Starting phenix.real_space_refine on Sun Dec 10 23:30:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mi9_23843/12_2023/7mi9_23843.pdb" } resolution = 3.89 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= -0.000 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: 5 Type Number sf(0) Gaussians P 170 5.49 5 S 74 5.16 5 C 9521 2.51 5 N 2935 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 234": "NH1" <-> "NH2" Residue "A ARG 253": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A ARG 279": "NH1" <-> "NH2" Residue "A ARG 307": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 349": "OE1" <-> "OE2" Residue "A ARG 365": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 386": "NH1" <-> "NH2" Residue "A ARG 393": "NH1" <-> "NH2" Residue "A ARG 413": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ARG 469": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 493": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "B ARG 278": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 307": "NH1" <-> "NH2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "B ARG 336": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 365": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 386": "NH1" <-> "NH2" Residue "B PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 393": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 432": "NH1" <-> "NH2" Residue "B GLU 433": "OE1" <-> "OE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B ARG 469": "NH1" <-> "NH2" Residue "B ARG 487": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 532": "NH1" <-> "NH2" Residue "B ARG 533": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C ARG 253": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ARG 278": "NH1" <-> "NH2" Residue "C ARG 279": "NH1" <-> "NH2" Residue "C ARG 302": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 313": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "C ARG 344": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 386": "NH1" <-> "NH2" Residue "C ARG 393": "NH1" <-> "NH2" 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 469": "NH1" <-> "NH2" Residue "C ARG 487": "NH1" <-> "NH2" Residue "C ARG 493": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C ARG 507": "NH1" <-> "NH2" Residue "C ARG 515": "NH1" <-> "NH2" Residue "C GLU 517": "OE1" <-> "OE2" Residue "C ARG 532": "NH1" <-> "NH2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D ARG 278": "NH1" <-> "NH2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D GLU 305": "OE1" <-> "OE2" Residue "D ARG 307": "NH1" <-> "NH2" Residue "D ARG 313": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ARG 344": "NH1" <-> "NH2" Residue "D ARG 365": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 386": "NH1" <-> "NH2" Residue "D ARG 393": "NH1" <-> "NH2" Residue "D GLU 401": "OE1" <-> "OE2" 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 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 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 19": "NH1" <-> "NH2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" 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 19": "NH1" <-> "NH2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F ARG 44": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 15924 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2772 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 20, 'TRANS': 327} Chain: "B" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2696 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 18, 'TRANS': 319} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2707 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 18, 'TRANS': 320} Chain: "D" Number of atoms: 2696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2696 Classifications: {'peptide': 339} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 320} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 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: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1639 Classifications: {'DNA': 80} Link IDs: {'rna3p': 79} Chain: "H" Number of atoms: 1468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1468 Classifications: {'DNA': 72} Link IDs: {'rna3p': 71} Chain: "I" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 250 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "J" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Time building chain proxies: 9.10, per 1000 atoms: 0.57 Number of scatterers: 15924 At special positions: 0 Unit cell: (119.574, 103.806, 185.274, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 170 15.00 O 3224 8.00 N 2935 7.00 C 9521 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: 8.24 Conformation dependent library (CDL) restraints added in 2.3 seconds 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2864 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 45.9% alpha, 9.2% beta 47 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 5.99 Creating SS restraints... Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.604A pdb=" N LEU A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 316 through 343 removed outlier: 3.914A pdb=" N CYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 330 " --> pdb=" O ARG A 326 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS A 331 " --> pdb=" O TRP A 327 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 358 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 385 through 390 Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 419 through 438 removed outlier: 4.467A pdb=" N PHE A 425 " --> pdb=" O ALA A 421 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 428 " --> pdb=" O SER A 424 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ARG A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 467 No H-bonds generated for 'chain 'A' and resid 465 through 467' Processing helix chain 'A' and resid 468 through 473 Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'A' and resid 487 through 491 removed outlier: 3.798A pdb=" N PHE A 491 " --> pdb=" O THR A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.591A pdb=" N LYS A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG A 507 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA A 510 " --> pdb=" O LYS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'B' and resid 253 through 257 removed outlier: 3.931A pdb=" N THR B 257 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 302 through 315 removed outlier: 3.671A pdb=" N THR B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N PHE B 315 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' Processing helix chain 'B' and resid 353 through 368 Processing helix chain 'B' and resid 374 through 386 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 390 through 395 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 424 through 437 removed outlier: 3.694A pdb=" N ARG B 432 " --> pdb=" O ALA B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 463 Processing helix chain 'B' and resid 465 through 469 Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 501 through 518 Processing helix chain 'B' and resid 531 through 546 removed outlier: 4.477A pdb=" N ALA B 539 " --> pdb=" O LEU B 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 277 Processing helix chain 'C' and resid 303 through 315 removed outlier: 3.574A pdb=" N ARG C 307 " --> pdb=" O ASN C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 333 removed outlier: 3.617A pdb=" N CYS C 320 " --> pdb=" O ASP C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 353 through 358 removed outlier: 3.880A pdb=" N MET C 358 " --> pdb=" O PRO C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 366 removed outlier: 3.689A pdb=" N MET C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 removed outlier: 3.717A pdb=" N GLY C 378 " --> pdb=" O GLU C 374 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU C 380 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 394 removed outlier: 3.729A pdb=" N MET C 394 " --> pdb=" O PHE C 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 391 through 394' Processing helix chain 'C' and resid 417 through 441 removed outlier: 3.938A pdb=" N LEU C 422 " --> pdb=" O PRO C 418 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 466 Processing helix chain 'C' and resid 467 through 472 removed outlier: 4.395A pdb=" N LEU C 471 " --> pdb=" O PRO C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 483 removed outlier: 3.973A pdb=" N VAL C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 518 removed outlier: 3.748A pdb=" N ALA C 510 " --> pdb=" O LYS C 506 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU C 517 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN C 518 " --> pdb=" O ARG C 514 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 548 Processing helix chain 'D' and resid 255 through 257 No H-bonds generated for 'chain 'D' and resid 255 through 257' Processing helix chain 'D' and resid 269 through 279 removed outlier: 4.156A pdb=" N ARG D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 313 Processing helix chain 'D' and resid 316 through 342 removed outlier: 3.908A pdb=" N CYS D 320 " --> pdb=" O ASP D 316 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG D 326 " --> pdb=" O ASN D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 368 Processing helix chain 'D' and resid 375 through 392 removed outlier: 3.633A pdb=" N SER D 392 " --> pdb=" O PHE D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 441 removed outlier: 3.623A pdb=" N ARG D 432 " --> pdb=" O ALA D 428 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU D 433 " --> pdb=" O MET D 429 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 3.681A pdb=" N LEU D 471 " --> pdb=" O PRO D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 483 removed outlier: 3.679A pdb=" N ASN D 483 " --> pdb=" O MET D 479 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 518 removed outlier: 3.577A pdb=" N MET D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU D 517 " --> pdb=" O GLU D 513 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLN D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 547 Processing helix chain 'E' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG E 19 " --> pdb=" O ARG E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 52 Processing helix chain 'F' and resid 13 through 26 removed outlier: 4.611A pdb=" N ARG F 19 " --> pdb=" O ARG F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 52 Processing sheet with id=AA1, first strand: chain 'A' and resid 222 through 226 removed outlier: 6.832A pdb=" N LEU A 222 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 8.694A pdb=" N ALA A 261 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU A 224 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N PHE A 263 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 226 " --> pdb=" O PHE A 263 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 247 through 253 removed outlier: 7.087A pdb=" N ILE A 242 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU A 251 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N LEU A 240 " --> pdb=" O GLU A 251 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 