Starting phenix.real_space_refine on Fri Mar 15 01:45:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xg6_22174/03_2024/6xg6_22174_updated.pdb" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 479 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians K 2 8.98 5 P 4 5.49 5 Mg 2 5.21 5 S 43 5.16 5 Be 2 3.05 5 C 6203 2.51 5 N 1708 2.21 5 O 1855 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 89": "OE1" <-> "OE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ARG 402": "NH1" <-> "NH2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A TYR 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A GLU 674": "OE1" <-> "OE2" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B PHE 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ASP 347": "OD1" <-> "OD2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 581": "OE1" <-> "OE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ARG 658": "NH1" <-> "NH2" Residue "B GLU 695": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9825 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4856 Classifications: {'peptide': 607} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 588} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4903 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 594} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 33 Unusual residues: {' K': 1, ' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.59, per 1000 atoms: 0.57 Number of scatterers: 9825 At special positions: 0 Unit cell: (94.424, 92.796, 135.124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) K 2 19.00 S 43 16.00 P 4 15.00 Mg 2 11.99 F 6 9.00 O 1855 8.00 N 1708 7.00 C 6203 6.00 Be 2 4.00 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: 4.00 Conformation dependent library (CDL) restraints added in 1.8 seconds 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2328 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 8 sheets defined 40.9% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 95 through 103 removed outlier: 3.816A pdb=" N ASP A 99 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 134 removed outlier: 3.814A pdb=" N PHE A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE A 113 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 171 Processing helix chain 'A' and resid 179 through 185 Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.563A pdb=" N MET A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 265 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.676A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 313 " --> pdb=" O TRP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 384 No H-bonds generated for 'chain 'A' and resid 382 through 384' Processing helix chain 'A' and resid 411 through 432 Processing helix chain 'A' and resid 434 through 443 Processing helix chain 'A' and resid 445 through 454 Processing helix chain 'A' and resid 458 through 467 removed outlier: 3.916A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 486 No H-bonds generated for 'chain 'A' and resid 483 through 486' Processing helix chain 'A' and resid 505 through 510 Processing helix chain 'A' and resid 512 through 519 Processing helix chain 'A' and resid 532 through 539 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 576 through 589 removed outlier: 4.061A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 582 " --> pdb=" O GLU A 578 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET A 583 " --> pdb=" O THR A 579 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA A 584 " --> pdb=" O GLU A 580 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.500A pdb=" N ARG A 619 " --> pdb=" O MET A 615 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN A 625 " --> pdb=" O PHE A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.909A pdb=" N ALA A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 removed outlier: 4.111A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 3.501A pdb=" N GLN A 666 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.861A pdb=" N ASN A 694 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 697 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL A 698 " --> pdb=" O GLU A 695 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 699 " --> pdb=" O LEU A 696 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 109 through 133 removed outlier: 4.052A pdb=" N PHE B 112 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE B 113 " --> pdb=" O GLU B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 171 Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 205 through 210 Processing helix chain 'B' and resid 262 through 265 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 308 through 318 removed outlier: 3.548A pdb=" N GLU B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 Processing helix chain 'B' and resid 376 through 378 No H-bonds generated for 'chain 'B' and resid 376 through 378' Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 409 through 432 removed outlier: 3.919A pdb=" N LYS B 413 " --> pdb=" O ALA B 409 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 removed outlier: 3.552A pdb=" N LYS B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.630A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.589A pdb=" N ALA