Starting phenix.real_space_refine on Wed Feb 14 21:18:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kck_22811/02_2024/7kck_22811_updated.pdb" } resolution = 3.26 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= 0.003 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 425 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: 7 Type Number sf(0) Gaussians K 2 8.98 5 P 6 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 6203 2.51 5 N 1710 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 99": "OD1" <-> "OD2" Residue "A GLU 115": "OE1" <-> "OE2" Residue "A GLU 125": "OE1" <-> "OE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A GLU 312": "OE1" <-> "OE2" 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 GLU 457": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 521": "OD1" <-> "OD2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 632": "OE1" <-> "OE2" Residue "A GLU 633": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 670": "OD1" <-> "OD2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "B GLU 216": "OE1" <-> "OE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 312": "OE1" <-> "OE2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 385": "NH1" <-> "NH2" Residue "B ASP 392": "OD1" <-> "OD2" Residue "B ASP 395": "OD1" <-> "OD2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B GLU 435": "OE1" <-> "OE2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 515": "OE1" <-> "OE2" Residue "B GLU 523": "OE1" <-> "OE2" Residue "B PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 532": "OD1" <-> "OD2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B PHE 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 633": "OE1" <-> "OE2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B GLU 643": "OE1" <-> "OE2" Residue "B ARG 658": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.48, per 1000 atoms: 0.56 Number of scatterers: 9825 At special positions: 0 Unit cell: (94.424, 86.284, 131.868, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 2 19.00 S 43 16.00 P 6 15.00 Mg 2 11.99 O 1859 8.00 N 1710 7.00 C 6203 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: 3.94 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: 48 helices and 9 sheets defined 40.8% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 109 through 134 removed outlier: 4.087A pdb=" N PHE A 112 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.788A pdb=" N MET A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 265 removed outlier: 4.004A pdb=" N LYS A 262 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLU A 263 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 277 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: 3.552A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.869A 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 454 removed outlier: 3.911A pdb=" N GLU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASP A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 453 " --> pdb=" O ARG A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 removed outlier: 3.636A pdb=" N ASP A 463 " --> pdb=" O GLU A 459 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 Processing helix chain 'A' and resid 505 through 510 removed outlier: 3.896A pdb=" N HIS A 510 " --> pdb=" O HIS A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 516 Processing helix chain 'A' and resid 532 through 539 removed outlier: 3.846A pdb=" N LEU A 537 " --> pdb=" O GLU A 533 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 576 through 589 removed outlier: 3.713A pdb=" N GLU A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 623 removed outlier: 4.090A pdb=" N HIS A 620 " --> pdb=" O GLY A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 638 removed outlier: 3.988A pdb=" N ALA A 635 " --> pdb=" O GLN A 631 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLN A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 637 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 638 " --> pdb=" O ARG A 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 