233 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295 Processing sheet with id=AA4, first strand: chain 'A' and resid 519 through 521 Processing sheet with id=AA5, first strand: chain 'B' and resid 225 through 226 removed outlier: 6.132A pdb=" N VAL B 260 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LEU B 286 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU B 262 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TRP B 285 " --> pdb=" O MET B 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.759A pdb=" N ILE B 242 " --> pdb=" O VAL B 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 491 through 492 Processing sheet with id=AA8, first strand: chain 'B' and resid 519 through 520 Processing sheet with id=AA9, first strand: chain 'D' and resid 224 through 225 removed outlier: 7.982A pdb=" N LEU D 224 " --> pdb=" O ALA D 261 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL D 260 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL D 283 " --> pdb=" O THR D 296 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR D 296 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS D 295 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL C 283 " --> pdb=" O THR C 296 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N LEU C 222 " --> pdb=" O SER C 258 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL C 260 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 224 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LEU C 262 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 226 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 248 through 253 removed outlier: 4.881A pdb=" N ALA C 250 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 491 through 493 Processing sheet with id=AB3, first strand: chain 'C' and resid 519 through 521 Processing sheet with id=AB4, first strand: chain 'D' and resid 231 through 236 Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 32 removed outlier: 5.515A pdb=" N TRP E 30 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLN E 37 " --> pdb=" O TRP E 30 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 79 " --> pdb=" O ILE E 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 80 removed outlier: 3.879A pdb=" N SER E 79 " --> pdb=" O ILE F 65 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN F 37 " --> pdb=" O TRP F 30 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TRP F 30 " --> pdb=" O GLN F 37 " (cutoff:3.500A) 510 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 121 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 5.28 Time building geometry restraints manager: 8.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3916 1.33 - 1.45: 4233 1.45 - 1.57: 8019 1.57 - 1.69: 336 1.69 - 1.82: 124 Bond restraints: 16628 Sorted by residual: bond pdb=" N GLY C 345 " pdb=" CA GLY C 345 " ideal model delta sigma weight residual 1.442 1.476 -0.034 7.70e-03 1.69e+04 1.98e+01 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.506 -0.047 1.25e-02 6.40e+03 1.44e+01 bond pdb=" N ILE A 328 " pdb=" CA ILE A 328 " ideal model delta sigma weight residual 1.452 1.496 -0.044 1.18e-02 7.18e+03 1.40e+01 bond pdb=" O3' DT H 27 " pdb=" P DT H 28 " ideal model delta sigma weight residual 1.607 1.661 -0.054 1.50e-02 4.44e+03 1.29e+01 bond pdb=" CA ALA B 437 " pdb=" C ALA B 437 " ideal model delta sigma weight residual 1.523 1.479 0.043 1.41e-02 5.03e+03 9.47e+00 ... (remaining 16623 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.32: 793 104.32 - 111.80: 8008 111.80 - 119.29: 5695 119.29 - 126.77: 8128 126.77 - 134.26: 601 Bond angle restraints: 23225 Sorted by residual: angle pdb=" N ILE B 524 " pdb=" CA ILE B 524 " pdb=" C ILE B 524 " ideal model delta sigma weight residual 113.71 107.60 6.11 9.50e-01 1.11e+00 4.13e+01 angle pdb=" C ARG B 412 " pdb=" N ARG B 413 " pdb=" CA ARG B 413 " ideal model delta sigma weight residual 121.80 108.89 12.91 2.44e+00 1.68e-01 2.80e+01 angle pdb=" N PHE B 388 " pdb=" CA PHE B 388 " pdb=" C PHE B 388 " ideal model delta sigma weight residual 113.17 106.74 6.43 1.26e+00 6.30e-01 2.60e+01 angle pdb=" C4' DG H 39 " pdb=" C3' DG H 39 " pdb=" O3' DG H 39 " ideal model delta sigma weight residual 110.00 117.44 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C4' DT H 6 " pdb=" C3' DT H 6 " pdb=" O3' DT H 6 " ideal model delta sigma weight residual 110.00 117.40 -7.40 1.50e+00 4.44e-01 2.43e+01 ... (remaining 23220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.99: 8490 34.99 - 69.97: 925 69.97 - 104.96: 41 104.96 - 139.94: 8 139.94 - 174.93: 5 Dihedral angle restraints: 9469 sinusoidal: 5001 harmonic: 4468 Sorted by residual: dihedral pdb=" CA ILE A 215 " pdb=" C ILE A 215 " pdb=" N PRO A 216 " pdb=" CA PRO A 216 " ideal model delta harmonic sigma weight residual 180.00 150.13 29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LEU A 478 " pdb=" C LEU A 478 " pdb=" N MET A 479 " pdb=" CA MET A 479 " ideal model delta harmonic sigma weight residual 180.00 151.66 28.34 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA GLU B 243 " pdb=" C GLU B 243 " pdb=" N GLU B 244 " pdb=" CA GLU B 244 " ideal model delta harmonic sigma weight residual 180.00 152.69 27.31 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 9466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 2146 0.074 - 0.149: 355 0.149 - 0.223: 19 0.223 - 0.297: 1 0.297 - 0.372: 5 Chirality restraints: 2526 Sorted by residual: chirality pdb=" C3' DT H 6 " pdb=" C4' DT H 6 " pdb=" O3' DT H 6 " pdb=" C2' DT H 6 " both_signs ideal model delta sigma weight residual False -2.66 -2.29 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' DT