Starting phenix.real_space_refine on Wed Jun 26 14:47:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs0_38612/06_2024/8xs0_38612.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs0_38612/06_2024/8xs0_38612.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/8xs0_38612/06_2024/8xs0_38612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs0_38612/06_2024/8xs0_38612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs0_38612/06_2024/8xs0_38612.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xs0_38612/06_2024/8xs0_38612.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= 0.008 sd= 0.057 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 30 5.16 5 C 6826 2.51 5 N 1696 2.21 5 O 1801 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 520": "OE1" <-> "OE2" Residue "A TYR 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 661": "NH1" <-> "NH2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "A ASP 685": "OD1" <-> "OD2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 113": "OD1" <-> "OD2" Residue "B ARG 178": "NH1" <-> "NH2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 572": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 611": "NH1" <-> "NH2" Residue "B ARG 661": "NH1" <-> "NH2" Residue "B TYR 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 685": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10353 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5129 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 30, 'TRANS': 657} Chain breaks: 1 Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 5224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5224 Classifications: {'peptide': 700} Incomplete info: {'truncation_to_alanine': 96} Link IDs: {'PTRANS': 31, 'TRANS': 668} Unresolved non-hydrogen bonds: 387 Unresolved non-hydrogen angles: 482 Unresolved non-hydrogen dihedrals: 325 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 8, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 19, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 230 Time building chain proxies: 6.25, per 1000 atoms: 0.60 Number of scatterers: 10353 At special positions: 0 Unit cell: (88.62, 138.205, 103.39, 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 30 16.00 O 1801 8.00 N 1696 7.00 C 6826 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: 4.32 Conformation dependent library (CDL) restraints added in 2.2 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2656 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 2 sheets defined 71.0% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 26 Processing helix chain 'A' and resid 36 through 42 removed outlier: 3.742A pdb=" N ILE A 42 " --> pdb=" O TYR A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 68 Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 112 removed outlier: 3.781A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Proline residue: A 104 - end of helix removed outlier: 4.099A pdb=" N LEU A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix Processing helix chain 'A' and resid 117 through 125 removed outlier: 6.183A pdb=" N ALA A 122 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 142 removed outlier: 6.845A pdb=" N MET A 139 " --> pdb=" O ASN A 136 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 142 " --> pdb=" O MET A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 151 Processing helix chain 'A' and resid 152 through 184 Processing helix chain 'A' and resid 207 through 220 Processing helix chain 'A' and resid 233 through 252 Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 279 through 305 removed outlier: 3.967A pdb=" N THR A 285 " --> pdb=" O ILE A 281 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLU A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 355 through 377 Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.237A pdb=" N ILE A 381 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE A 383 " --> pdb=" O ILE A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 391 Processing helix chain 'A' and resid 392 through 396 removed outlier: 3.586A pdb=" N ILE A 396 " --> pdb=" O LEU A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 438 Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.748A pdb=" N ALA A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ILE A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 523 removed outlier: 3.723A pdb=" N THR A 496 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.959A pdb=" N PHE A 514 " --> pdb=" O ALA A 510 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLY