Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 02:17:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlb_22238/04_2023/6xlb_22238.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 7178 2.51 5 N 1828 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 284": "OE1" <-> "OE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ASP 352": "OD1" <-> "OD2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 366": "OD1" <-> "OD2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 479": "OE1" <-> "OE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 485": "OD1" <-> "OD2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 511": "OE1" <-> "OE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 523": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A ASP 552": "OD1" <-> "OD2" Residue "A ASP 556": "OD1" <-> "OD2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 329": "OE1" <-> "OE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ASP 352": "OD1" <-> "OD2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 366": "OD1" <-> "OD2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B ASP 406": "OD1" <-> "OD2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 411": "OD1" <-> "OD2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B GLU 479": "OE1" <-> "OE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 485": "OD1" <-> "OD2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B TYR 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 527": "OE1" <-> "OE2" Residue "B GLU 535": "OE1" <-> "OE2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B GLU 539": "OE1" <-> "OE2" Residue "B GLU 542": "OE1" <-> "OE2" Residue "B ASP 556": "OD1" <-> "OD2" Residue "B GLU 559": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B GLU 620": "OE1" <-> "OE2" Residue "B ASP 632": "OD1" <-> "OD2" Residue "C1 ASP 13": "OD1" <-> "OD2" Residue "C1 GLU 22": "OE1" <-> "OE2" Residue "C1 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 51": "OE1" <-> "OE2" Residue "C1 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ASP 68": "OD1" <-> "OD2" Residue "C1 ASP 80": "OD1" <-> "OD2" Residue "C1 PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 90": "OE1" <-> "OE2" Residue "C1 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 103": "OE1" <-> "OE2" Residue "C1 TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ASP 110": "OD1" <-> "OD2" Residue "C1 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 119": "OE1" <-> "OE2" Residue "C1 GLU 130": "OE1" <-> "OE2" Residue "C1 ARG 136": "NH1" <-> "NH2" Residue "C1 ASP 145": "OD1" <-> "OD2" Residue "C1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 228": "OE1" <-> "OE2" Residue "C1 GLU 231": "OE1" <-> "OE2" Residue "C1 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ARG 244": "NH1" <-> "NH2" Residue "C1 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 256": "OE1" <-> "OE2" Residue "C1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 271": "OE1" <-> "OE2" Residue "C1 PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 304": "OE1" <-> "OE2" Residue "C1 PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 GLU 310": "OE1" <-> "OE2" Residue "C1 ARG 327": "NH1" <-> "NH2" Residue "C1 TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C1 ARG 338": "NH1" <-> "NH2" Residue "D1 PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 97": "OE1" <-> "OE2" Residue "D1 PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 136": "NH1" <-> "NH2" Residue "D1 ASP 145": "OD1" <-> "OD2" Residue "D1 TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 219": "OE1" <-> "OE2" Residue "D1 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 231": "OE1" <-> "OE2" Residue "D1 PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 244": "NH1" <-> "NH2" Residue "D1 PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 271": "OE1" <-> "OE2" Residue "D1 GLU 276": "OE1" <-> "OE2" Residue "D1 PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 GLU 304": "OE1" <-> "OE2" Residue "D1 GLU 307": "OE1" <-> "OE2" Residue "D1 ASP 326": "OD1" <-> "OD2" Residue "D1 ARG 327": "NH1" <-> "NH2" Residue "D1 PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D1 ARG 338": "NH1" <-> "NH2" Residue "D1 PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11180 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3304 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 15, 'TRANS': 390} Chain: "B" Number of atoms: 3304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3304 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 15, 'TRANS': 390} Chain: "C1" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Chain: "D1" Number of atoms: 2286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2286 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain breaks: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.57 Number of scatterers: 11180 At special positions: 0 Unit cell: (97.008, 107.328, 108.