G 10 " pdb=" C4' DT G 10 " pdb=" O3' DT G 10 " pdb=" C2' DT G 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.29 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C3' DG H 10 " pdb=" C4' DG H 10 " pdb=" O3' DG H 10 " pdb=" C2' DG H 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.31 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 2523 not shown) Planarity restraints: 2421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 466 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.06e+01 pdb=" N PRO A 467 " -0.196 5.00e-02 4.00e+02 pdb=" CA PRO A 467 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 467 " 0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA D 370 " -0.062 5.00e-02 4.00e+02 9.52e-02 1.45e+01 pdb=" N PRO D 371 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 371 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 371 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 550 " 0.046 5.00e-02 4.00e+02 7.03e-02 7.90e+00 pdb=" N PRO C 551 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 551 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 551 " 0.039 5.00e-02 4.00e+02 ... (remaining 2418 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 337 2.59 - 3.16: 14547 3.16 - 3.74: 29004 3.74 - 4.32: 38425 4.32 - 4.90: 58256 Nonbonded interactions: 140569 Sorted by model distance: nonbonded pdb=" O ARG B 413 " pdb=" OP2 DT H 30 " model vdw 2.008 3.040 nonbonded pdb=" O GLN C 361 " pdb=" NE2 GLN C 361 " model vdw 2.117 2.520 nonbonded pdb=" O LEU A 323 " pdb=" CB TRP A 327 " model vdw 2.176 2.752 nonbonded pdb=" OD2 ASP A 490 " pdb=" NH2 ARG A 507 " model vdw 2.197 2.520 nonbonded pdb=" O PRO B 353 " pdb=" CD2 LEU B 357 " model vdw 2.202 3.460 ... (remaining 140564 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' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'B' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'C' and (resid 221 through 379 or (resid 380 through 381 and (name N or n \ ame CA or name C or name O )) or resid 382 through 558)) selection = (chain 'D' and resid 221 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.800 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 49.710 Find NCS groups from input model: 0.880 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4923 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 : 0.006 0.054 16628 Z= 0.385 Angle : 0.907 12.909 23225 Z= 0.546 Chirality : 0.053 0.372 2526 Planarity : 0.007 0.113 2421 Dihedral : 24.159 174.930 6605 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 38.70 Ramachandran Plot: Outliers : 0.58 % Allowed : 13.16 % Favored : 86.25 % Rotamer: Outliers : 2.08 % Allowed : 1.85 % Favored : 96.06 % Cbeta Deviations : 0.07 % 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: -3.37 (0.20), residues: 1542 helix: -1.59 (0.19), residues: 677 sheet: -2.83 (0.46), residues: 111 loop : -2.78 (0.20), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP B 434 HIS 0.009 0.002 HIS A 295 PHE 0.018 0.002 PHE B 556 TYR 0.037 0.003 TYR B 387 ARG 0.024 0.001 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 357 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 7 residues processed: 376 average time/residue: 0.3650 time to fit residues: 186.8181 Evaluate side-chains 203 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.690 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2050 time to fit residues: 4.5227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.6980 chunk 126 optimal weight: 0.1980 chunk 70 optimal weight: 0.3980 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 GLN A 390 HIS A 538 GLN B 555 ASN C 265 ASN ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN E 32 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5087 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16628 Z= 0.247 Angle : 0.775 10.980 23225 Z= 0.418 Chirality : 0.046 0.196 2526 Planarity : 0.007 0.063 2421 Dihedral : 27.525 178.674 3595 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 26.31 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.27 % Favored : 90.60 % Rotamer: Outliers : 2.55 % Allowed : 13.12 % Favored : 84.34 % 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: -2.85 (0.20), residues: 1542 helix: -1.12 (0.19), residues: 696 sheet: -2.07 (0.53), residues: 94 loop : -2.64 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 327 HIS 0.023 0.002 HIS B 366 PHE 0.023 0.002 PHE C 292 TYR 0.023 0.002 TYR A 527 ARG 0.009 0.001 ARG D 515 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 231 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 outliers start: 33 outliers final: 14 residues processed: 252 average time/residue: 0.3109 time to fit residues: 113.0014 Evaluate side-chains 183 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 169 time to evaluate : 1.416 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1514 time to fit residues: 5.8149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 0.0470 chunk 103 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 164 optimal weight: 5.9990 chunk 135 optimal weight: 0.8980 chunk 150 optimal weight: 0.0060 chunk 51 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.9896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 HIS ** C 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS D 301 HIS E 32 GLN F 32 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16628 Z= 0.241 Angle : 0.711 8.065 23225 Z= 0.385 Chirality : 0.043 0.210 2526 Planarity : 0.006 0.059 2421 Dihedral : 27.213 178.248 3595 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.01 % Favored : 90.86 % Rotamer: Outliers : 1.70 % Allowed : 17.52 % Favored : 80.79 % 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: -2.61 (0.20), residues: 1542 helix: -0.90 (0.19), residues: 695 sheet: -1.72 (0.53), residues: 94 loop : -2.58 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 343 HIS 0.016 0.002 HIS B 366 PHE 0.023 0.002 PHE C 263 TYR 0.022 0.002 TYR A 527 ARG 0.010 0.001 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 191 time to evaluate : 1.660 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: 22 outliers final: 5 residues processed: 205 average time/residue: 0.3033 time to fit residues: 91.9714 Evaluate side-chains 160 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 155 time to evaluate : 1.546 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1532 time to fit residues: 3.4682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 152 optimal weight: 3.9990 chunk 161 optimal weight: 10.0000 chunk 79 optimal weight: 0.1980 chunk 144 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 522 HIS A 538 GLN ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN C 334 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5463 moved from start: 0.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16628 Z= 0.291 Angle : 0.730 10.009 23225 Z= 0.395 Chirality : 0.044 0.179 2526 Planarity : 0.006 0.056 2421 Dihedral : 27.078 177.306 3595 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.66 % Favored : 90.21 % Rotamer: Outliers : 2.39 % Allowed : 19.91 % Favored : 77.70 % 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: -2.53 (0.20), residues: 1542 helix: -0.72 (0.20), residues: 693 sheet: -1.87 (0.49), residues: 109 loop : -2.64 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP A 327 HIS 0.009 0.001 HIS B 366 PHE 0.019 0.002 PHE A 455 TYR 0.023 0.002 TYR A 527 ARG 0.006 0.001 ARG D 515 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 167 time to evaluate : 1.457 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 outliers start: 31 outliers final: 10 residues processed: 191 average time/residue: 0.2918 time to fit residues: 81.7265 Evaluate side-chains 157 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.430 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1546 time to fit residues: 4.7425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 111 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 451 HIS C 301 HIS ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN F 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5586 moved from start: 0.6650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16628 Z= 0.266 Angle : 0.713 10.281 23225 Z= 0.387 Chirality : 0.043 0.193 2526 Planarity : 0.006 0.092 2421 Dihedral : 26.959 177.624 3595 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.14 % Favored : 90.79 % Rotamer: Outliers : 1.70 % Allowed : 21.91 % Favored : 76.39 % 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: -2.44 (0.20), residues: 1542 helix: -0.58 (0.20), residues: 683 sheet: -2.02 (0.47), residues: 115 loop : -2.59 (0.20), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 327 HIS 0.013 0.002 HIS D 274 PHE 0.019 0.002 PHE D 449 TYR 0.022 0.002 TYR A 527 ARG 0.006 0.001 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 176 time to evaluate : 1.553 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 outliers start: 22 outliers final: 6 residues processed: 190 average time/residue: 0.3050 time to fit residues: 84.2414 Evaluate side-chains 147 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 1.425 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2226 time to fit residues: 4.2274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 39 optimal weight: 0.0870 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 390 HIS B 366 HIS B 390 HIS B 451 HIS ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN C 451 HIS ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5534 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16628 Z= 0.211 Angle : 0.682 9.460 23225 Z= 0.365 Chirality : 0.041 0.157 2526 Planarity : 0.005 0.054 2421 Dihedral : 26.848 174.640 3595 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 1.77 % Allowed : 23.92 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.21), residues: 1542 helix: -0.26 (0.20), residues: 686 sheet: -1.77 (0.50), residues: 107 loop : -2.55 (0.20), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP A 327 HIS 0.005 0.001 HIS C 390 PHE 0.024 0.002 PHE A 455 TYR 0.018 0.001 TYR A 527 ARG 0.011 0.000 ARG C 302 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.634 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 outliers start: 23 outliers final: 10 residues processed: 171 average time/residue: 0.2857 time to fit residues: 72.9370 Evaluate side-chains 147 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.518 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1888 time to fit residues: 5.1939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 117 optimal weight: 0.2980 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 0.1980 chunk 160 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 74 optimal weight: 7.