631 through 638' Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.976A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 680 removed outlier: 3.859A pdb=" N ASP A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 4.235A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 109 through 133 removed outlier: 3.982A pdb=" N PHE B 112 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 3.896A 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 187 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: 3.559A pdb=" N TYR B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.591A pdb=" N SER B 356 " --> pdb=" O MET B 352 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' 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 Processing helix chain 'B' and resid 434 through 454 removed outlier: 6.326A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 removed outlier: 3.501A pdb=" N GLU B 462 " --> pdb=" O GLN B 458 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 489 removed outlier: 3.666A pdb=" N ARG B 489 " --> pdb=" O GLU B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 509 Processing helix chain 'B' and resid 512 through 518 Processing helix chain 'B' and resid 532 through 539 Processing helix chain 'B' and resid 550 through 556 removed outlier: 3.812A pdb=" N VAL B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 589 removed outlier: 3.755A pdb=" N GLU B 580 " --> pdb=" O GLU B 576 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU B 581 " --> pdb=" O LYS B 577 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU B 582 " --> pdb=" O GLU B 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG B 587 " --> pdb=" O MET B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 623 Processing helix chain 'B' and resid 632 through 638 removed outlier: 3.913A pdb=" N LEU B 637 " --> pdb=" O GLU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 659 removed outlier: 3.885A pdb=" N ASN B 655 " --> pdb=" O ILE B 651 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 680 removed outlier: 3.538A pdb=" N GLN B 666 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 700 removed outlier: 4.385A pdb=" N GLY B 691 " --> pdb=" O ARG B 687 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS B 699 " --> pdb=" O GLU B 695 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 284 through 287 removed outlier: 3.997A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 370 through 373 removed outlier: 7.125A pdb=" N LEU A 365 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA A 364 " --> pdb=" O ILE A 387 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N GLY A 389 " --> pdb=" O ALA A 364 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR A 366 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL A 391 " --> pdb=" O TYR A 366 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 547 through 549 removed outlier: 6.132A pdb=" N ILE A 497 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 597 through 599 removed outlier: 7.015A pdb=" N LEU A 642 " --> pdb=" O LYS A 598 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 284 through 287 removed outlier: 3.899A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 230 through 233 Processing sheet with id= G, first strand: chain 'B' and resid 363 through 366 removed outlier: 7.424A pdb=" N ALA B 364 " --> pdb=" O ILE B 387 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 389 " --> pdb=" O ALA B 364 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N TYR B 366 " --> pdb=" O GLY B 389 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 391 " --> pdb=" O TYR B 366 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 546 through 549 removed outlier: 3.580A pdb=" N TYR B 499 " --> pdb=" O ILE B 548 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 597 through 599 removed outlier: 7.066A pdb=" N LEU B 642 " --> pdb=" O LYS B 598 " (cutoff:3.500A) 357 hydrogen bonds defined for protein. 