 (t) REVERT: B 220 ARG cc_start: 0.5709 (OUTLIER) cc_final: 0.5359 (mmm160) REVERT: B 227 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6216 (mm-40) REVERT: B 248 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.5935 (ttp80) REVERT: B 351 LYS cc_start: 0.6667 (tptp) cc_final: 0.6443 (tptt) REVERT: B 479 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6498 (ptt) REVERT: B 488 THR cc_start: 0.8499 (p) cc_final: 0.8250 (p) REVERT: B 518 GLN cc_start: 0.6112 (mp10) cc_final: 0.5423 (mp10) REVERT: C 201 VAL cc_start: 0.7427 (t) cc_final: 0.7147 (p) REVERT: C 227 GLN cc_start: 0.8103 (pp30) cc_final: 0.7622 (pt0) REVERT: C 256 GLU cc_start: 0.7696 (mt-10) cc_final: 0.7337 (mt-10) REVERT: C 336 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6502 (mmm160) REVERT: C 517 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7015 (tm-30) REVERT: C 543 THR cc_start: 0.8724 (p) cc_final: 0.8445 (p) REVERT: D 301 HIS cc_start: 0.7425 (p-80) cc_final: 0.7072 (p90) REVERT: D 379 ILE cc_start: 0.1719 (OUTLIER) cc_final: 0.1334 (tp) REVERT: D 394 MET cc_start: 0.4757 (mmt) cc_final: 0.4206 (mmt) REVERT: D 457 ARG cc_start: 0.7511 (mtm180) cc_final: 0.7244 (mtm-85) REVERT: D 464 MET cc_start: 0.5186 (OUTLIER) cc_final: 0.4045 (tpt) REVERT: D 479 MET cc_start: 0.4619 (OUTLIER) cc_final: 0.3279 (tmm) REVERT: D 513 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6613 (pt0) REVERT: D 517 GLU cc_start: 0.5790 (mm-30) cc_final: 0.4496 (tt0) REVERT: E 47 LYS cc_start: 0.8422 (mttm) cc_final: 0.8104 (mttt) REVERT: E 65 ILE cc_start: 0.8467 (pt) cc_final: 0.8214 (pt) REVERT: E 75 LYS cc_start: 0.8218 (ptpp) cc_final: 0.7690 (tptp) REVERT: E 84 THR cc_start: 0.9035 (OUTLIER) cc_final: 0.8726 (t) REVERT: F 29 CYS cc_start: 0.7938 (t) cc_final: 0.7620 (m) REVERT: F 32 GLN cc_start: 0.6968 (tp40) cc_final: 0.6688 (tt0) REVERT: F 42 ARG cc_start: 0.7692 (mmm-85) cc_final: 0.7314 (tmm160) REVERT: F 91 GLN cc_start: 0.8584 (pm20) cc_final: 0.8365 (pm20) outliers start: 178 outliers final: 27 residues processed: 575 average time/residue: 0.4013 time to fit residues: 303.4746 Evaluate side-chains 288 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 248 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ASP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain B residue 220 ARG Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain B residue 248 ARG Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 416 LYS Chi-restraints excluded: chain B residue 479 MET Chi-restraints excluded: chain B residue 538 GLN Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 410 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 509 ILE Chi-restraints excluded: chain D residue 248 ARG Chi-restraints excluded: chain D residue 325 ARG Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 464 MET Chi-restraints excluded: chain D residue 479 MET Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 515 ARG Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 55 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.0570 chunk 76 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 142 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 86 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 165 optimal weight: 0.6980 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 ASN B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 ASN B 522 HIS C 310 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 HIS D 451 HIS ** D 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 13 ASN ** E 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15941 Z= 0.265 Angle : 0.796 8.718 21835 Z= 0.418 Chirality : 0.048 0.192 2361 Planarity : 0.007 0.131 2644 Dihedral : 18.291 142.241 2797 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 4.77 % Allowed : 14.63 % Favored : 80.60 % 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: -1.35 (0.19), residues: 1773 helix: 0.15 (0.17), residues: 845 sheet: -0.70 (0.46), residues: 124 loop : -2.11 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 327 HIS 0.008 0.001 HIS B 295 PHE 0.024 0.002 PHE B 425 TYR 0.029 0.002 TYR A 553 ARG 0.010 0.001 ARG D 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 290 time to evaluate : 1.542 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: A 29 MET cc_start: 0.7761 (ttm) cc_final: 0.7342 (ttm) REVERT: A 35 PHE cc_start: 0.9072 (t80) cc_final: 0.8661 (t80) REVERT: A 69 HIS cc_start: 0.7559 (t70) cc_final: 0.7300 (t70) REVERT: A 90 GLU cc_start: 0.6596 (mt-10) cc_final: 0.5976 (pt0) REVERT: A 256 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7111 (tt0) REVERT: A 280 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8574 (pm20) REVERT: A 358 MET cc_start: 0.6952 (mmm) cc_final: 0.6193 (ppp) REVERT: A 374 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8238 (tp30) REVERT: A 394 MET cc_start: 0.8031 (ptt) cc_final: 0.7727 (ptt) REVERT: A 429 MET cc_start: 0.8443 (tmm) cc_final: 0.8229 (tmm) REVERT: A 474 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.7251 (m-30) REVERT: B 389 GLN cc_start: 0.7850 (OUTLIER) cc_final: 0.7377 (mt0) REVERT: B 518 GLN cc_start: 0.6785 (mp10) cc_final: 0.6046 (mp10) REVERT: B 538 GLN cc_start: 0.7951 (mm110) cc_final: 0.7568 (mm-40) REVERT: B 555 ASN cc_start: 0.7161 (m110) cc_final: 0.6770 (m110) REVERT: C 227 GLN cc_start: 0.8409 (pp30) cc_final: 0.8111 (pp30) REVERT: C 236 ASP cc_start: 0.6893 (OUTLIER) cc_final: 0.6664 (p0) REVERT: C 280 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7766 (pp20) REVERT: C 291 TRP cc_start: 0.7168 (t-100) cc_final: 0.6303 (t60) REVERT: C 336 ARG cc_start: 0.7536 (mmp80) cc_final: 0.6651 (mmm160) REVERT: C 373 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7495 (pp) REVERT: C 418 PRO cc_start: 0.8546 (Cg_exo) cc_final: 0.8343 (Cg_endo) REVERT: C 479 MET cc_start: 0.8971 (mmt) cc_final: 0.8491 (mmm) REVERT: C 517 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6935 (tp30) REVERT: D 291 TRP cc_start: 0.4507 (t-100) cc_final: 0.4189 (t-100) REVERT: D 301 HIS cc_start: 0.7402 (p-80) cc_final: 0.6889 (p90) REVERT: D 318 GLU cc_start: 0.5852 (pp20) cc_final: 0.5530 (mp0) REVERT: D 379 ILE cc_start: 0.2870 (OUTLIER) cc_final: 0.2381 (tp) REVERT: D 430 LEU cc_start: 0.5622 (mt) cc_final: 0.5109 (mp) REVERT: E 2 GLU cc_start: 0.8014 (tt0) cc_final: 0.7691 (tt0) REVERT: E 24 MET cc_start: 0.8569 (tpp) cc_final: 0.8299 (tpp) REVERT: E 47 LYS cc_start: 0.8514 (mttm) cc_final: 0.8034 (mttt) REVERT: E 61 ASP cc_start: 0.8104 (m-30) cc_final: 0.7730 (m-30) REVERT: E 75 LYS cc_start: 0.8304 (ptpp) cc_final: 0.7780 (tptp) REVERT: E 79 SER cc_start: 0.8345 (t) cc_final: 0.8082 (m) REVERT: E 84 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8720 (t) REVERT: F 42 ARG cc_start: 0.7638 (mmm-85) cc_final: 0.7308 (ttp-170) REVERT: F 91 GLN cc_start: 0.8283 (pm20) cc_final: 0.7963 (pm20) outliers start: 71 outliers final: 35 residues processed: 337 average time/residue: 0.3139 time to fit residues: 149.4614 Evaluate side-chains 263 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 220 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 206 HIS Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 280 GLU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 431 THR Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 360 LEU Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 13 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 165 optimal weight: 0.9990 chunk 178 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15941 Z= 0.319 Angle : 0.736 10.748 21835 Z= 0.385 Chirality : 0.046 0.164 2361 Planarity : 0.006 0.120 2644 Dihedral : 17.289 140.146 2710 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.71 % Favored : 93.23 % Rotamer: Outliers : 3.83 % Allowed : 17.92 % Favored : 78.26 % 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: -0.89 (0.19), residues: 1773 helix: 0.69 (0.18), residues: 832 sheet: -0.52 (0.44), residues: 129 loop : -2.02 (0.20), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 343 HIS 0.007 0.001 HIS B 295 PHE 0.021 0.002 PHE A 153 TYR 0.021 0.002 TYR A 21 ARG 0.015 0.001 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 234 time to evaluate : 1.867 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: A 8 ILE cc_start: 0.8874 (mp) cc_final: 0.8608 (mp) REVERT: A 29 MET cc_start: 0.8219 (ttm) cc_final: 0.7892 (ttm) REVERT: A 35 PHE cc_start: 0.9151 (t80) cc_final: 0.8773 (t80) REVERT: A 120 GLN cc_start: 0.6914 (OUTLIER) cc_final: 0.6660 (tt0) REVERT: A 146 ARG cc_start: 0.8112 (mmt180) cc_final: 0.7881 (mmt180) REVERT: A 232 TYR cc_start: 0.8136 (t80) cc_final: 0.7788 (t80) REVERT: A 251 GLU cc_start: 0.8106 (pm20) cc_final: 0.7656 (pt0) REVERT: A 256 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7206 (tt0) REVERT: A 394 MET cc_start: 0.8654 (ptt) cc_final: 0.8423 (ptp) REVERT: A 429 MET cc_start: 0.8836 (tmm) cc_final: 0.8592 (tmm) REVERT: A 479 MET cc_start: 0.6614 (ttm) cc_final: 0.6211 (ttm) REVERT: A 526 LYS cc_start: 0.8215 (mttm) cc_final: 0.7769 (mptt) REVERT: B 227 GLN cc_start: 0.7180 (pm20) cc_final: 0.6922 (mp10) REVERT: B 302 ARG cc_start: 0.7680 (tpp-160) cc_final: 0.7417 (mmt-90) REVERT: B 343 TRP cc_start: 0.8696 (t-100) cc_final: 0.8407 (t-100) REVERT: B 351 LYS cc_start: 0.7353 (tptt) cc_final: 0.7033 (tptt) REVERT: B 389 GLN cc_start: 0.7989 (OUTLIER) cc_final: 0.7559 (mt0) REVERT: B 407 PHE cc_start: 0.6059 (m-10) cc_final: 0.5830 (m-10) REVERT: B 465 MET cc_start: 0.8481 (ptt) cc_final: 0.8232 (ptp) REVERT: B 506 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8374 (mttm) REVERT: B 555 ASN cc_start: 0.7270 (m110) cc_final: 0.7022 (m110) REVERT: C 227 GLN cc_start: 0.8430 (pp30) cc_final: 0.7742 (pp30) REVERT: C 236 ASP cc_start: 0.6981 (OUTLIER) cc_final: 0.6411 (p0) REVERT: C 280 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7945 (pp20) REVERT: C 291 TRP cc_start: 0.7054 (t-100) cc_final: 0.6404 (t60) REVERT: C 293 MET cc_start: 0.4377 (mpp) cc_final: 0.4067 (mpp) REVERT: C 336 ARG cc_start: 0.7581 (mmp80) cc_final: 0.6728 (mmm160) REVERT: C 361 GLN cc_start: 0.9213 (mm110) cc_final: 0.8785 (mm110) REVERT: C 373 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7470 (pp) REVERT: C 465 MET cc_start: 0.8637 (ttt) cc_final: 0.8380 (ttp) REVERT: C 517 GLU cc_start: 0.7470 (mm-30) cc_final: 0.6966 (tp30) REVERT: C 536 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 312 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7679 (pp30) REVERT: D 379 ILE cc_start: 0.2796 (pt) cc_final: 0.2421 (tp) REVERT: D 394 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.3967 (mmt) REVERT: D 430 LEU cc_start: 0.5871 (mt) cc_final: 0.5391 (mp) REVERT: E 22 LYS cc_start: 0.8995 (pptt) cc_final: 0.8579 (pttm) REVERT: E 61 ASP cc_start: 0.8426 (m-30) cc_final: 0.8120 (m-30) REVERT: E 75 LYS cc_start: 0.8376 (ptpp) cc_final: 0.7975 (tptp) REVERT: E 84 THR cc_start: 0.9148 (OUTLIER) cc_final: 0.8900 (t) REVERT: F 10 ASP cc_start: 0.7759 (m-30) cc_final: 0.7532 (m-30) REVERT: F 42 ARG cc_start: 0.7955 (mmm-85) cc_final: 0.7456 (ttp-170) REVERT: F 91 GLN cc_start: 0.8218 (pm20) cc_final: 0.7776 (pm20) outliers start: 57 outliers final: 28 residues processed: 276 average time/residue: 0.3298 time to fit residues: 127.6255 Evaluate side-chains 231 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 194 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 420 ASN Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 254 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 373 LEU Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 394 MET Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 84 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.4980 chunk 124 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 18 optimal weight: 0.4980 chunk 79 optimal weight: 0.0270 chunk 111 optimal weight: 0.4980 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 157 optimal weight: 0.1980 chunk 47 optimal weight: 0.0470 overall best weight: 0.2536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 HIS ** B 390 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6830 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15941 Z= 0.180 Angle : 0.637 8.133 21835 Z= 0.330 Chirality : 0.042 0.215 2361 Planarity : 0.005 0.053 2644 Dihedral : 16.815 141.018 2696 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.89 % Allowed : 19.66 % Favored : 77.45 % 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: -0.48 (0.20), residues: 1773 helix: 1.17 (0.18), residues: 829 sheet: -0.77 (0.40), residues: 152 loop : -1.91 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 17 HIS 0.004 0.001 HIS A 274 PHE 0.016 0.001 PHE A 153 TYR 0.020 0.001 TYR B 427 ARG 0.007 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 1.693 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 69 HIS cc_start: 0.7666 (t-90) cc_final: 0.6994 (t70) REVERT: A 77 SER cc_start: 0.7250 (t) cc_final: 0.7006 (t) REVERT: A 105 LYS cc_start: 0.8065 (mttm) cc_final: 0.7602 (mtmm) REVERT: A 251 GLU cc_start: 0.7976 (pm20) cc_final: 0.7672 (pt0) REVERT: A 256 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7109 (tt0) REVERT: A 479 MET cc_start: 0.6679 (ttm) cc_final: 0.6317 (ttm) REVERT: A 485 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6649 (mt-10) REVERT: A 526 LYS cc_start: 0.8196 (mttm) cc_final: 0.7596 (mptt) REVERT: B 225 TYR cc_start: 0.7611 (m-10) cc_final: 0.7376 (m-80) REVERT: B 227 GLN cc_start: 0.7521 (pm20) cc_final: 0.7308 (mp10) REVERT: B 302 ARG cc_start: 0.7637 (tpp-160) cc_final: 0.7357 (mmt180) REVERT: B 351 LYS cc_start: 0.7463 (tptt) cc_final: 0.7174 (tptt) REVERT: B 389 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7504 (mt0) REVERT: B 416 LYS cc_start: 0.7958 (mttm) cc_final: 0.7757 (mmtp) REVERT: B 506 LYS cc_start: 0.8559 (ttmt) cc_final: 0.8271 (mttm) REVERT: C 247 VAL cc_start: 0.8600 (t) cc_final: 0.8348 (p) REVERT: C 291 TRP cc_start: 0.7140 (t-100) cc_final: 0.6439 (t60) REVERT: C 336 ARG cc_start: 0.7450 (OUTLIER) cc_final: 0.6998 (mmm160) REVERT: C 358 MET cc_start: 0.8527 (ppp) cc_final: 0.8077 (ppp) REVERT: C 500 LEU cc_start: 0.7372 (mm) cc_final: 0.6935 (mm) REVERT: C 517 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6606 (tp30) REVERT: C 536 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 301 HIS cc_start: 0.7772 (p-80) cc_final: 0.7516 (p90) REVERT: D 312 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7520 (pp30) REVERT: D 379 ILE cc_start: 0.2757 (pt) cc_final: 0.2423 (tp) REVERT: D 429 MET cc_start: 0.5820 (mmm) cc_final: 0.4491 (ptp) REVERT: D 431 THR cc_start: 0.6373 (p) cc_final: 0.5943 (p) REVERT: D 451 HIS cc_start: 0.3966 (OUTLIER) cc_final: 0.2792 (m-70) REVERT: D 455 PHE cc_start: 0.4964 (m-80) cc_final: 0.4476 (m-80) REVERT: D 479 MET cc_start: 0.1935 (mmt) cc_final: 0.1655 (mmt) REVERT: E 61 ASP cc_start: 0.8459 (m-30) cc_final: 