A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 540 through 548 removed outlier: 3.764A pdb=" N TRP A 548 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 572 removed outlier: 3.540A pdb=" N VAL A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix removed outlier: 3.584A pdb=" N TYR A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 601 removed outlier: 4.029A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 610 removed outlier: 4.314A pdb=" N GLY A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 638 removed outlier: 4.544A pdb=" N HIS A 615 " --> pdb=" O ARG A 611 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A 622 " --> pdb=" O GLN A 618 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 665 removed outlier: 3.608A pdb=" N ILE A 651 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR A 652 " --> pdb=" O PRO A 648 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR A 658 " --> pdb=" O LEU A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.670A pdb=" N GLU A 669 " --> pdb=" O TYR A 665 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N HIS A 670 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 665 through 670' Processing helix chain 'A' and resid 673 through 677 removed outlier: 3.865A pdb=" N CYS A 677 " --> pdb=" O GLU A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 694 removed outlier: 3.837A pdb=" N PHE A 690 " --> pdb=" O LEU A 686 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 691 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ALA A 692 " --> pdb=" O GLU A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 27 removed outlier: 4.170A pdb=" N LEU B 27 " --> pdb=" O LEU B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 42 Processing helix chain 'B' and resid 59 through 67 Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 112 removed outlier: 3.618A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) Proline residue: B 104 - end of helix removed outlier: 3.808A pdb=" N LEU B 107 " --> pdb=" O LEU B 103 " (cutoff:3.500A) Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 117 through 125 removed outlier: 3.643A pdb=" N ASN B 121 " --> pdb=" O ASN B 118 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA B 122 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 184 removed outlier: 3.610A pdb=" N VAL B 156 " --> pdb=" O PHE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 218 Processing helix chain 'B' and resid 233 through 255 Processing helix chain 'B' and resid 274 through 278 removed outlier: 3.623A pdb=" N GLN B 277 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 278 " --> pdb=" O GLY B 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 278' Processing helix chain 'B' and resid 279 through 303 removed outlier: 3.617A pdb=" N TYR B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR B 285 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU B 287 " --> pdb=" O TYR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.525A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 376 Processing helix chain 'B' and resid 377 through 387 removed outlier: 4.253A pdb=" N ILE B 381 " --> pdb=" O TYR B 377 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 383 " --> pdb=" O ILE B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 391 Processing helix chain 'B' and resid 392 through 396 Processing helix chain 'B' and resid 401 through 408 removed outlier: 4.012A pdb=" N GLU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 406 " --> pdb=" O PRO B 402 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR B 407 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ALA B 408 " --> pdb=" O VAL B 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 401 through 408' Processing helix chain 'B' and resid 409 through 440 removed outlier: 3.673A pdb=" N GLU B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER B 415 " --> pdb=" O THR B 411 " (cutoff:3.500A) Proline residue: B 418 - end of helix removed outlier: 3.764A pdb=" N PHE B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Proline residue: B 430 - end of helix removed outlier: 3.505A pdb=" N ALA B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 468 removed outlier: 3.778A pdb=" N ALA B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 484 removed outlier: 3.645A pdb=" N LYS B 479 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 481 " --> pdb=" O VAL B 478 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 482 " --> pdb=" O LYS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 