894 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: 2.70 Time building geometry restraints manager: 4.26 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: 3248 1.34 - 1.46: 2033 1.46 - 1.58: 4626 1.58 - 1.69: 10 1.69 - 1.81: 78 Bond restraints: 9995 Sorted by residual: bond pdb=" O3A ANP A 803 " pdb=" PB ANP A 803 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.16e+01 bond pdb=" O3A ANP B 803 " pdb=" PB ANP B 803 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.10e+01 bond pdb=" N3B ANP B 803 " pdb=" PG ANP B 803 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.68e+01 bond pdb=" O5' ANP A 803 " pdb=" PA ANP A 803 " ideal model delta sigma weight residual 1.655 1.577 0.078 2.00e-02 2.50e+03 1.51e+01 ... (remaining 9990 not shown) Histogram of bond angle deviations from ideal: 99.49 - 106.38: 229 106.38 - 113.28: 5487 113.28 - 120.17: 3550 120.17 - 127.07: 4134 127.07 - 133.97: 88 Bond angle restraints: 13488 Sorted by residual: angle pdb=" PB ANP A 803 " pdb=" N3B ANP A 803 " pdb=" PG ANP A 803 " ideal model delta sigma weight residual 126.95 110.61 16.34 3.00e+00 1.11e-01 2.97e+01 angle pdb=" PB ANP B 803 " pdb=" N3B ANP B 803 " pdb=" PG ANP B 803 " ideal model delta sigma weight residual 126.95 110.67 16.28 3.00e+00 1.11e-01 2.94e+01 angle pdb=" O1B ANP A 803 " pdb=" PB ANP A 803 " pdb=" O2B ANP A 803 " ideal model delta sigma weight residual 120.08 109.00 11.08 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N SER A 401 " pdb=" CA SER A 401 " pdb=" C SER A 401 " ideal model delta sigma weight residual 112.97 109.09 3.88 1.06e+00 8.90e-01 1.34e+01 angle pdb=" O1B ANP B 803 " pdb=" PB ANP B 803 " pdb=" O2B ANP B 803 " ideal model delta sigma weight residual 120.08 109.12 10.96 3.00e+00 1.11e-01 1.33e+01 ... (remaining 13483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5462 17.95 - 35.89: 558 35.89 - 53.84: 106 53.84 - 71.79: 23 71.79 - 89.74: 12 Dihedral angle restraints: 6161 sinusoidal: 2578 harmonic: 3583 Sorted by residual: dihedral pdb=" CA ALA A 608 " pdb=" C ALA A 608 " pdb=" N MET A 609 " pdb=" CA MET A 609 " ideal model delta harmonic sigma weight residual 180.00 162.53 17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA LEU A 613 " pdb=" C LEU A 613 " pdb=" N GLU A 614 " pdb=" CA GLU A 614 " ideal model delta harmonic sigma weight residual -180.00 -163.53 -16.47 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA TYR B 277 " pdb=" C TYR B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual 180.00 -163.71 -16.29 0 5.00e+00 4.00e-02 1.06e+01 ... (remaining 6158 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1305 0.056 - 0.111: 192 0.111 - 0.167: 20 0.167 - 0.223: 0 0.223 - 0.279: 2 Chirality restraints: 1519 Sorted by residual: chirality pdb=" C3' ANP B 803 " pdb=" C2' ANP B 803 " pdb=" C4' ANP B 803 " pdb=" O3' ANP B 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C3' ANP A 803 " pdb=" C2' ANP A 803 " pdb=" C4' ANP A 803 " pdb=" O3' ANP A 803 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ASP B 378 " pdb=" N ASP B 378 " pdb=" C ASP B 378 " pdb=" CB ASP B 378 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 1516 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 511 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO A 512 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 512 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 512 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 685 " -0.031 5.00e-02 4.00e+02 4.71e-02 3.54e+00 pdb=" N PRO B 686 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 686 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 686 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 475 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 476 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 476 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 476 " -0.020 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.63: 140 2.63 - 3.26: 10381 3.26 - 3.89: 19947 3.89 - 4.51: 27350 4.51 - 5.14: 41834 Nonbonded interactions: 99652 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 801 " model vdw 2.008 2.170 nonbonded pdb="MG MG A 801 " pdb=" O3G ANP A 