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 2152 8.00 N 1828 7.00 C 7178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.71 Conformation dependent library (CDL) restraints added in 1.6 seconds 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2640 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 271 through 275 Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.582A pdb=" N TYR A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 404 removed outlier: 3.955A pdb=" N VAL A 387 " --> pdb=" O LYS A 383 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A 388 " --> pdb=" O ILE A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 428 removed outlier: 4.188A pdb=" N LYS A 412 " --> pdb=" O GLU A 408 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LYS A 419 " --> pdb=" O SER A 415 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ASN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 436 Processing helix chain 'A' and resid 453 through 459 Processing helix chain 'A' and resid 474 through 480 removed outlier: 3.614A pdb=" N LYS A 480 " --> pdb=" O LYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 490 removed outlier: 4.287A pdb=" N ALA A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 487 " --> pdb=" O PHE A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 510 Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.842A pdb=" N LYS A 538 " --> pdb=" O ALA A 534 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLU A 542 " --> pdb=" O LYS A 538 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR A 543 " --> pdb=" O GLU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 582 through 590 Processing helix chain 'A' and resid 602 through 605 Processing helix chain 'A' and resid 615 through 628 Processing helix chain 'A' and resid 632 through 651 Processing helix chain 'A' and resid 656 through 672 removed outlier: 4.392A pdb=" N PHE A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.501A pdb=" N THR B 274 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 280 Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.523A pdb=" N TYR B 285 " --> pdb=" O THR B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 406 removed outlier: 3.700A pdb=" N VAL B 387 " --> pdb=" O LYS B 383 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE B 388 " --> pdb=" O ILE B 384 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 428 removed outlier: 3.800A pdb=" N LYS B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LYS B 419 " --> pdb=" O SER B 415 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 436 Processing helix chain 'B' and resid 453 through 460 Processing helix chain 'B' and resid 474 through 479 Processing helix chain 'B' and resid 484 through 490 Processing helix chain 'B' and resid 501 through 510 removed outlier: 3.591A pdb=" N ALA B 505 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 541 removed outlier: 3.532A pdb=" N GLU B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 541 " --> pdb=" O GLU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 555 Processing helix chain 'B' and resid 582 through 591 removed outlier: 3.603A pdb=" N ALA B 591 " --> pdb=" O ARG B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 605 Processing helix chain 'B' and resid 615 through 628 Processing helix chain 'B' and resid 632 through 651 Processing helix chain 'B' and resid 656 through 672 removed outlier: 4.139A pdb=" N PHE B 660 " --> pdb=" O GLU B 656 " (cutoff:3.500A) Processing helix chain 'C1' and resid 16 through 28 Processing helix chain 'C1' and resid 117 through 121 Processing helix chain 'C1' and resid 122 through 131 removed outlier: 3.631A pdb=" N LEUC1 126 " --> pdb=" O GLUC1 122 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILEC1 127 " --> pdb=" O ALAC1 123 " (cutoff:3.500A) Processing helix chain 'C1' and resid 131 through 150 removed outlier: 3.916A pdb=" N GLYC1 143 " --> pdb=" O PHEC1 139 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYSC1 144 " --> pdb=" O GLNC1 140 " (cutoff:3.500A) Processing helix chain 'C1' and resid 225 through 233 Processing helix chain 'C1' and resid 235 through 244 Processing helix chain 'C1' and resid 326 through 336 Processing helix chain 'C1' and resid 337 through 344 Processing helix chain 'D1' and resid 16 through 28 Processing helix chain 'D1' and resid 117 through 121 Processing helix chain 'D1' and resid 122 through 131 removed outlier: 3.994A pdb=" N LEUD1 126 " --> pdb=" O GLUD1 122 " (cutoff:3.500A) Processing helix chain 'D1' and resid 131 through 150 removed outlier: 3.910A pdb=" N GLYD1 143 " --> pdb=" O PHED1 139 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYSD1 144 " --> pdb=" O GLND1 140 " (cutoff:3.500A) Processing helix chain 'D1' and resid 225 through 233 Processing helix chain 'D1' and resid 235 through 244 Processing helix chain 'D1' and resid 324 through 336 Processing helix chain 'D1' and resid 337 through 344 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 308 removed outlier: 3.619A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 451 through 452 removed outlier: 4.321A pdb=" N ASN A 442 " --> pdb=" O PHE A 496 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N LEU A 495 " --> pdb=" O ASN A 466 