486 through 523 removed outlier: 4.186A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 572 removed outlier: 3.888A pdb=" N VAL B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Proline residue: B 560 - end of helix removed outlier: 3.648A pdb=" N TYR B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 601 removed outlier: 4.110A pdb=" N ILE B 581 " --> pdb=" O PRO B 577 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 611 removed outlier: 4.398A pdb=" N GLY B 610 " --> pdb=" O GLU B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 638 Processing helix chain 'B' and resid 642 through 665 Proline residue: B 648 - end of helix Processing helix chain 'B' and resid 665 through 670 removed outlier: 3.556A pdb=" N GLU B 669 " --> pdb=" O TYR B 665 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N HIS B 670 " --> pdb=" O GLY B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 665 through 670' Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 686 through 694 removed outlier: 4.148A pdb=" N PHE B 690 " --> pdb=" O LEU B 686 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA B 692 " --> pdb=" O GLU B 688 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 228 through 229 removed outlier: 3.655A pdb=" N ILE A 194 " --> pdb=" O VAL A 313 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 228 through 231 removed outlier: 5.534A pdb=" N ALA B 310 " --> pdb=" O ALA B 230 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 313 " --> pdb=" O ILE B 194 " (cutoff:3.500A) 644 hydrogen bonds defined for protein. 1845 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: 3.04 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3164 1.34 - 1.46: 2275 1.46 - 1.58: 5131 1.58 - 1.70: 0 1.70 - 1.81: 46 Bond restraints: 10616 Sorted by residual: bond pdb=" CA LEU B 348 " pdb=" CB LEU B 348 " ideal model delta sigma weight residual 1.528 1.486 0.042 2.61e-02 1.47e+03 2.63e+00 bond pdb=" CA LEU B 195 " pdb=" CB LEU B 195 " ideal model delta sigma weight residual 1.524 1.503 0.022 1.46e-02 4.69e+03 2.21e+00 bond pdb=" C TYR B 549 " pdb=" N PRO B 550 " ideal model delta sigma weight residual 1.336 1.319 0.017 1.20e-02 6.94e+03 1.94e+00 bond pdb=" CG LEU A 649 " pdb=" CD2 LEU A 649 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CA ILE B 689 " pdb=" CB ILE B 689 " ideal model delta sigma weight residual 1.545 1.534 0.012 1.05e-02 9.07e+03 1.26e+00 ... (remaining 10611 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 290 106.97 - 113.74: 6077 113.74 - 120.51: 4265 120.51 - 127.28: 3771 127.28 - 134.05: 114 Bond angle restraints: 14517 Sorted by residual: angle pdb=" C THR B 223 " pdb=" N PHE B 224 " pdb=" CA PHE B 224 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 angle pdb=" N VAL A 675 " pdb=" CA VAL A 675 " pdb=" C VAL A 675 " ideal model delta sigma weight residual 112.80 107.70 5.10 1.15e+00 7.56e-01 1.97e+01 angle pdb=" N GLU A 679 " pdb=" CA GLU A 679 " pdb=" C GLU A 679 " ideal model delta sigma weight residual 110.06 115.77 -5.71 1.43e+00 4.89e-01 1.60e+01 angle pdb=" N GLU B 241 " pdb=" CA GLU B 241 " pdb=" CB GLU B 241 " ideal model delta sigma weight residual 110.28 115.98 -5.70 1.55e+00 4.16e-01 1.35e+01 angle pdb=" C LYS B 663 " pdb=" N PHE B 664 " pdb=" CA PHE B 664 " ideal model delta sigma weight residual 122.08 116.61 5.47 1.53e+00 4.27e-01 1.28e+01 ... (remaining 14512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 5570 15.83 - 31.66: 504 31.66 - 47.49: 114 47.49 - 63.32: 16 63.32 - 79.15: 4 Dihedral angle restraints: 6208 sinusoidal: 2115 harmonic: 4093 Sorted by residual: dihedral pdb=" CA ALA B 34 " pdb=" C ALA B 34 " pdb=" N PRO B 35 " pdb=" CA PRO B 35 " ideal model delta harmonic sigma weight residual 180.00 -129.23 -50.77 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA ALA A 34 " pdb=" C ALA A 34 " pdb=" N PRO A 35 " pdb=" CA PRO A 35 " ideal model delta harmonic sigma weight residual -180.00 -130.98 -49.02 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA GLY B 441 " pdb=" C GLY B 441 " pdb=" N ILE B 442 " pdb=" CA ILE B 442 " ideal model delta harmonic sigma weight residual 180.00 146.66 33.34 0 5.00e+00 4.00e-02 4.45e+01 ... (remaining 6205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1579 0.076 - 0.153: 169 0.153 - 0.229: 2 0.229 - 0.306: 1 0.306 - 0.382: 1 Chirality restraints: 1752 Sorted by residual: chirality pdb=" CB ILE A 256 " pdb=" CA ILE A 256 " pdb=" CG1 ILE A 256 " pdb=" CG2 ILE A 256 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CG LEU A 564 " pdb=" CB LEU A 