B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 488 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 483 through 489' Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 519 removed outlier: 4.596A pdb=" N LYS B 519 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.719A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL B 589 " --> pdb=" O TRP B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 621 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.539A pdb=" N GLN B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 660 removed outlier: 3.802A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 679 removed outlier: 4.243A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 4.192A pdb=" N GLY B 691 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 285 through 287 removed outlier: 6.354A pdb=" N ILE A 143 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 219 " --> pdb=" O TYR A 229 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 370 through 373 removed outlier: 6.704A pdb=" N LEU A 365 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 546 through 549 removed outlier: 6.299A pdb=" N LEU A 525 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 597 through 599 removed outlier: 7.674A pdb=" N LEU A 642 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 285 through 287 removed outlier: 6.888A pdb=" N ILE B 143 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER B 219 " --> pdb=" O TYR B 229 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 363 through 366 removed outlier: 7.391A pdb=" N ALA B 364 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY B 389 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR B 366 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL B 391 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 546 through 549 removed outlier: 3.637A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 598 through 600 removed outlier: 3.556A pdb=" N LYS B 598 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 644 " --> pdb=" O LYS B 598 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 870 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: 2.81 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3240 1.34 - 1.46: 1814 1.46 - 1.58: 4854 1.58 - 1.69: 7 1.69 - 1.81: 78 Bond restraints: 9993 Sorted by residual: bond pdb=" BE BEF A 902 " pdb=" F2 BEF A 902 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" BE BEF B 902 " pdb=" F2 BEF B 902 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF B 902 " pdb=" F3 BEF B 902 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF A 902 " pdb=" F3 BEF A 902 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" BE BEF A 902 " pdb=" F1 BEF A 902 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 ... (remaining 9988 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.44: 298 107.44 - 114.64: 6023 114.64 - 121.84: 5025 121.84 - 129.04: 2077 129.04 - 136.23: 57 Bond angle restraints: 13480 Sorted by residual: angle pdb=" CA PRO B 662 " pdb=" N PRO B 662 " pdb=" CD PRO B 662 " ideal model delta sigma weight residual 112.00 104.59 7.41 1.40e+00 5.10e-01 2.80e+01 angle pdb=" F2 BEF B 902 " pdb=" BE BEF B 902 " pdb=" F3 BEF B 902 " ideal model delta sigma weight residual 119.96 107.31 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" F2 BEF A 902 " pdb=" BE BEF A 902 " pdb=" F3 BEF A 902 " ideal model delta sigma weight residual 119.96 107.42 12.54 3.00e+00 1.11e-01 1.75e+01 angle pdb=" F1 BEF A 902 " pdb=" BE BEF A 902 " pdb=" F3 BEF A 902 " ideal model delta sigma weight residual 120.12 109.96 10.16 3.00e+00 1.11e-01 1.15e+01 angle pdb=" F1 BEF B 902 " pdb=" BE BEF B 902 " pdb=" F3 BEF B 902 " ideal model delta sigma weight residual 120.12 110.11 10.01 3.00e+00 1.11e-01 1.11e+01 ... (remaining 13475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.87: 5661 22.87 - 45.74: 402 45.74 - 68.62: 33 68.62 - 91.49: 21 91.49 - 114.36: 2 Dihedral angle restraints: 6119 sinusoidal: 2536 harmonic: 3583 Sorted by residual: dihedral pdb=" O1B ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PB ADP A 901 " pdb=" PA ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -174.36 114.36 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" O2A ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PA ADP B 901 " pdb=" PB ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 -172.11 112.11 1 2.00e+01 2.50e-03 3.30e+01 dihedral pdb=" O2A ADP A 901 " pdb=" O3A ADP A 901 " pdb=" PA ADP A 901 " pdb=" PB ADP A 901 " ideal model delta sinusoidal sigma weight residual -60.00 -131.18 71.18 1 2.00e+01 2.50e-03 1.63e+01 ... (remaining 6116 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 950 0.029 - 0.058: 385 0.058 - 0.087: 109 0.087 - 0.116: 66 0.116 - 0.144: 9 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CB ILE A 113 " pdb=" CA ILE A 113 " pdb=" CG1 ILE A 113 " pdb=" CG2 ILE A 113 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE B 254 " pdb=" N ILE B 254 " pdb=" C ILE B 254 " pdb=" CB ILE B 254 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 chirality pdb=" CA ILE B 143 " pdb=" N ILE B 143 " pdb=" C ILE B 143 " pdb=" CB ILE B 143 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.63e-01 ... (remaining 1516 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 661 " 0.094 5.00e-02 