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N TYR A 468 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N LEU A 497 " --> pdb=" O TYR A 468 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE A 470 " --> pdb=" O LEU A 497 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE A 467 " --> pdb=" O VAL A 518 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 563 removed outlier: 7.828A pdb=" N PHE A 609 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N VAL A 561 " --> pdb=" O PHE A 609 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 611 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N VAL A 563 " --> pdb=" O ILE A 611 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 301 through 307 removed outlier: 6.349A pdb=" N LYS B 338 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N SER B 367 " --> pdb=" O LYS B 338 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N TYR B 340 " --> pdb=" O SER B 367 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 451 through 452 removed outlier: 4.182A pdb=" N ASN B 442 " --> pdb=" O PHE B 496 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N LEU B 495 " --> pdb=" O ASN B 466 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N TYR B 468 " --> pdb=" O LEU B 495 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N LEU B 497 " --> pdb=" O TYR B 468 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE B 470 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N ILE B 467 " --> pdb=" O VAL B 518 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 563 removed outlier: 6.690A pdb=" N LYS B 560 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 611 " --> pdb=" O LYS B 560 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 562 " --> pdb=" O ILE B 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C1' and resid 13 through 15 Processing sheet with id=AA8, first strand: chain 'C1' and resid 41 through 53 removed outlier: 7.073A pdb=" N LEUC1 74 " --> pdb=" O LYSC1 45 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N VALC1 47 " --> pdb=" O THRC1 72 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N THRC1 72 " --> pdb=" O VALC1 47 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N SERC1 49 " --> pdb=" O LYSC1 70 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYSC1 70 " --> pdb=" O SERC1 49 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLUC1 51 " --> pdb=" O ASPC1 68 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASPC1 68 " --> pdb=" O GLUC1 51 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEUC1 69 " --> pdb=" O GLUC1 97 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLUC1 97 " --> pdb=" O LEUC1 69 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLUC1 90 " --> pdb=" O PHEC1 114 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C1' and resid 213 through 218 removed outlier: 6.941A pdb=" N ILEC1 216 " --> pdb=" O THRC1 318 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THRC1 318 " --> pdb=" O ILEC1 216 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEUC1 218 " --> pdb=" O LYSC1 316 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYSC1 316 " --> pdb=" O LEUC1 218 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERC1 274 " --> pdb=" O VALC1 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C1' and resid 213 through 218 removed outlier: 6.941A pdb=" N ILEC1 216 " --> pdb=" O THRC1 318 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N THRC1 318 " --> pdb=" O ILEC1 216 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEUC1 218 " --> pdb=" O LYSC1 316 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYSC1 316 " --> pdb=" O LEUC1 218 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERC1 274 " --> pdb=" O VALC1 282 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C1' and resid 221 through 222 Processing sheet with id=AB3, first strand: chain 'D1' and resid 14 through 15 Processing sheet with id=AB4, first strand: chain 'D1' and resid 41 through 53 removed outlier: 8.051A pdb=" N LYSD1 43 " --> pdb=" O HISD1 78 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N HISD1 78 " --> pdb=" O LYSD1 43 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N LYSD1 45 " --> pdb=" O GLUD1 76 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N GLUD1 76 " --> pdb=" O LYSD1 45 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N VALD1 47 " --> pdb=" O LEUD1 74 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEUD1 74 " --> pdb=" O VALD1 47 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEUD1 69 " --> pdb=" O GLUD1 97 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLUD1 97 " --> pdb=" O LEUD1 69 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D1' and resid 214 through 218 removed outlier: 5.248A pdb=" N THRD1 214 " --> pdb=" O GLYD1 319 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N HISD1 284 " --> pdb=" O LEUD1 272 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N LEUD1 272 " --> pdb=" O HISD1 284 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LYSD1 286 " --> pdb=" O SERD1 270 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SERD1 