564 " pdb=" CD1 LEU A 564 " pdb=" CD2 LEU A 564 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA TRP A 613 " pdb=" N TRP A 613 " pdb=" C TRP A 613 " pdb=" CB TRP A 613 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 1749 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 341 " 0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO A 342 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 342 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 342 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 38 " 0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO A 39 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 39 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 39 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 103 " -0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO B 104 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO B 104 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 104 " -0.031 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 410 2.71 - 3.26: 11714 3.26 - 3.80: 16624 3.80 - 4.35: 19230 4.35 - 4.90: 31855 Nonbonded interactions: 79833 Sorted by model distance: nonbonded pdb=" OH TYR B 164 " pdb=" OG SER B 653 " model vdw 2.158 2.440 nonbonded pdb=" O ASN A 136 " pdb=" ND2 ASN A 141 " model vdw 2.159 2.520 nonbonded pdb=" O ASN A 114 " pdb=" OG1 THR A 119 " model vdw 2.187 2.440 nonbonded pdb=" ND2 ASN A 351 " pdb=" O LYS A 438 " model vdw 2.195 2.520 nonbonded pdb=" O LYS B 144 " pdb=" OG1 THR B 639 " model vdw 2.210 2.440 ... (remaining 79828 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' and (resid 3 through 473 or resid 486 through 702)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.080 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.590 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 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 : 0.004 0.042 10616 Z= 0.288 Angle : 0.839 11.703 14517 Z= 0.468 Chirality : 0.046 0.382 1752 Planarity : 0.006 0.070 1794 Dihedral : 12.990 79.155 3552 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.60 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.93 (0.24), residues: 1382 helix: 0.86 (0.19), residues: 799 sheet: -5.70 (0.64), residues: 10 loop : -2.81 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 336 HIS 0.004 0.001 HIS A 447 PHE 0.026 0.002 PHE A 664 TYR 0.017 0.002 TYR B 693 ARG 0.008 0.001 ARG A 611 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 198 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 56 ARG cc_start: 0.8067 (ptt180) cc_final: 0.7759 (tmm-80) REVERT: A 248 LYS cc_start: 0.9653 (mmpt) cc_final: 0.9389 (mmmt) REVERT: A 513 PHE cc_start: 0.7369 (m-80) cc_final: 0.6780 (m-80) REVERT: B 237 ASN cc_start: 0.8800 (m110) cc_final: 0.8592 (m110) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.1900 time to fit residues: 55.1942 Evaluate side-chains 159 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 7.9990 chunk 41 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 125 optimal weight: 0.1980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.233 Angle : 0.738 9.567 14517 Z= 0.371 Chirality : 0.044 0.334 1752 Planarity : 0.005 0.069 1794 Dihedral : 5.818 47.259 1475 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 13.10 % Favored : 86.76 % Rotamer: Outliers : 2.66 % Allowed : 11.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.80 (0.24), residues: 1382 helix: 0.96 (0.18), residues: 826 sheet: -5.17 (0.82), residues: 10 loop : -2.94 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 336 HIS 0.003 0.001 HIS A 447 PHE 0.027 0.002 PHE B 514 TYR 0.025 0.002 TYR A 171 ARG 0.004 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 170 time to evaluate : 1.252 Fit side-chains REVERT: A 56 ARG cc_start: 0.8022 (ptt180) cc_final: 0.7768 (tmm-80) REVERT: A 248 LYS cc_start: 0.9669 (mmpt) cc_final: 0.9441 (mmmt) REVERT: A 377 TYR cc_start: 0.6303 (p90) cc_final: 0.5044 (p90) REVERT: A 378 MET cc_start: 0.7658 (mmp) cc_final: 0.6814 (mmm) REVERT: B 367 ASN cc_start: 0.8740 (m-40) cc_final: 0.8537 (m-40) REVERT: B 437 SER cc_start: 0.9176 (t) cc_final: 0.8944 (t) REVERT: B 589 LEU cc_start: 0.8442 (mp) cc_final: 0.8236 (mp) outliers start: 27 outliers final: 16 residues processed: 183 average time/residue: 0.1897 time to fit residues: 51.8511 Evaluate side-chains 168 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 85 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 125 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 353 ASN B 628 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10616 