803 " model vdw 2.009 2.170 nonbonded pdb="MG MG B 801 " pdb=" O3G ANP B 803 " model vdw 2.013 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 801 " model vdw 2.038 2.170 nonbonded pdb=" O1B ANP A 803 " pdb=" O2A ANP A 803 " model vdw 2.161 3.040 ... (remaining 99647 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 801 through 803)) selection = (chain 'B' and (resid 70 through 351 or resid 363 through 554 or resid 573 throu \ gh 704 or resid 801 through 803)) } 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: 0.010 Normalize map: mean=0, sd=1: 2.060 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: 7.550 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 29.580 Find NCS groups from input model: 0.570 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 0.144 9995 Z= 0.280 Angle : 0.657 16.340 13488 Z= 0.326 Chirality : 0.041 0.279 1519 Planarity : 0.004 0.071 1714 Dihedral : 15.215 89.736 3833 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.09 % Allowed : 0.56 % Favored : 99.34 % 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: -0.31 (0.25), residues: 1206 helix: 0.40 (0.24), residues: 495 sheet: 0.30 (0.41), residues: 182 loop : -0.90 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.002 0.000 HIS A 506 PHE 0.016 0.001 PHE B 531 TYR 0.009 0.001 TYR B 218 ARG 0.006 0.000 ARG A 412 *********************** 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 134 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 133 time to evaluate : 1.049 Fit side-chains REVERT: A 699 LYS cc_start: 0.7914 (ptpt) cc_final: 0.7120 (tptt) REVERT: B 290 ARG cc_start: 0.7154 (mmp-170) cc_final: 0.6926 (mmp-170) REVERT: B 348 MET cc_start: 0.7744 (ppp) cc_final: 0.7443 (ppp) REVERT: B 537 LEU cc_start: 0.8798 (mt) cc_final: 0.8537 (mt) REVERT: B 677 MET cc_start: 0.8486 (mmt) cc_final: 0.8083 (mmt) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2303 time to fit residues: 43.0217 Evaluate side-chains 106 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 SER 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: 3.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN B 420 GLN B 538 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 9995 Z= 0.426 Angle : 0.667 8.924 13488 Z= 0.343 Chirality : 0.046 0.172 1519 Planarity : 0.005 0.055 1714 Dihedral : 6.543 52.475 1399 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.13 % Allowed : 11.58 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.24), residues: 1206 helix: 0.11 (0.23), residues: 510 sheet: -0.06 (0.39), residues: 186 loop : -0.85 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 299 HIS 0.004 0.001 HIS A 506 PHE 0.017 0.002 PHE A 441 TYR 0.017 0.002 TYR A 218 ARG 0.006 0.001 ARG A 402 *********************** 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 132 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.230 Fit side-chains REVERT: A 349 LYS cc_start: 0.7690 (pttt) cc_final: 0.7235 (ptpp) REVERT: A 699 LYS cc_start: 0.8098 (ptpt) cc_final: 0.7593 (tptt) REVERT: B 290 ARG cc_start: 0.7512 (mmp-170) cc_final: 0.7170 (mmp-170) REVERT: B 537 LEU cc_start: 0.8935 (mt) cc_final: 0.8648 (mt) REVERT: B 554 ILE cc_start: 0.8619 (mm) cc_final: 0.8410 (mm) REVERT: B 598 LYS cc_start: 0.7930 (pptt) cc_final: 0.7610 (pptt) outliers start: 12 outliers final: 8 residues processed: 127 average time/residue: 0.2441 time to fit residues: 43.7413 Evaluate side-chains 113 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 684 ASP Chi-restraints excluded: chain B residue 698 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9995 Z= 0.178 Angle : 0.528 9.020 13488 Z= 0.272 Chirality : 0.041 0.159 1519 Planarity : 0.004 0.044 1714 Dihedral : 5.946 56.842 1398 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.60 % Allowed : 14.97 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.24), residues: 1206 helix: 0.18 (0.23), residues: 509 sheet: 0.15 (0.39), residues: 176 loop : -0.84 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 585 HIS 0.002 0.000 HIS B 538 PHE 0.012 0.001 