270 " --> pdb=" O LYSD1 286 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D1' and resid 221 through 222 512 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3581 1.34 - 1.46: 2506 1.46 - 1.58: 5281 1.58 - 1.69: 0 1.69 - 1.81: 38 Bond restraints: 11406 Sorted by residual: bond pdb=" CA GLU A 544 " pdb=" C GLU A 544 " ideal model delta sigma weight residual 1.521 1.529 -0.008 1.14e-02 7.69e+03 5.05e-01 bond pdb=" CA GLU A 656 " pdb=" CB GLU A 656 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.58e-02 4.01e+03 4.65e-01 bond pdb=" CA ASP A 637 " pdb=" CB ASP A 637 " ideal model delta sigma weight residual 1.528 1.539 -0.010 1.66e-02 3.63e+03 3.90e-01 bond pdb=" CB GLU A 656 " pdb=" CG GLU A 656 " ideal model delta sigma weight residual 1.520 1.537 -0.017 3.00e-02 1.11e+03 3.09e-01 bond pdb=" C GLU A 544 " pdb=" O GLU A 544 " ideal model delta sigma weight residual 1.244 1.238 0.005 1.00e-02 1.00e+04 2.98e-01 ... (remaining 11401 not shown) Histogram of bond angle deviations from ideal: 100.41 - 107.13: 253 107.13 - 113.86: 6399 113.86 - 120.58: 4591 120.58 - 127.30: 4029 127.30 - 134.02: 94 Bond angle restraints: 15366 Sorted by residual: angle pdb=" C TYR A 543 " pdb=" N GLU A 544 " pdb=" CA GLU A 544 " ideal model delta sigma weight residual 119.78 122.50 -2.72 1.24e+00 6.50e-01 4.81e+00 angle pdb=" CA GLU A 656 " pdb=" CB GLU A 656 " pdb=" CG GLU A 656 " ideal model delta sigma weight residual 114.10 117.93 -3.83 2.00e+00 2.50e-01 3.66e+00 angle pdb=" CA TRPC1 242 " pdb=" CB TRPC1 242 " pdb=" CG TRPC1 242 " ideal model delta sigma weight residual 113.60 117.21 -3.61 1.90e+00 2.77e-01 3.61e+00 angle pdb=" C LEU A 509 " pdb=" N LYS A 510 " pdb=" CA LYS A 510 " ideal model delta sigma weight residual 121.54 125.05 -3.51 1.91e+00 2.74e-01 3.38e+00 angle pdb=" C LEU B 509 " pdb=" N LYS B 510 " pdb=" CA LYS B 510 " ideal model delta sigma weight residual 121.54 124.88 -3.34 1.91e+00 2.74e-01 3.05e+00 ... (remaining 15361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 6418 17.95 - 35.90: 415 35.90 - 53.85: 81 53.85 - 71.80: 23 71.80 - 89.75: 19 Dihedral angle restraints: 6956 sinusoidal: 2902 harmonic: 4054 Sorted by residual: dihedral pdb=" CB GLUC1 228 " pdb=" CG GLUC1 228 " pdb=" CD GLUC1 228 " pdb=" OE1 GLUC1 228 " ideal model delta sinusoidal sigma weight residual 0.00 -86.78 86.78 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA ASNC1 152 " pdb=" CB ASNC1 152 " pdb=" CG ASNC1 152 " pdb=" OD1 ASNC1 152 " ideal model delta sinusoidal sigma weight residual 120.00 -174.79 -65.21 2 2.00e+01 2.50e-03 9.89e+00 dihedral pdb=" CB GLUD1 324 " pdb=" CG GLUD1 324 " pdb=" CD GLUD1 324 " pdb=" OE1 GLUD1 324 " ideal model delta sinusoidal sigma weight residual 0.00 84.92 -84.92 1 3.00e+01 1.11e-03 9.72e+00 ... (remaining 6953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1031 0.029 - 0.058: 438 0.058 - 0.086: 112 0.086 - 0.115: 100 0.115 - 0.144: 13 Chirality restraints: 1694 Sorted by residual: chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA ILE A 319 " pdb=" N ILE A 319 " pdb=" C ILE A 319 " pdb=" CB ILE A 319 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA ILEC1 50 " pdb=" N ILEC1 50 " pdb=" C ILEC1 50 " pdb=" CB ILEC1 50 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 1691 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VALD1 224 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.03e+00 pdb=" N PROD1 225 " -0.062 5.00e-02 4.00e+02 pdb=" CA PROD1 225 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROD1 225 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VALC1 224 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PROC1 225 " 0.054 5.00e-02 4.00e+02 pdb=" CA PROC1 225 " -0.016 5.00e-02 4.00e+02 pdb=" CD PROC1 225 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " -0.020 5.00e-02 4.00e+02 3.03e-02 1.47e+00 pdb=" N PRO A 355 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.017 5.00e-02 4.00e+02 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1964 2.77 - 3.30: 10804 3.30 - 3.83: 18776 3.83 - 4.37: 22534 4.37 - 4.90: 38408 Nonbonded interactions: 92486 Sorted by model distance: nonbonded pdb=" OE1 GLU B 586 " pdb=" OG SER B 604 " model vdw 2.235 2.440 nonbonded pdb=" O ILEC1 239 " pdb=" OG1 THRC1 243 " model vdw 2.243 2.440 nonbonded pdb=" O ILED1 239 " pdb=" OG1 THRD1 243 " model vdw 2.254 2.440 nonbonded pdb=" OH TYR A 456 " pdb=" O GLU A 493 " model vdw 2.254 2.440 nonbonded pdb=" OG SER B 446 " pdb=" O GLU B 449 " model vdw 2.255 2.440 ... (remaining 92481 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 'A' selection = chain 'B' } ncs_group { reference = chain 'C1' selection = chain 'D1' } 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: 4.130 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: 8.390 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 32.730 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 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 : 0.002 0.021 11406 Z= 0.099 Angle : 0.428 5.953 15366 Z= 0.238 Chirality : 0.040 0.144 1694 Planarity : 0.003 0.036 1960 Dihedral : 13.651 