Z= 0.193 Angle : 0.703 10.458 14517 Z= 0.348 Chirality : 0.043 0.307 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.573 48.240 1475 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 2.66 % Allowed : 15.86 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % 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: -0.47 (0.24), residues: 1382 helix: 1.17 (0.19), residues: 829 sheet: None (None), residues: 0 loop : -2.79 (0.27), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.032 0.002 PHE B 224 TYR 0.024 0.001 TYR A 171 ARG 0.002 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.160 Fit side-chains revert: symmetry clash REVERT: A 248 LYS cc_start: 0.9669 (mmpt) cc_final: 0.9440 (mmmt) REVERT: B 432 LEU cc_start: 0.9151 (tt) cc_final: 0.8936 (tp) REVERT: B 437 SER cc_start: 0.9106 (t) cc_final: 0.8878 (t) outliers start: 27 outliers final: 15 residues processed: 183 average time/residue: 0.1879 time to fit residues: 51.1373 Evaluate side-chains 173 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 158 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 628 GLN Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 0.6980 chunk 94 optimal weight: 0.0670 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 HIS ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.187 Angle : 0.689 9.794 14517 Z= 0.341 Chirality : 0.042 0.294 1752 Planarity : 0.005 0.065 1794 Dihedral : 5.443 48.125 1475 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.00 % Favored : 88.86 % Rotamer: Outliers : 3.94 % Allowed : 17.14 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.30 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.24), residues: 1382 helix: 1.17 (0.19), residues: 836 sheet: None (None), residues: 0 loop : -2.75 (0.27), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.003 0.001 HIS A 447 PHE 0.028 0.002 PHE B 513 TYR 0.047 0.001 TYR A 171 ARG 0.002 0.000 ARG A 523 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 165 time to evaluate : 1.110 Fit side-chains REVERT: A 186 ASP cc_start: 0.8515 (m-30) cc_final: 0.8308 (m-30) REVERT: A 229 VAL cc_start: 0.9446 (m) cc_final: 0.9244 (t) REVERT: A 248 LYS cc_start: 0.9677 (mmpt) cc_final: 0.9450 (mmmt) REVERT: A 377 TYR cc_start: 0.6457 (p90) cc_final: 0.6079 (p90) REVERT: A 378 MET cc_start: 0.7815 (mmp) cc_final: 0.7570 (mtp) REVERT: B 437 SER cc_start: 0.9136 (t) cc_final: 0.8882 (t) outliers start: 40 outliers final: 21 residues processed: 189 average time/residue: 0.1744 time to fit residues: 49.7599 Evaluate side-chains 177 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 156 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 308 GLN Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 631 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 30.0000 chunk 119 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10616 Z= 0.220 Angle : 0.697 10.674 14517 Z= 0.344 Chirality : 0.042 0.283 1752 Planarity : 0.005 0.066 1794 Dihedral : 5.381 48.244 1475 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 4.43 % Allowed : 18.13 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.23 % 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: -0.42 (0.24), residues: 1382 helix: 1.22 (0.19), residues: 832 sheet: -4.07 (1.30), residues: 10 loop : -2.75 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.026 0.001 PHE A 513 TYR 0.041 0.001 TYR A 171 ARG 0.003 0.000 ARG B 611 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 155 time to evaluate : 1.446 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8529 (m-30) cc_final: 0.8297 (m-30) REVERT: A 229 VAL cc_start: 0.9455 (m) cc_final: 0.9249 (t) REVERT: A 248 LYS cc_start: 0.9670 (mmpt) cc_final: 0.9451 (mmmt) REVERT: A 377 TYR cc_start: 0.6470 (p90) cc_final: 0.5395 (p90) REVERT: A 563 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8476 (ttp) REVERT: B 369 PHE cc_start: 0.8846 (t80) cc_final: 0.8579 (t80) REVERT: B 437 SER cc_start: 0.9176 (t) cc_final: 0.8884 (t) outliers start: 45 outliers final: 27 residues processed: 182 average time/residue: 0.1784 time to fit residues: 48.6875 Evaluate side-chains 174 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 146 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 563 MET Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 133 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10616 Z= 0.204 Angle : 0.684 10.142 14517 Z= 0.336 Chirality : 0.042 0.261 1752 Planarity : 0.005 0.065 1794 Dihedral : 5.308 48.039 1475 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 