0.8253 (m-30) REVERT: E 65 ILE cc_start: 0.8601 (pt) cc_final: 0.8340 (mt) REVERT: E 75 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7845 (tptp) REVERT: E 84 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8842 (t) REVERT: E 88 ILE cc_start: 0.8700 (mm) cc_final: 0.8428 (mt) REVERT: F 2 GLU cc_start: 0.7533 (tt0) cc_final: 0.7271 (tt0) REVERT: F 42 ARG cc_start: 0.7977 (mmm-85) cc_final: 0.7479 (ttp-170) REVERT: F 75 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7333 (mmmt) REVERT: F 91 GLN cc_start: 0.8320 (pm20) cc_final: 0.7801 (pm20) outliers start: 43 outliers final: 22 residues processed: 271 average time/residue: 0.3069 time to fit residues: 120.1920 Evaluate side-chains 235 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 389 GLN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 438 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain F residue 84 THR Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 10.0000 chunk 99 optimal weight: 0.1980 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 72 optimal weight: 0.2980 chunk 150 optimal weight: 9.9990 chunk 121 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 15941 Z= 0.323 Angle : 0.694 7.322 21835 Z= 0.366 Chirality : 0.046 0.221 2361 Planarity : 0.005 0.051 2644 Dihedral : 16.711 140.185 2687 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.50 % Allowed : 18.79 % Favored : 76.71 % 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: -0.45 (0.20), residues: 1773 helix: 1.22 (0.18), residues: 827 sheet: -0.91 (0.38), residues: 167 loop : -1.89 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 327 HIS 0.006 0.001 HIS A 522 PHE 0.020 0.002 PHE A 35 TYR 0.018 0.002 TYR A 450 ARG 0.005 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 215 time to evaluate : 1.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9169 (mp) cc_final: 0.8944 (mp) REVERT: A 69 HIS cc_start: 0.7148 (t-90) cc_final: 0.6463 (t70) REVERT: A 105 LYS cc_start: 0.8192 (mttm) cc_final: 0.7700 (mtmm) REVERT: A 166 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: A 256 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7302 (tt0) REVERT: A 374 GLU cc_start: 0.8605 (mp0) cc_final: 0.8281 (tp30) REVERT: A 412 ARG cc_start: 0.7027 (ttm110) cc_final: 0.6644 (mtm-85) REVERT: A 479 MET cc_start: 0.6754 (ttm) cc_final: 0.6439 (ttm) REVERT: A 485 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7028 (mt-10) REVERT: A 526 LYS cc_start: 0.8358 (mttm) cc_final: 0.7792 (mptt) REVERT: B 227 GLN cc_start: 0.7862 (pm20) cc_final: 0.7484 (pm20) REVERT: B 351 LYS cc_start: 0.7780 (tptt) cc_final: 0.7512 (tptt) REVERT: B 389 GLN cc_start: 0.7869 (mp10) cc_final: 0.7645 (mm-40) REVERT: B 506 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8415 (mttm) REVERT: B 518 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6309 (mp10) REVERT: C 291 TRP cc_start: 0.7096 (t-100) cc_final: 0.6525 (t60) REVERT: C 336 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7178 (mtp85) REVERT: C 358 MET cc_start: 0.8653 (ppp) cc_final: 0.8335 (ppp) REVERT: C 465 MET cc_start: 0.8127 (ttt) cc_final: 0.7593 (ttm) REVERT: C 517 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6939 (tm-30) REVERT: C 536 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: D 301 HIS cc_start: 0.7808 (p-80) cc_final: 0.7450 (p90) REVERT: D 312 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7598 (pp30) REVERT: D 321 LEU cc_start: 0.5657 (mm) cc_final: 0.5450 (mt) REVERT: D 362 ASP cc_start: 0.7622 (m-30) cc_final: 0.7268 (t70) REVERT: D 379 ILE cc_start: 0.2842 (pt) cc_final: 0.2538 (tp) REVERT: D 413 ARG cc_start: 0.2090 (OUTLIER) cc_final: 0.0373 (mtm110) REVERT: D 451 HIS cc_start: 0.3983 (OUTLIER) cc_final: 0.3001 (m-70) REVERT: D 455 PHE cc_start: 0.4515 (m-80) cc_final: 0.4196 (m-80) REVERT: E 2 GLU cc_start: 0.7987 (tt0) cc_final: 0.7778 (tt0) REVERT: E 61 ASP cc_start: 0.8550 (m-30) cc_final: 0.8274 (m-30) REVERT: E 75 LYS cc_start: 0.8520 (ptpp) cc_final: 0.8280 (tptt) REVERT: E 84 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9073 (t) REVERT: F 2 GLU cc_start: 0.7611 (tt0) cc_final: 0.7372 (tt0) REVERT: F 10 ASP cc_start: 0.7792 (m-30) cc_final: 0.7562 (m-30) REVERT: F 42 ARG cc_start: 0.8020 (mmm-85) cc_final: 0.7464 (ttp-170) REVERT: F 49 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7876 (mm-30) REVERT: F 91 GLN cc_start: 0.8373 (pm20) cc_final: 0.7796 (pm20) outliers start: 67 outliers final: 41 residues processed: 264 average time/residue: 0.3040 time to fit residues: 115.3125 Evaluate side-chains 243 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 1.