4.00e+02 1.37e-01 3.01e+01 pdb=" N PRO B 662 " -0.237 5.00e-02 4.00e+02 pdb=" CA PRO B 662 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO B 662 " 0.071 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 380 " 0.023 5.00e-02 4.00e+02 3.51e-02 1.97e+00 pdb=" N PRO B 381 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 381 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 381 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 475 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO A 476 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.017 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.67: 170 2.67 - 3.28: 10670 3.28 - 3.90: 20014 3.90 - 4.52: 26535 4.52 - 5.14: 40533 Nonbonded interactions: 97922 Sorted by model distance: nonbonded pdb=" F1 BEF A 902 " pdb="MG MG A 903 " model vdw 2.048 2.120 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 903 " model vdw 2.096 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 903 " model vdw 2.105 2.170 nonbonded pdb=" O1B ADP B 901 " pdb="MG MG B 903 " model vdw 2.127 2.170 nonbonded pdb=" O1A ADP B 901 " pdb="MG MG B 903 " model vdw 2.144 2.170 ... (remaining 97917 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 70 through 554 or resid 573 through 626 or resid 631 throu \ gh 704 or resid 901 through 904)) selection = (chain 'B' and (resid 70 through 351 or resid 363 through 554 or resid 573 throu \ gh 704 or resid 901 through 904)) } 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 individual isotropic 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 7.410 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.820 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 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 : 0.003 0.096 9993 Z= 0.171 Angle : 0.548 12.652 13480 Z= 0.267 Chirality : 0.038 0.144 1519 Planarity : 0.004 0.137 1714 Dihedral : 15.405 114.361 3791 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.25), residues: 1206 helix: 0.92 (0.25), residues: 495 sheet: 1.25 (0.42), residues: 177 loop : -0.55 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 309 HIS 0.002 0.000 HIS B 129 PHE 0.011 0.001 PHE A 112 TYR 0.006 0.001 TYR A 106 ARG 0.004 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 1.107 Fit side-chains REVERT: A 94 THR cc_start: 0.6615 (p) cc_final: 0.6403 (p) REVERT: A 495 ARG cc_start: 0.6708 (ptm-80) cc_final: 0.6346 (ttp80) REVERT: A 606 HIS cc_start: 0.7263 (m90) cc_final: 0.6952 (m90) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2535 time to fit residues: 58.2692 Evaluate side-chains 119 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 GLN ** B 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.075 9993 Z= 0.683 Angle : 0.890 10.355 13480 Z= 0.450 Chirality : 0.053 0.227 1519 Planarity : 0.007 0.073 1714 Dihedral : 7.594 151.445 1356 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.45 % Allowed : 11.49 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.24), residues: 1206 helix: -0.38 (0.22), residues: 514 sheet: 0.00 (0.39), residues: 187 loop : -0.76 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 299 HIS 0.016 0.003 HIS A 88 PHE 0.017 0.003 PHE B 209 TYR 0.017 0.003 TYR A 437 ARG 0.010 0.001 ARG B 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 1.103 Fit side-chains REVERT: A 279 ASN cc_start: 0.8736 (OUTLIER) cc_final: 0.8291 (t160) REVERT: A 396 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8054 (tt) outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 0.2399 time to fit residues: 44.3444 Evaluate side-chains 114 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 ASN Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 624 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 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 479 GLN A 655 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9993 Z= 0.180 Angle : 0.580 8.564 13480 Z= 0.289 Chirality : 0.040 0.162 1519 Planarity : 0.004 0.064 1714 Dihedral : 6.547 130.475 1356 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.07 % Allowed : 14.41 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1206 helix: 0.08 (0.23), residues: 507 sheet: 0.17 (0.39), residues: 184 loop : -0.74 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.004 0.001 HIS B 144 PHE 0.012 0.001 PHE A 112 TYR 0.009 0.001 TYR A 327 ARG 0.006 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 1.155 Fit side-chains REVERT: A 99 ASP cc_start: 0.7942 (t0) cc_final: 0.7659 (t0) REVERT: A 300 MET cc_start: 0.7700 (mmm) cc_final: 0.7433 (mmt) REVERT: A 327 TYR cc_start: 0.8643 (m-80) cc_final: 0.8291 (m-80) REVERT: B 98 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8549 (mt) outliers start: 22 outliers final: 12 residues processed: 137 average time/residue: 0.2298 time to fit residues: 43.7169 Evaluate side-chains 121 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 655 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 116 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 ASN A 479 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 GLN B 419 GLN B 645 ASN B 655 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9993 Z= 0.374 Angle : 0.665 9.472 13480 Z= 0.331 Chirality : 0.044 0.157 1519 Planarity : 0.005 0.058 1714 Dihedral : 7.013 143.065 1356 