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5553 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16628 Z= 0.208 Angle : 0.677 9.882 23225 Z= 0.361 Chirality : 0.041 0.170 2526 Planarity : 0.005 0.051 2421 Dihedral : 26.755 167.890 3595 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 0.69 % Allowed : 25.00 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.09 (0.21), residues: 1542 helix: -0.21 (0.21), residues: 690 sheet: -1.62 (0.49), residues: 107 loop : -2.57 (0.20), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP A 327 HIS 0.008 0.001 HIS A 390 PHE 0.023 0.002 PHE A 508 TYR 0.016 0.001 TYR A 527 ARG 0.005 0.000 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 151 time to evaluate : 1.462 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: 9 outliers final: 2 residues processed: 159 average time/residue: 0.3091 time to fit residues: 71.7635 Evaluate side-chains 133 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 131 time to evaluate : 1.653 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1654 time to fit residues: 2.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 96 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 31 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.7912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16628 Z= 0.213 Angle : 0.689 9.741 23225 Z= 0.364 Chirality : 0.041 0.164 2526 Planarity : 0.005 0.050 2421 Dihedral : 26.664 170.384 3595 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.43 % Favored : 91.50 % Rotamer: Outliers : 0.85 % Allowed : 26.00 % Favored : 73.15 % 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: -2.08 (0.21), residues: 1542 helix: -0.19 (0.20), residues: 690 sheet: -1.61 (0.48), residues: 106 loop : -2.57 (0.20), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.003 TRP A 327 HIS 0.005 0.001 HIS A 390 PHE 0.031 0.002 PHE A 315 TYR 0.015 0.001 TYR A 527 ARG 0.007 0.000 ARG C 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 144 time to evaluate : 1.657 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: 151 average time/residue: 0.2969 time to fit residues: 68.1105 Evaluate side-chains 134 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 130 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1536 time to fit residues: 3.0278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5758 moved from start: 0.8722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16628 Z= 0.304 Angle : 0.756 10.508 23225 Z= 0.405 Chirality : 0.045 0.256 2526 Planarity : 0.006 0.053 2421 Dihedral : 26.669 171.574 3595 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 27.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.12 % Favored : 89.82 % Rotamer: Outliers : 1.08 % Allowed : 26.00 % Favored : 72.92 % 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: -2.26 (0.20), residues: 1542 helix: -0.33 (0.20), residues: 689 sheet: -2.10 (0.41), residues: 129 loop : -2.60 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP A 327 HIS 0.011 0.002 HIS B 451 PHE 0.028 0.002 PHE A 315 TYR 0.020 0.002 TYR A 527 ARG 0.009 0.001 ARG C 396 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 1 residues processed: 159 average time/residue: 0.3205 time to fit residues: 74.2698 Evaluate side-chains 131 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.717 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1465 time to fit residues: 2.4433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5883 moved from start: 0.9865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 16628 Z= 0.367 Angle : 0.840 12.572 23225 Z= 0.449 Chirality : 0.047 0.236 2526 Planarity : 0.007 0.083 2421 Dihedral : 26.696 171.338 3595 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 30.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 0.62 % Allowed : 27.39 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.25 % 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: -2.51 (0.20), residues: 1542 helix: -0.57 (0.20), residues: 684 sheet: -2.26 (0.38), residues: 143 loop : -2.67 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.003 TRP A 327 HIS 0.017 0.002 HIS C 390 PHE 0.027 0.003 PHE A 315 TYR 0.020 0.002 TYR A 527 ARG 0.033 0.001 ARG B 325 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3084 Ramachandran restraints generated. 1542 Oldfield, 0 Emsley, 1542 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 159 average time/residue: 0.3279 time to fit residues: 75.8759 Evaluate side-chains 138 residues out of total 1298 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 134 time to evaluate : 1.535 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1779 time to fit residues: 3.3694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 16 optimal weight: 0.0980 chunk 24 optimal weight: 3.9990 chunk 116 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 555 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 HIS C 483 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.160795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.142286 restraints weight = 64840.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.142201 restraints weight = 53169.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.142610 restraints weight = 40424.818| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6064 moved from start: 1.0085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16628 Z= 0.231 Angle : 0.758 11.115 23225 Z= 0.401 Chirality : 0.043 0.247 2526 Planarity : 0.006 0.048 2421 Dihedral : 26.603 171.015 3595 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 0.39 % Allowed : 27.85 % Favored : 71.76 % 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: -2.28 (0.21), residues: 1542 helix: -0.39 (0.20), residues: 687 sheet: -1.65 (0.44), residues: 114 loop : -2.65 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP A 327 HIS 0.009 0.001 HIS D 366 PHE 0.036 0.002 PHE A 407 TYR 0.015 0.001 TYR A 527 ARG 0.009 0.001 ARG C 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2871.76 seconds wall clock time: 53 minutes 20.34 seconds (3200.34 seconds total)