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 276 CYS Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 541 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 536 GLU Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 413 ARG Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 524 ILE Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 0.0060 chunk 158 optimal weight: 8.9990 chunk 34 optimal weight: 0.0980 chunk 103 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 176 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.2202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.6795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15941 Z= 0.304 Angle : 0.665 14.123 21835 Z= 0.346 Chirality : 0.044 0.218 2361 Planarity : 0.005 0.075 2644 Dihedral : 16.563 141.834 2685 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.96 % Allowed : 20.40 % Favored : 75.64 % 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 (0.20), residues: 1773 helix: 1.25 (0.18), residues: 825 sheet: -0.86 (0.38), residues: 177 loop : -1.87 (0.21), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 327 HIS 0.007 0.001 HIS C 366 PHE 0.015 0.002 PHE D 391 TYR 0.014 0.001 TYR A 21 ARG 0.031 0.001 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ILE cc_start: 0.9228 (mp) cc_final: 0.9021 (mp) REVERT: A 105 LYS cc_start: 0.8210 (mttm) cc_final: 0.7748 (mtmm) REVERT: A 256 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7154 (tt0) REVERT: A 361 GLN cc_start: 0.7877 (tt0) cc_final: 0.7529 (tp40) REVERT: A 479 MET cc_start: 0.6864 (ttm) cc_final: 0.6526 (ttm) REVERT: A 485 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7114 (mt-10) REVERT: A 526 LYS cc_start: 0.8367 (mttm) cc_final: 0.7798 (mptt) REVERT: B 227 GLN cc_start: 0.8013 (pm20) cc_final: 0.7673 (pm20) REVERT: B 358 MET cc_start: 0.8671 (mmm) cc_final: 0.8179 (mmt) REVERT: B 416 LYS cc_start: 0.8226 (mttm) cc_final: 0.7902 (mmtm) REVERT: B 506 LYS cc_start: 0.8598 (ttmt) cc_final: 0.8362 (mttm) REVERT: B 518 GLN cc_start: 0.7385 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: C 291 TRP cc_start: 0.7045 (t-100) cc_final: 0.6408 (t60) REVERT: C 293 MET cc_start: 0.4627 (mpp) cc_final: 0.4385 (mpp) REVERT: C 336 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.6631 (mtp85) REVERT: C 358 MET cc_start: 0.8677 (ppp) cc_final: 0.8435 (ppp) REVERT: C 361 GLN cc_start: 0.9243 (mm110) cc_final: 0.8906 (mm110) REVERT: C 465 MET cc_start: 0.8288 (ttt) cc_final: 0.7686 (ttm) REVERT: C 517 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7108 (tm-30) REVERT: C 536 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: D 230 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4117 (tptt) REVERT: D 301 HIS cc_start: 0.7893 (p-80) cc_final: 0.7523 (p90) REVERT: D 312 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.7543 (pp30) REVERT: D 358 MET cc_start: 0.6037 (mpt) cc_final: 0.5507 (ttt) REVERT: D 362 ASP cc_start: 0.7612 (m-30) cc_final: 0.7343 (t70) REVERT: D 429 MET cc_start: 0.6104 (mmm) cc_final: 0.4790 (ptp) REVERT: D 451 HIS cc_start: 0.4106 (OUTLIER) cc_final: 0.3148 (m-70) REVERT: D 455 PHE cc_start: 0.4440 (m-80) cc_final: 0.4141 (m-80) REVERT: E 61 ASP cc_start: 0.8454 (m-30) cc_final: 0.8186 (m-30) REVERT: E 75 LYS cc_start: 0.8378 (ptpp) cc_final: 0.8153 (tptt) REVERT: F 10 ASP cc_start: 0.7681 (m-30) cc_final: 0.7468 (m-30) REVERT: F 42 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7404 (ttp-170) REVERT: F 91 GLN cc_start: 0.8399 (pm20) cc_final: 0.7792 (pm20) outliers start: 59 outliers final: 37 residues processed: 242 average time/residue: 0.2864 time to fit residues: 100.9949 Evaluate side-chains 224 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 181 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 293 MET Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 476 THR Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 368 MET Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 226 VAL Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 94 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 100 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 chunk 148 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15941 Z= 0.221 Angle : 0.625 11.310 21835 Z= 0.324 Chirality : 0.043 0.283 2361 Planarity : 0.005 0.051 2644 Dihedral : 16.498 142.121 2684 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.75 % Allowed : 21.34 % Favored : 75.91 % 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: -0.23 (0.20), residues: 1773 helix: 1.39 (0.18), residues: 827 sheet: -0.54 (0.40), residues: 161 loop : -1.83 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 327 HIS 0.007 0.001 HIS C 366 PHE 0.015 0.001 PHE B 407 TYR 0.015 0.001 TYR D 527 ARG 0.006 0.000 ARG D 344 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8182 (mttm) cc_final: 0.7746 (mtmm) REVERT: A 256 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7131 (tt0) REVERT: A 361 GLN cc_start: 0.7893 (tt0) cc_final: 0.7553 (tp40) REVERT: A 412 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6892 (ttm110) REVERT: A 454 ARG cc_start: 0.7566 (ptp90) cc_final: 0.7258 (ptm160) REVERT: A 479 MET cc_start: 0.6799 (ttm) cc_final: 0.6428 (ttm) REVERT: A 485 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7109 (mt-10) REVERT: A 526 LYS cc_start: 0.8339 (mttm) cc_final: 0.7795 (mptt) REVERT: B 227 GLN cc_start: 0.8036 (pm20) cc_final: 0.7713 (pm20) REVERT: B 358 MET cc_start: 0.8810 (mmm) cc_final: 0.8378 (mmt) REVERT: B 416 LYS cc_start: 0.8173 (mttm) cc_final: 0.7900 (mmtp) REVERT: B 506 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8307 (mttm) REVERT: B 518 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6199 (mp10) REVERT: C 291 TRP cc_start: 0.7161 (t-100) cc_final: 0.6420 (t60) REVERT: C 293 MET cc_start: 0.4749 (mpp) cc_final: 0.4489 (mpp) REVERT: C 336 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6808 (mtp85) REVERT: C 361 GLN cc_start: 0.9281 (mm110) cc_final: 0.9050 (mm110) REVERT: C 517 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7080 (tm-30) REVERT: C 536 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: D 230 LYS cc_start: 0.5425 (OUTLIER) cc_final: 0.4029 (tptt) REVERT: D 253 ARG cc_start: 0.7487 (tpt90) cc_final: 0.6617 (ptp-110) REVERT: D 301 HIS cc_start: 0.7605 (p-80) cc_final: 0.6861 (p90) REVERT: D 305 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8015 (mt-10) REVERT: D 312 GLN cc_start: 0.7789 (OUTLIER) cc_final: 0.7519 (pp30) REVERT: D 358 MET cc_start: 0.6045 (mpt) cc_final: 0.5471 (ttp) REVERT: D 362 ASP cc_start: 0.7648 (m-30) cc_final: 0.7337 (t70) REVERT: D 429 MET cc_start: 0.6263 (mmm) cc_final: 0.5028 (ptp) REVERT: D 451 HIS cc_start: 0.3890 (OUTLIER) cc_final: 0.3080 (m-70) REVERT: D 455 PHE cc_start: 0.4481 (m-80) cc_final: 0.4281 (m-80) REVERT: F 2 GLU cc_start: 0.7684 (tt0) cc_final: 0.7455 (tt0) REVERT: F 10 ASP cc_start: 0.7789 (m-30) cc_final: 0.7548 (m-30) REVERT: F 42 ARG cc_start: 0.7990 (mmm-85) cc_final: 0.7406 (ttp-170) REVERT: F 91 GLN cc_start: 0.8504 (pm20) cc_final: 0.7867 (pm20) outliers start: 41 outliers final: 24 residues processed: 234 average time/residue: 0.2915 time to fit residues: 99.6590 Evaluate side-chains 213 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 506 LYS Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 254 LEU Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain F residue 73 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.2980 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 137 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN D 555 ASN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 moved from start: 0.7278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15941 Z= 0.226 Angle : 0.629 10.857 21835 Z= 0.324 Chirality : 0.042 0.201 2361 Planarity : 0.005 0.065 2644 Dihedral : 16.462 142.225 2684 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.36 % Allowed : 21.41 % Favored : 75.23 % 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: -0.20 (0.20), residues: 1773 helix: 1.44 (0.18), residues: 828 sheet: -0.82 (0.38), residues: 177 loop : -1.79 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 327 HIS 0.007 0.001 HIS C 366 PHE 0.014 0.001 PHE D 468 TYR 0.012 0.001 TYR D 527 ARG 0.010 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 191 time to evaluate : 1.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8146 (mttm) cc_final: 0.7744 (mtmm) REVERT: A 256 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7149 (tt0) REVERT: A 358 MET cc_start: 0.7751 (mmp) cc_final: 0.6238 (tmm) REVERT: A 361 GLN cc_start: 0.7873 (tt0) cc_final: 0.7560 (tp40) REVERT: A 454 ARG cc_start: 0.7611 (ptp90) cc_final: 0.7286 (mtm110) REVERT: A 479 MET cc_start: 0.6658 (ttm) cc_final: 0.6279 (ttm) REVERT: A 485 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7127 (mt-10) REVERT: B 227 GLN cc_start: 0.8109 (pm20) cc_final: 0.7841 (pm20) REVERT: B 358 MET cc_start: 0.8913 (mmm) cc_final: 0.8622 (mmm) REVERT: B 368 MET cc_start: 0.7670 (mmm) cc_final: 0.7460 (mmm) REVERT: B 416 LYS cc_start: 0.8182 (mttm) cc_final: 0.7934 (mmtp) REVERT: B 518 GLN cc_start: 0.7270 (OUTLIER) cc_final: 0.6072 (mp10) REVERT: C 291 TRP cc_start: 0.7166 (t-100) cc_final: 0.6400 (t60) REVERT: C 293 MET cc_start: 0.4806 (mpp) cc_final: 0.4536 (mpp) REVERT: C 336 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7199 (mtp85) REVERT: C 465 MET cc_start: 0.8431 (ttt) cc_final: 0.7925 (ttm) REVERT: C 517 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7102 (tm-30) REVERT: C 536 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: D 230 LYS cc_start: 0.5538 (OUTLIER) cc_final: 0.4096 (tptt) REVERT: D 253 ARG cc_start: 0.7525 (tpt90) cc_final: 0.6616 (ptp-110) REVERT: D 296 THR cc_start: 0.8587 (m) cc_final: 0.8156 (p) REVERT: D 301 HIS cc_start: 0.7738 (p-80) cc_final: 0.7127 (p90) REVERT: D 305 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8011 (mt-10) REVERT: D 312 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7406 (pp30) REVERT: D 358 MET cc_start: 0.6024 (mpt) cc_final: 0.5508 (ttt) REVERT: D 362 ASP cc_start: 0.7584 (m-30) cc_final: 0.7340 (t70) REVERT: D 429 MET cc_start: 0.6483 (mmm) cc_final: 0.5214 (ptp) REVERT: D 451 HIS cc_start: 