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.30 % Allowed : 16.01 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.24), residues: 1206 helix: 0.03 (0.23), residues: 504 sheet: -0.28 (0.38), residues: 184 loop : -0.82 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 299 HIS 0.008 0.001 HIS A 88 PHE 0.013 0.002 PHE B 621 TYR 0.016 0.002 TYR B 513 ARG 0.005 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.211 Fit side-chains REVERT: A 88 HIS cc_start: 0.6969 (OUTLIER) cc_final: 0.5339 (p-80) REVERT: A 292 MET cc_start: 0.5988 (pmm) cc_final: 0.5732 (ptp) REVERT: A 300 MET cc_start: 0.7794 (mmm) cc_final: 0.7531 (mmt) REVERT: A 643 GLU cc_start: 0.7718 (mp0) cc_final: 0.7450 (mp0) REVERT: B 98 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8661 (mt) REVERT: B 113 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7832 (pt) outliers start: 35 outliers final: 22 residues processed: 135 average time/residue: 0.2268 time to fit residues: 43.1088 Evaluate side-chains 126 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 230 GLN Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 479 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9993 Z= 0.245 Angle : 0.597 9.063 13480 Z= 0.295 Chirality : 0.042 0.152 1519 Planarity : 0.004 0.055 1714 Dihedral : 6.744 136.710 1356 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 13.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.01 % Allowed : 18.55 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1206 helix: 0.09 (0.24), residues: 504 sheet: -0.32 (0.38), residues: 184 loop : -0.84 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 231 HIS 0.005 0.001 HIS A 88 PHE 0.014 0.001 PHE B 621 TYR 0.012 0.001 TYR B 513 ARG 0.007 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 111 time to evaluate : 1.166 Fit side-chains REVERT: A 88 HIS cc_start: 0.6771 (OUTLIER) cc_final: 0.4948 (p-80) REVERT: A 292 MET cc_start: 0.5978 (pmm) cc_final: 0.5762 (ptp) REVERT: A 300 MET cc_start: 0.7738 (mmm) cc_final: 0.7461 (mmt) REVERT: B 98 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8619 (mt) REVERT: B 113 ILE cc_start: 0.7826 (OUTLIER) cc_final: 0.7597 (pt) outliers start: 32 outliers final: 22 residues processed: 135 average time/residue: 0.2265 time to fit residues: 43.4477 Evaluate side-chains 128 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 0.0030 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 479 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 GLN B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9993 Z= 0.208 Angle : 0.576 10.763 13480 Z= 0.283 Chirality : 0.041 0.151 1519 Planarity : 0.004 0.057 1714 Dihedral : 6.580 134.292 1356 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.20 % Allowed : 18.46 % Favored : 78.34 % 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: -0.61 (0.25), residues: 1206 helix: 0.08 (0.24), residues: 515 sheet: -0.31 (0.38), residues: 183 loop : -0.82 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 231 HIS 0.004 0.001 HIS A 88 PHE 0.013 0.001 PHE B 112 TYR 0.011 0.001 TYR A 437 ARG 0.008 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 113 time to evaluate : 1.249 Fit side-chains REVERT: A 88 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.4684 (p-80) REVERT: A 300 MET cc_start: 0.7724 (mmm) cc_final: 0.7455 (mmt) REVERT: A 643 GLU cc_start: 0.7806 (mp0) cc_final: 0.7361 (mp0) REVERT: B 98 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8582 (mt) outliers start: 34 outliers final: 26 residues processed: 137 average time/residue: 0.2164 time to fit residues: 42.3288 Evaluate side-chains 132 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 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 188 GLN A 479 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9993 Z= 0.272 Angle : 0.605 8.797 13480 Z= 0.298 Chirality : 0.042 0.149 1519 Planarity : 0.004 0.060 1714 Dihedral : 6.724 137.683 1356 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.52 % Allowed : 17.80 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1206 helix: 0.06 (0.23), residues: 515 sheet: -0.34 (0.38), residues: 184 loop : -0.81 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 585 HIS 0.005 0.001 HIS A 88 PHE 0.010 0.001 PHE A 112 TYR 0.012 0.002 TYR A 437 ARG 0.010 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 105 time to evaluate : 1.135 Fit side-chains REVERT: A 88 HIS cc_start: 0.6759 (OUTLIER) cc_final: 0.4932 (p-80) REVERT: A 300 MET cc_start: 0.7735 (mmm) cc_final: 0.7463 (mmt) REVERT: A 643 GLU cc_start: 0.7760 (mp0) cc_final: 0.7333 (mp0) REVERT: B 98 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8655 (mt) REVERT: B 113 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7641 (pt) outliers start: 48 outliers final: 31 residues processed: 141 average time/residue: 0.2041 time to fit residues: 41.9303 Evaluate side-chains 140 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 106 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 153 THR Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 506 HIS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 479 GLN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9993 Z= 0.198 Angle : 0.581 13.595 13480 Z= 0.284 Chirality : 0.041 0.165 1519 Planarity : 0.004 0.059 1714 Dihedral : 6.502 