PHE B 531 TYR 0.010 0.001 TYR B 206 ARG 0.004 0.000 ARG A 634 *********************** 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 137 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 1.200 Fit side-chains REVERT: A 349 LYS cc_start: 0.7637 (pttt) cc_final: 0.7217 (ptpp) REVERT: A 699 LYS cc_start: 0.8026 (ptpt) cc_final: 0.7283 (tptt) REVERT: B 290 ARG cc_start: 0.7380 (mmp-170) cc_final: 0.7043 (mmp-170) REVERT: B 352 MET cc_start: 0.7524 (tpp) cc_final: 0.7062 (mpp) REVERT: B 537 LEU cc_start: 0.8921 (mt) cc_final: 0.8549 (mt) REVERT: B 598 LYS cc_start: 0.7728 (pptt) cc_final: 0.7024 (ptpt) outliers start: 17 outliers final: 9 residues processed: 134 average time/residue: 0.2102 time to fit residues: 40.5881 Evaluate side-chains 113 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 613 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.4980 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9995 Z= 0.321 Angle : 0.590 9.123 13488 Z= 0.301 Chirality : 0.043 0.161 1519 Planarity : 0.004 0.039 1714 Dihedral : 6.150 54.331 1398 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.26 % Allowed : 17.70 % Favored : 80.04 % 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: -0.64 (0.24), residues: 1206 helix: 0.09 (0.23), residues: 519 sheet: -0.25 (0.38), residues: 186 loop : -0.90 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 585 HIS 0.004 0.001 HIS B 538 PHE 0.014 0.002 PHE A 441 TYR 0.012 0.002 TYR B 206 ARG 0.005 0.000 ARG A 634 *********************** 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 132 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 1.118 Fit side-chains REVERT: A 110 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7961 (pt0) REVERT: A 349 LYS cc_start: 0.7807 (pttt) cc_final: 0.7375 (ptpp) REVERT: A 699 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7553 (tptt) REVERT: B 290 ARG cc_start: 0.7504 (mmp-170) cc_final: 0.7188 (mmp-170) REVERT: B 352 MET cc_start: 0.7621 (tpp) cc_final: 0.7104 (mpp) REVERT: B 537 LEU cc_start: 0.8916 (mt) cc_final: 0.8632 (mt) REVERT: B 598 LYS cc_start: 0.7891 (pptt) cc_final: 0.7136 (ptpt) outliers start: 24 outliers final: 12 residues processed: 127 average time/residue: 0.2104 time to fit residues: 38.2818 Evaluate side-chains 113 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 613 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9995 Z= 0.390 Angle : 0.618 9.683 13488 Z= 0.316 Chirality : 0.044 0.162 1519 Planarity : 0.004 0.037 1714 Dihedral : 6.387 56.245 1398 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 18.93 % Favored : 78.06 % 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: -0.06 (0.23), residues: 524 sheet: -0.48 (0.38), residues: 186 loop : -0.97 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 585 HIS 0.003 0.001 HIS A 506 PHE 0.015 0.002 PHE B 239 TYR 0.014 0.002 TYR A 286 ARG 0.004 0.000 ARG A 634 *********************** 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 147 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 1.195 Fit side-chains REVERT: A 110 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: A 349 LYS cc_start: 0.7913 (pttt) cc_final: 0.7451 (ptpp) REVERT: A 699 LYS cc_start: 0.8039 (ptpt) cc_final: 0.7555 (tptt) REVERT: B 352 MET cc_start: 0.7672 (tpp) cc_final: 0.7176 (mpp) REVERT: B 537 LEU cc_start: 0.8950 (mt) cc_final: 0.8653 (mt) REVERT: B 580 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7303 (mp0) REVERT: B 598 LYS cc_start: 0.8040 (pptt) cc_final: 0.7225 (ptpt) REVERT: B 695 GLU cc_start: 0.7886 (pp20) cc_final: 0.7540 (pp20) outliers start: 32 outliers final: 19 residues processed: 138 average time/residue: 0.2212 time to fit residues: 43.3179 Evaluate side-chains 126 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 GLN A 504 ASN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 GLN B 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 9995 Z= 0.363 Angle : 0.615 10.356 13488 Z= 0.311 Chirality : 0.044 0.166 1519 Planarity : 0.004 0.035 1714 Dihedral : 6.367 56.600 1398 