0.3899 (OUTLIER) cc_final: 0.3086 (m-70) REVERT: E 25 HIS cc_start: 0.8411 (OUTLIER) cc_final: 0.7192 (m-70) REVERT: F 10 ASP cc_start: 0.7752 (m-30) cc_final: 0.7491 (m-30) REVERT: F 42 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7423 (ttp-170) REVERT: F 91 GLN cc_start: 0.8507 (pm20) cc_final: 0.7856 (pm20) outliers start: 50 outliers final: 28 residues processed: 225 average time/residue: 0.2919 time to fit residues: 95.7754 Evaluate side-chains 215 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 180 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 56 VAL Chi-restraints excluded: chain F residue 73 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 98 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 154 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 295 HIS C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.7402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15941 Z= 0.205 Angle : 0.620 9.775 21835 Z= 0.319 Chirality : 0.042 0.163 2361 Planarity : 0.004 0.056 2644 Dihedral : 16.446 142.203 2684 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.89 % Allowed : 22.15 % Favored : 74.97 % 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 (0.20), residues: 1773 helix: 1.53 (0.18), residues: 826 sheet: -0.85 (0.38), residues: 177 loop : -1.76 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 327 HIS 0.012 0.001 HIS D 295 PHE 0.015 0.001 PHE B 407 TYR 0.012 0.001 TYR A 21 ARG 0.007 0.000 ARG D 325 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 1.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8117 (mttm) cc_final: 0.7750 (mtmm) REVERT: A 256 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7123 (tt0) REVERT: A 358 MET cc_start: 0.7777 (mmp) cc_final: 0.6284 (tmm) REVERT: A 361 GLN cc_start: 0.7732 (tt0) cc_final: 0.7416 (tp40) REVERT: A 454 ARG cc_start: 0.7598 (ptp90) cc_final: 0.7367 (mtm110) REVERT: A 479 MET cc_start: 0.6568 (ttm) cc_final: 0.6163 (ttm) REVERT: A 485 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7167 (mt-10) REVERT: B 227 GLN cc_start: 0.8123 (pm20) cc_final: 0.7902 (pm20) REVERT: B 358 MET cc_start: 0.8930 (mmm) cc_final: 0.8634 (mmm) REVERT: B 368 MET cc_start: 0.7547 (mmm) cc_final: 0.7342 (mmm) REVERT: B 416 LYS cc_start: 0.8197 (mttm) cc_final: 0.7967 (mmtp) REVERT: B 518 GLN cc_start: 0.7252 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: C 291 TRP cc_start: 0.7171 (t-100) cc_final: 0.6379 (t60) REVERT: C 293 MET cc_start: 0.4835 (mpp) cc_final: 0.4541 (mpp) REVERT: C 336 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6971 (mtp85) REVERT: C 465 MET cc_start: 0.8408 (ttt) cc_final: 0.7928 (ttm) REVERT: C 500 LEU cc_start: 0.7631 (mm) cc_final: 0.7207 (mm) REVERT: C 517 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6970 (tm-30) REVERT: C 536 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: D 230 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.4124 (tptt) REVERT: D 253 ARG cc_start: 0.7503 (tpt90) cc_final: 0.6834 (ptm-80) REVERT: D 265 ASN cc_start: 0.7394 (m-40) cc_final: 0.7133 (m-40) REVERT: D 296 THR cc_start: 0.8653 (m) cc_final: 0.8260 (p) REVERT: D 301 HIS cc_start: 0.7730 (p-80) cc_final: 0.7058 (p90) REVERT: D 305 GLU cc_start: 0.8259 (mt-10) cc_final: 0.8026 (mt-10) REVERT: D 312 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7406 (pp30) REVERT: D 358 MET cc_start: 0.6098 (mpt) cc_final: 0.5630 (ttt) REVERT: D 362 ASP cc_start: 0.7569 (m-30) cc_final: 0.7324 (t70) REVERT: D 429 MET cc_start: 0.6599 (mmm) cc_final: 0.5330 (ptp) REVERT: D 430 LEU cc_start: 0.6615 (mt) cc_final: 0.6349 (mt) REVERT: E 25 HIS cc_start: 0.8401 (OUTLIER) cc_final: 0.7177 (m-70) REVERT: F 2 GLU cc_start: 0.7570 (tt0) cc_final: 0.7336 (tt0) REVERT: F 10 ASP cc_start: 0.7646 (m-30) cc_final: 0.7331 (m-30) REVERT: F 42 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7470 (ttp-170) REVERT: F 91 GLN cc_start: 0.8494 (pm20) cc_final: 0.7836 (pm20) outliers start: 43 outliers final: 30 residues processed: 220 average time/residue: 0.3162 time to fit residues: 101.7660 Evaluate side-chains 217 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 389 GLN Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 5.9990 chunk 172 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 chunk 144 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 88 optimal weight: 0.0870 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15941 Z= 0.198 Angle : 0.610 9.049 21835 Z= 0.315 Chirality : 0.041 0.172 2361 Planarity : 0.004 0.053 2644 Dihedral : 16.421 141.868 2684 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.89 % Allowed : 22.28 % Favored : 74.83 % 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 (0.20), residues: 1773 helix: 1.49 (0.18), residues: 833 sheet: -0.72 (0.40), residues: 168 loop : -1.77 (0.21), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 327 HIS 0.011 0.001 HIS D 295 PHE 0.015 0.001 PHE A 425 TYR 0.019 0.001 TYR B 387 ARG 0.007 0.000 ARG D 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3546 Ramachandran restraints generated. 