132.938 1356 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.86 % Allowed : 19.02 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.25), residues: 1206 helix: 0.00 (0.23), residues: 530 sheet: -0.27 (0.38), residues: 183 loop : -0.87 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 231 HIS 0.004 0.001 HIS A 88 PHE 0.018 0.001 PHE B 621 TYR 0.011 0.001 TYR A 437 ARG 0.013 0.000 ARG A 623 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 115 time to evaluate : 1.106 Fit side-chains REVERT: A 88 HIS cc_start: 0.6555 (OUTLIER) cc_final: 0.4638 (p-80) REVERT: A 300 MET cc_start: 0.7689 (mmm) cc_final: 0.7429 (mmt) REVERT: A 643 GLU cc_start: 0.7714 (mp0) cc_final: 0.7275 (mp0) REVERT: B 98 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (mt) REVERT: B 113 ILE cc_start: 0.7618 (OUTLIER) cc_final: 0.7380 (pt) outliers start: 41 outliers final: 31 residues processed: 148 average time/residue: 0.2175 time to fit residues: 46.0647 Evaluate side-chains 139 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 105 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 479 GLN A 496 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9993 Z= 0.227 Angle : 0.596 10.517 13480 Z= 0.290 Chirality : 0.041 0.149 1519 Planarity : 0.004 0.061 1714 Dihedral : 6.559 134.540 1356 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 4.05 % Allowed : 19.21 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.24), residues: 1206 helix: -0.02 (0.23), residues: 531 sheet: -0.29 (0.38), residues: 183 loop : -0.89 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.010 0.001 PHE A 112 TYR 0.012 0.001 TYR A 437 ARG 0.009 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 109 time to evaluate : 1.089 Fit side-chains REVERT: A 88 HIS cc_start: 0.6616 (OUTLIER) cc_final: 0.4671 (p-80) REVERT: A 300 MET cc_start: 0.7679 (mmm) cc_final: 0.7420 (mmt) REVERT: A 643 GLU cc_start: 0.7686 (mp0) cc_final: 0.7315 (mp0) REVERT: B 98 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 113 ILE cc_start: 0.7700 (OUTLIER) cc_final: 0.7459 (pt) outliers start: 43 outliers final: 35 residues processed: 140 average time/residue: 0.2025 time to fit residues: 40.5398 Evaluate side-chains 144 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 113 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 463 ASP Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 553 ASP Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 496 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9993 Z= 0.182 Angle : 0.581 10.416 13480 Z= 0.283 Chirality : 0.040 0.150 1519 Planarity : 0.004 0.059 1714 Dihedral : 6.415 131.749 1356 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.20 % Allowed : 20.34 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.25), residues: 1206 helix: 0.03 (0.23), residues: 531 sheet: -0.17 (0.38), residues: 183 loop : -0.87 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 585 HIS 0.003 0.001 HIS A 88 PHE 0.019 0.001 PHE B 621 TYR 0.011 0.001 TYR A 498 ARG 0.010 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2412 Ramachandran restraints generated. 1206 Oldfield, 0 Emsley, 1206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 1.077 Fit side-chains REVERT: A 88 HIS cc_start: 0.6510 (OUTLIER) cc_final: 0.4608 (p-80) REVERT: A 300 MET cc_start: 0.7643 (mmm) cc_final: 0.7391 (mmt) REVERT: B 98 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8589 (mt) outliers start: 34 outliers final: 29 residues processed: 140 average time/residue: 0.2046 time to fit residues: 41.1202 Evaluate side-chains 141 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 396 ILE Chi-restraints excluded: chain A residue 412 ARG Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 496 ASN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 613 LEU Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 656 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 292 MET Chi-restraints excluded: chain B residue 298 ILE Chi-restraints excluded: chain B residue 301 MET Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 460 VAL Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain B residue 490 MET Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 553 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 26 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN A 496 ASN ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 655 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.122486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101210 restraints weight = 16563.097| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.24 r_work: 0.3223 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9993 Z= 0.222 Angle : 0.595 10.759 13480 Z= 0.290 Chirality : 0.041 0.150 1519 Planarity : 0.004 0.059 1714 Dihedral : 6.491 133.258 1356 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.48 % Allowed : 20.06 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1206 helix: 0.03 (0.23), residues: 531 sheet: -0.17 (0.38), residues: 183 loop : -0.91 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 585 HIS 0.004 0.001 HIS A 88 PHE 0.010 0.001 PHE A 112 TYR 0.014 0.001 TYR B 315 ARG 0.010 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2115.86 seconds wall clock time: 39 minutes 0.76 seconds (2340.76 seconds total)