89.751 4316 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.20), residues: 1368 helix: -1.42 (0.20), residues: 518 sheet: -1.62 (0.29), residues: 284 loop : -1.58 (0.23), residues: 566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 353 time to evaluate : 1.433 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: symmetry clash outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.3041 time to fit residues: 140.4675 Evaluate side-chains 194 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 430 GLN A 442 ASN ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 ASN ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 508 GLN ** B 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C1 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN C1 212 ASN D1 78 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11406 Z= 0.266 Angle : 0.622 8.466 15366 Z= 0.326 Chirality : 0.045 0.190 1694 Planarity : 0.004 0.048 1960 Dihedral : 3.793 17.141 1466 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.01 % 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: -1.17 (0.22), residues: 1368 helix: -0.10 (0.23), residues: 522 sheet: -1.15 (0.30), residues: 278 loop : -1.07 (0.25), residues: 568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 1.318 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 outliers start: 25 outliers final: 16 residues processed: 199 average time/residue: 0.2709 time to fit residues: 74.1186 Evaluate side-chains 157 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 141 time to evaluate : 1.565 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1100 time to fit residues: 5.3755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 592 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 58 GLN ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 314 GLN D1 284 HIS ** D1 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 11406 Z= 0.228 Angle : 0.596 10.436 15366 Z= 0.306 Chirality : 0.044 0.176 1694 Planarity : 0.004 0.047 1960 Dihedral : 3.909 18.183 1466 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.45 % 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: -0.89 (0.22), residues: 1368 helix: 0.11 (0.23), residues: 526 sheet: -1.03 (0.30), residues: 278 loop : -0.88 (0.25), residues: 564 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.491 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 outliers start: 18 outliers final: 9 residues processed: 186 average time/residue: 0.2599 time to fit residues: 67.1568 Evaluate side-chains 149 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.473 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1094 time to fit residues: 3.6571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.0370 chunk 83 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 212 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 11406 Z= 0.203 Angle : 0.587 9.051 15366 Z= 0.305 Chirality : 0.044 0.155 1694 Planarity : 0.004 0.042 1960 Dihedral : 4.046 18.506 1466 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 2.50 % 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: -0.70 (0.23), residues: 1368 helix: 0.24 (0.23), residues: 526 sheet: -0.85 (0.29), residues: 296 loop : -0.77 (0.26), residues: 546 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 165 time to evaluate : 1.463 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 outliers start: 31 outliers final: 12 residues processed: 186 average time/residue: 0.2486 time to fit residues: 65.4463 Evaluate side-chains 145 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1177 time to fit residues: 4.5459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 0.0670 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 11406 Z= 0.228 Angle : 0.597 8.778 15366 Z= 0.307 Chirality : 0.045 0.210 1694 Planarity : 0.004 0.041 1960 Dihedral : 4.095 19.015 1466 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 1.29 % 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: -0.58 (0.23), residues: 1368 helix: 0.33 (0.23), residues: 526 sheet: -0.74 (0.30), residues: 300 loop : -0.71 (0.26), residues: 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 146 time to evaluate : 1.459 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 outliers start: 16 outliers final: 9 residues processed: 154 average time/residue: 0.2770 time to fit residues: 59.1491 Evaluate side-chains 132 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1747 time to fit residues: 4.3366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 5.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 11406 Z= 0.179 Angle : 0.588 9.586 15366 Z= 0.301 Chirality : 0.044 0.174 1694 Planarity : 0.004 0.045 1960 Dihedral : 4.058 18.830 1466 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.13 % 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: -0.40 (0.23), residues: 1368 helix: 0.50 (0.24), residues: 524 sheet: -0.53 (0.32), residues: 280 loop : -0.73 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 150 average time/residue: 0.2391 time to fit residues: 51.8402 Evaluate side-chains 130 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 122 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1225 time to fit residues: 3.