3.74 % Allowed : 19.11 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.23 % 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 (0.24), residues: 1382 helix: 1.30 (0.19), residues: 831 sheet: -3.91 (1.26), residues: 10 loop : -2.70 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.002 0.000 HIS A 447 PHE 0.026 0.001 PHE B 513 TYR 0.035 0.001 TYR A 171 ARG 0.007 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8534 (m-30) cc_final: 0.8283 (m-30) REVERT: A 229 VAL cc_start: 0.9458 (m) cc_final: 0.9242 (t) REVERT: A 248 LYS cc_start: 0.9669 (mmpt) cc_final: 0.9452 (mmmt) REVERT: A 378 MET cc_start: 0.7949 (mmm) cc_final: 0.7329 (mmm) REVERT: A 631 MET cc_start: 0.8991 (tpp) cc_final: 0.8753 (tpp) REVERT: B 86 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8868 (p) REVERT: B 369 PHE cc_start: 0.8872 (t80) cc_final: 0.8632 (t80) REVERT: B 437 SER cc_start: 0.9159 (t) cc_final: 0.8887 (t) outliers start: 38 outliers final: 26 residues processed: 182 average time/residue: 0.1726 time to fit residues: 47.3762 Evaluate side-chains 178 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 151 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 511 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10616 Z= 0.203 Angle : 0.692 10.037 14517 Z= 0.339 Chirality : 0.042 0.254 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.242 48.013 1475 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.51 % Favored : 88.35 % Rotamer: Outliers : 4.14 % Allowed : 19.61 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.23 % 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: -0.26 (0.24), residues: 1382 helix: 1.41 (0.19), residues: 820 sheet: -2.39 (1.31), residues: 15 loop : -2.74 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.030 0.001 PHE B 513 TYR 0.034 0.001 TYR A 171 ARG 0.006 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 153 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8521 (m-30) cc_final: 0.8277 (m-30) REVERT: A 229 VAL cc_start: 0.9462 (m) cc_final: 0.9246 (t) REVERT: A 248 LYS cc_start: 0.9676 (mmpt) cc_final: 0.9462 (mmmt) REVERT: B 86 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8875 (p) REVERT: B 369 PHE cc_start: 0.8857 (t80) cc_final: 0.8640 (t80) REVERT: B 437 SER cc_start: 0.9125 (t) cc_final: 0.8836 (t) outliers start: 42 outliers final: 26 residues processed: 180 average time/residue: 0.1818 time to fit residues: 49.3917 Evaluate side-chains 177 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 26 optimal weight: 0.0570 chunk 25 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10616 Z= 0.196 Angle : 0.706 14.434 14517 Z= 0.338 Chirality : 0.042 0.244 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.206 47.792 1475 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.65 % Favored : 88.21 % Rotamer: Outliers : 3.65 % Allowed : 20.89 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % 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: -0.19 (0.24), residues: 1382 helix: 1.39 (0.19), residues: 826 sheet: -2.38 (1.29), residues: 15 loop : -2.62 (0.27), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.002 0.000 HIS A 447 PHE 0.028 0.001 PHE B 513 TYR 0.031 0.001 TYR A 171 ARG 0.005 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 154 time to evaluate : 1.177 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8524 (m-30) cc_final: 0.8278 (m-30) REVERT: A 229 VAL cc_start: 0.9457 (m) cc_final: 0.9241 (t) REVERT: A 248 LYS cc_start: 0.9678 (mmpt) cc_final: 0.9462 (mmmt) REVERT: B 86 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8872 (p) REVERT: B 300 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8335 (tppt) REVERT: B 437 SER cc_start: 0.9107 (t) cc_final: 0.8804 (t) outliers start: 37 outliers final: 28 residues processed: 177 average time/residue: 0.1812 time to fit residues: 48.7911 Evaluate side-chains 176 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10616 Z= 0.215 Angle : 0.719 18.156 14517 Z= 0.343 Chirality : 0.042 0.251 1752 Planarity : 0.005 0.062 1794 Dihedral : 5.203 47.790 1475 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.72 % Favored : 88.13 % Rotamer: Outliers : 3.55 % Allowed : 21.18 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1382 helix: 1.41 (0.19), residues: 822 sheet: -2.33 (1.28), residues: 15 loop : -2.66 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 61 HIS 0.002 0.001 HIS A 701 PHE 0.030 0.001 PHE B 513 TYR 0.040 0.001 TYR A 586 ARG 0.006 0.000 ARG B 661 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.252 