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.20 % Allowed : 19.21 % Favored : 77.59 % 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: -0.88 (0.24), residues: 1206 helix: -0.07 (0.23), residues: 522 sheet: -0.53 (0.38), residues: 185 loop : -1.02 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 585 HIS 0.004 0.001 HIS A 506 PHE 0.015 0.002 PHE B 239 TYR 0.012 0.002 TYR A 286 ARG 0.004 0.000 ARG A 634 *********************** 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 146 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.276 Fit side-chains REVERT: A 110 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8003 (pt0) REVERT: A 349 LYS cc_start: 0.7911 (pttt) cc_final: 0.7435 (ptpp) REVERT: A 491 ARG cc_start: 0.7104 (OUTLIER) cc_final: 0.6810 (tpt170) REVERT: A 573 CYS cc_start: 0.4917 (t) cc_final: 0.4525 (t) REVERT: A 699 LYS cc_start: 0.8041 (ptpt) cc_final: 0.7558 (tptt) REVERT: B 163 MET cc_start: 0.8649 (mtp) cc_final: 0.8402 (mtm) REVERT: B 349 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8484 (tttm) REVERT: B 352 MET cc_start: 0.7662 (tpp) cc_final: 0.7181 (mpp) REVERT: B 537 LEU cc_start: 0.8950 (mt) cc_final: 0.8656 (mt) REVERT: B 580 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7438 (mp0) REVERT: B 598 LYS cc_start: 0.8015 (pptt) cc_final: 0.7245 (ptpt) REVERT: B 677 MET cc_start: 0.8563 (mmt) cc_final: 0.8295 (tpp) REVERT: B 695 GLU cc_start: 0.7828 (pp20) cc_final: 0.7535 (pp20) outliers start: 34 outliers final: 20 residues processed: 135 average time/residue: 0.2243 time to fit residues: 43.6694 Evaluate side-chains 128 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 106 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 394 GLU Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9995 Z= 0.176 Angle : 0.536 8.871 13488 Z= 0.272 Chirality : 0.041 0.173 1519 Planarity : 0.004 0.036 1714 Dihedral : 5.788 54.499 1398 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.17 % Allowed : 20.72 % 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: -0.72 (0.24), residues: 1206 helix: 0.06 (0.23), residues: 527 sheet: -0.41 (0.39), residues: 175 loop : -0.94 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 585 HIS 0.002 0.001 HIS A 144 PHE 0.009 0.001 PHE B 239 TYR 0.009 0.001 TYR B 344 ARG 0.003 0.000 ARG A 634 *********************** 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 143 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.157 Fit side-chains REVERT: A 110 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: A 699 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7557 (tptt) REVERT: B 352 MET cc_start: 0.7610 (tpp) cc_final: 0.7130 (mpp) REVERT: B 517 MET cc_start: 0.8340 (mmm) cc_final: 0.8106 (tpp) REVERT: B 537 LEU cc_start: 0.8932 (mt) cc_final: 0.8555 (mt) REVERT: B 580 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7415 (mp0) REVERT: B 598 LYS cc_start: 0.7764 (pptt) cc_final: 0.6908 (ptpp) REVERT: B 677 MET cc_start: 0.8591 (mmt) cc_final: 0.8328 (tpp) REVERT: B 695 GLU cc_start: 0.7799 (pp20) cc_final: 0.7502 (pp20) outliers start: 23 outliers final: 15 residues processed: 135 average time/residue: 0.2074 time to fit residues: 40.4280 Evaluate side-chains 124 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 108 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 683 VAL 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: 0.3980 chunk 22 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9995 Z= 0.233 Angle : 0.563 8.521 13488 Z= 0.282 Chirality : 0.042 0.170 1519 Planarity : 0.004 0.038 1714 Dihedral : 5.902 57.165 1398 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.98 % Allowed : 21.75 % Favored : 76.27 % 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: -0.73 (0.24), residues: 1206 helix: 0.06 (0.23), residues: 526 sheet: -0.41 (0.38), residues: 186 loop : -0.99 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 299 HIS 0.003 0.001 HIS A 620 PHE 0.011 0.001 PHE B 239 TYR 0.010 0.001 TYR B 206 ARG 0.003 0.000 ARG A 634 *********************** 