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 110 optimal weight: 0.1980 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN B 391 ASN ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 11406 Z= 0.180 Angle : 0.596 9.881 15366 Z= 0.304 Chirality : 0.044 0.208 1694 Planarity : 0.004 0.038 1960 Dihedral : 4.033 18.727 1466 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1368 helix: 0.52 (0.23), residues: 526 sheet: -0.55 (0.33), residues: 280 loop : -0.62 (0.26), residues: 562 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 1.526 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 outliers start: 11 outliers final: 4 residues processed: 154 average time/residue: 0.2622 time to fit residues: 56.9081 Evaluate side-chains 126 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 122 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1062 time to fit residues: 2.6388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.0670 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.1980 chunk 83 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 11406 Z= 0.181 Angle : 0.627 11.192 15366 Z= 0.317 Chirality : 0.044 0.184 1694 Planarity : 0.004 0.038 1960 Dihedral : 4.083 20.274 1466 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.48 % 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: -0.28 (0.23), residues: 1368 helix: 0.57 (0.24), residues: 524 sheet: -0.57 (0.33), residues: 280 loop : -0.55 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 133 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 134 average time/residue: 0.2601 time to fit residues: 49.6267 Evaluate side-chains 124 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 122 time to evaluate : 1.515 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1060 time to fit residues: 2.4194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.0030 chunk 125 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 380 GLN A 381 GLN ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN C1 247 GLN ** D1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.5014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 11406 Z= 0.215 Angle : 0.634 14.670 15366 Z= 0.324 Chirality : 0.044 0.191 1694 Planarity : 0.004 0.038 1960 Dihedral : 4.132 20.518 1466 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.40 % 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: -0.28 (0.23), residues: 1368 helix: 0.58 (0.24), residues: 524 sheet: -0.61 (0.32), residues: 280 loop : -0.55 (0.26), residues: 564 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 1.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 128 average time/residue: 0.2535 time to fit residues: 46.9514 Evaluate side-chains 119 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.499 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1244 time to fit residues: 2.4088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 0.0050 chunk 89 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN ** D1 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 284 HIS ** D1 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 11406 Z= 0.200 Angle : 0.645 10.717 15366 Z= 0.330 Chirality : 0.045 0.188 1694 Planarity : 0.004 0.037 1960 Dihedral : 4.169 20.793 1466 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 0.16 % 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: -0.30 (0.23), residues: 1368 helix: 0.53 (0.23), residues: 524 sheet: -0.59 (0.33), residues: 280 loop : -0.53 (0.26), residues: 564 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2736 Ramachandran restraints generated. 1368 Oldfield, 0 Emsley, 1368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 128 average time/residue: 0.2566 time to fit residues: 47.0598 Evaluate side-chains 121 residues out of total 1242 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.514 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1049 time to fit residues: 2.2488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 578 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 152 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.065786 restraints weight = 38657.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.067720 restraints weight = 24499.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069037 restraints weight = 18029.397| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 11406 Z= 0.213 Angle : 0.645 10.934 15366 Z= 0.328 Chirality : 0.045 0.195 1694 Planarity : 0.004 0.037 1960 Dihedral : 4.188 21.330 1466 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer Outliers : 0.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.23), residues: 1368 helix: 0.53 (0.23), residues: 526 sheet: -0.64 (0.33), residues: 280 loop : -0.54 (0.25), residues: 562 =============================================================================== Job complete usr+sys time: 2220.65 seconds wall clock time: 41 minutes 33.28 seconds (2493.28 seconds total)