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8517 (m-30) cc_final: 0.8282 (m-30) REVERT: A 229 VAL cc_start: 0.9463 (m) cc_final: 0.9245 (t) REVERT: A 248 LYS cc_start: 0.9681 (mmpt) cc_final: 0.9467 (mmmt) REVERT: A 351 ASN cc_start: 0.8727 (t0) cc_final: 0.8446 (t0) REVERT: A 513 PHE cc_start: 0.7170 (m-80) cc_final: 0.6597 (m-80) REVERT: B 86 VAL cc_start: 0.9089 (OUTLIER) cc_final: 0.8877 (p) REVERT: B 224 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7255 (m-80) REVERT: B 300 LYS cc_start: 0.8920 (ttmm) cc_final: 0.8329 (tppt) REVERT: B 437 SER cc_start: 0.9118 (t) cc_final: 0.8817 (t) outliers start: 36 outliers final: 30 residues processed: 175 average time/residue: 0.1792 time to fit residues: 47.2992 Evaluate side-chains 179 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 147 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 630 VAL Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 6.9990 chunk 62 optimal weight: 0.1980 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 84 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10616 Z= 0.193 Angle : 0.720 16.784 14517 Z= 0.343 Chirality : 0.042 0.235 1752 Planarity : 0.005 0.063 1794 Dihedral : 5.143 47.468 1475 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.22 % Favored : 88.64 % Rotamer: Outliers : 3.45 % Allowed : 21.48 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.23 % 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: -0.14 (0.24), residues: 1382 helix: 1.44 (0.19), residues: 820 sheet: -2.25 (1.25), residues: 15 loop : -2.57 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.032 0.001 PHE B 513 TYR 0.035 0.001 TYR A 586 ARG 0.005 0.000 ARG B 661 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 156 time to evaluate : 1.379 Fit side-chains revert: symmetry clash REVERT: A 186 ASP cc_start: 0.8530 (m-30) cc_final: 0.8291 (m-30) REVERT: A 229 VAL cc_start: 0.9456 (m) cc_final: 0.9243 (t) REVERT: A 248 LYS cc_start: 0.9683 (mmpt) cc_final: 0.9479 (mmmt) REVERT: A 351 ASN cc_start: 0.8696 (t0) cc_final: 0.8440 (t0) REVERT: A 513 PHE cc_start: 0.7138 (m-80) cc_final: 0.6479 (m-80) REVERT: A 517 TYR cc_start: 0.8623 (m-10) cc_final: 0.8196 (m-80) REVERT: B 18 VAL cc_start: 0.9636 (m) cc_final: 0.9430 (p) REVERT: B 86 VAL cc_start: 0.9096 (OUTLIER) cc_final: 0.8892 (p) REVERT: B 224 PHE cc_start: 0.7857 (OUTLIER) cc_final: 0.7448 (m-80) REVERT: B 300 LYS cc_start: 0.8902 (ttmm) cc_final: 0.8449 (tppt) REVERT: B 437 SER cc_start: 0.9105 (t) cc_final: 0.8800 (t) REVERT: B 563 MET cc_start: 0.8557 (tpp) cc_final: 0.8058 (ttt) outliers start: 35 outliers final: 30 residues processed: 178 average time/residue: 0.1734 time to fit residues: 46.8426 Evaluate side-chains 183 residues out of total 1207 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 575 ILE Chi-restraints excluded: chain A residue 579 ILE Chi-restraints excluded: chain A residue 606 TYR Chi-restraints excluded: chain A residue 627 PHE Chi-restraints excluded: chain A residue 693 TYR Chi-restraints excluded: chain A residue 694 ILE Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 224 PHE Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 381 ILE Chi-restraints excluded: chain B residue 383 PHE Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 570 PHE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 693 TYR Chi-restraints excluded: chain B residue 694 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.157232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116006 restraints weight = 20134.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113744 restraints weight = 16661.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.115334 restraints weight = 13099.330| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10616 Z= 0.189 Angle : 0.710 16.288 14517 Z= 0.337 Chirality : 0.042 0.236 1752 Planarity : 0.004 0.062 1794 Dihedral : 5.091 46.978 1475 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.43 % Favored : 88.42 % Rotamer: Outliers : 3.45 % Allowed : 21.28 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.28 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.24), residues: 1382 helix: 1.43 (0.19), residues: 822 sheet: -3.42 (1.10), residues: 10 loop : -2.48 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 61 HIS 0.002 0.001 HIS A 447 PHE 0.028 0.002 PHE B 369 TYR 0.033 0.001 TYR A 586 ARG 0.005 0.000 ARG B 661 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2006.79 seconds wall clock time: 36 minutes 35.44 seconds (2195.44 seconds total)