1773 Oldfield, 0 Emsley, 1773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8095 (mttm) cc_final: 0.7769 (mtmm) REVERT: A 256 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7104 (tt0) REVERT: A 358 MET cc_start: 0.7918 (mmp) cc_final: 0.6383 (tmm) REVERT: A 361 GLN cc_start: 0.7746 (tt0) cc_final: 0.7449 (tp40) REVERT: A 454 ARG cc_start: 0.7640 (ptp90) cc_final: 0.7429 (mtm110) REVERT: A 462 LEU cc_start: 0.7860 (tp) cc_final: 0.7313 (tp) REVERT: A 479 MET cc_start: 0.6528 (ttm) cc_final: 0.6146 (ttm) REVERT: A 485 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7192 (mt-10) REVERT: B 227 GLN cc_start: 0.8139 (pm20) cc_final: 0.7933 (pm20) REVERT: B 358 MET cc_start: 0.8967 (mmm) cc_final: 0.8669 (mmm) REVERT: B 368 MET cc_start: 0.7579 (mmm) cc_final: 0.7377 (mmm) REVERT: B 416 LYS cc_start: 0.8185 (mttm) cc_final: 0.7946 (mmtp) REVERT: C 291 TRP cc_start: 0.7323 (t-100) cc_final: 0.6456 (t60) REVERT: C 293 MET cc_start: 0.4866 (mpp) cc_final: 0.4550 (mpp) REVERT: C 336 ARG cc_start: 0.7573 (OUTLIER) cc_final: 0.6754 (mtp85) REVERT: C 465 MET cc_start: 0.8390 (ttt) cc_final: 0.7928 (ttm) REVERT: C 517 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6963 (tm-30) REVERT: C 536 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: D 230 LYS cc_start: 0.5607 (OUTLIER) cc_final: 0.4156 (tptt) REVERT: D 253 ARG cc_start: 0.7436 (tpt90) cc_final: 0.6840 (ptm-80) REVERT: D 265 ASN cc_start: 0.7157 (m-40) cc_final: 0.6906 (m-40) REVERT: D 296 THR cc_start: 0.8592 (m) cc_final: 0.8156 (p) REVERT: D 301 HIS cc_start: 0.7720 (p-80) cc_final: 0.6974 (p90) REVERT: D 305 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8046 (mt-10) REVERT: D 312 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.7429 (pp30) REVERT: D 358 MET cc_start: 0.6098 (mpt) cc_final: 0.5642 (ttt) REVERT: D 362 ASP cc_start: 0.7495 (m-30) cc_final: 0.7244 (t70) REVERT: D 429 MET cc_start: 0.6659 (mmm) cc_final: 0.5388 (ptp) REVERT: E 25 HIS cc_start: 0.8368 (OUTLIER) cc_final: 0.7094 (m-70) REVERT: F 2 GLU cc_start: 0.7510 (tt0) cc_final: 0.7232 (tt0) REVERT: F 42 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7457 (ttp-170) REVERT: F 91 GLN cc_start: 0.8497 (pm20) cc_final: 0.7858 (pm20) outliers start: 43 outliers final: 31 residues processed: 217 average time/residue: 0.2917 time to fit residues: 92.8926 Evaluate side-chains 213 residues out of total 1490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 320 CYS Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 434 TRP Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 518 GLN Chi-restraints excluded: chain B residue 527 TYR Chi-restraints excluded: chain B residue 529 ILE Chi-restraints excluded: chain B residue 555 ASN Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 248 ARG Chi-restraints excluded: chain C residue 256 GLU Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 322 ASN Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 ASN Chi-restraints excluded: chain C residue 375 VAL Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 536 GLU Chi-restraints excluded: chain D residue 230 LYS Chi-restraints excluded: chain D residue 236 ASP Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 292 PHE Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 312 GLN Chi-restraints excluded: chain E residue 8 SER Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 HIS Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 13 ASN Chi-restraints excluded: chain F residue 29 CYS Chi-restraints excluded: chain F residue 73 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 10.0000 chunk 153 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 40 optimal weight: 0.2980 chunk 144 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 ASN B 389 GLN C 312 GLN ** C 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN ** D 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.099984 restraints weight = 27963.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.102456 restraints weight = 14544.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.103129 restraints weight = 9454.927| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15941 Z= 0.270 Angle : 0.640 8.969 21835 Z= 0.331 Chirality : 0.043 0.188 2361 Planarity : 0.005 0.050 2644 Dihedral : 16.461 141.447 2684 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.62 % Allowed : 22.68 % Favored : 74.70 % 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 (0.20), residues: 1773 helix: 1.56 (0.18), residues: 819 sheet: -0.73 (0.40), residues: 165 loop : -1.70 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 327 HIS 0.010 0.001 HIS D 295 PHE 0.024 0.001 PHE A 425 TYR 0.020 0.001 TYR B 387 ARG 0.015 0.000 ARG F 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3281.50 seconds wall clock time: 60 minutes 25.44 seconds (3625.44 seconds total)