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 130 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 109 time to evaluate : 1.164 Fit side-chains REVERT: A 110 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.7921 (pt0) REVERT: A 583 MET cc_start: 0.6545 (tpp) cc_final: 0.6302 (tpp) REVERT: A 699 LYS cc_start: 0.8044 (ptpt) cc_final: 0.7588 (tptt) REVERT: B 352 MET cc_start: 0.7619 (tpp) cc_final: 0.7101 (mpp) REVERT: B 517 MET cc_start: 0.8336 (mmm) cc_final: 0.8109 (tpp) REVERT: B 537 LEU cc_start: 0.8943 (mt) cc_final: 0.8557 (mt) REVERT: B 580 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7421 (mp0) REVERT: B 598 LYS cc_start: 0.7827 (pptt) cc_final: 0.6973 (ptpp) REVERT: B 695 GLU cc_start: 0.7818 (pp20) cc_final: 0.7496 (pp20) outliers start: 21 outliers final: 17 residues processed: 124 average time/residue: 0.2217 time to fit residues: 39.5417 Evaluate side-chains 122 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 chunk 108 optimal weight: 8.9990 chunk 71 optimal weight: 5.9990 chunk 114 optimal weight: 0.0270 chunk 70 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9995 Z= 0.197 Angle : 0.551 8.458 13488 Z= 0.276 Chirality : 0.041 0.168 1519 Planarity : 0.004 0.036 1714 Dihedral : 5.782 58.628 1398 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.98 % Allowed : 21.66 % Favored : 76.37 % 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: 0.14 (0.23), residues: 522 sheet: -0.31 (0.38), residues: 185 loop : -0.94 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 299 HIS 0.002 0.000 HIS A 256 PHE 0.010 0.001 PHE B 239 TYR 0.010 0.001 TYR B 206 ARG 0.004 0.000 ARG A 623 *********************** 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 136 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: A 623 ARG cc_start: 0.6789 (mtm110) cc_final: 0.6376 (ttp-110) REVERT: A 699 LYS cc_start: 0.8041 (ptpt) cc_final: 0.7585 (tptt) REVERT: B 352 MET cc_start: 0.7703 (tpp) cc_final: 0.7193 (mpp) REVERT: B 517 MET cc_start: 0.8340 (mmm) cc_final: 0.8085 (tpp) REVERT: B 537 LEU cc_start: 0.8936 (mt) cc_final: 0.8545 (mt) REVERT: B 580 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7436 (mp0) REVERT: B 598 LYS cc_start: 0.7810 (pptt) cc_final: 0.7117 (ptpt) REVERT: B 695 GLU cc_start: 0.7784 (pp20) cc_final: 0.7475 (pp20) outliers start: 21 outliers final: 14 residues processed: 130 average time/residue: 0.2227 time to fit residues: 41.2405 Evaluate side-chains 121 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 0.0570 chunk 95 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9995 Z= 0.186 Angle : 0.552 8.557 13488 Z= 0.275 Chirality : 0.041 0.168 1519 Planarity : 0.004 0.036 1714 Dihedral : 5.594 55.420 1398 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.69 % Allowed : 21.56 % 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: -0.61 (0.24), residues: 1206 helix: 0.16 (0.23), residues: 521 sheet: -0.25 (0.38), residues: 185 loop : -0.95 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 231 HIS 0.003 0.001 HIS A 144 PHE 0.010 0.001 PHE A 239 TYR 0.010 0.001 TYR B 206 ARG 0.003 0.000 ARG A 623 ********************** 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 126 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.175 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: A 623 ARG cc_start: 0.6785 (mtm110) cc_final: 0.6401 (ttp-110) REVERT: A 699 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7594 (tptt) REVERT: B 352 MET cc_start: 0.7772 (tpp) cc_final: 0.7254 (mpp) REVERT: B 517 MET cc_start: 0.8348 (mmm) cc_final: 0.8088 (tpp) REVERT: B 537 LEU cc_start: 0.8924 (mt) cc_final: 0.8530 (mt) REVERT: B 580 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7442 (mp0) REVERT: B 598 LYS cc_start: 0.7760 (pptt) cc_final: 0.6928 (ptpp) REVERT: B 677 MET cc_start: 0.8633 (mmt) cc_final: 0.8391 (mpp) REVERT: B 695 GLU cc_start: 0.7766 (pp20) cc_final: 0.7481 (pp20) outliers start: 18 outliers final: 17 residues processed: 121 average time/residue: 0.2237 time to fit residues: 38.8423 Evaluate side-chains 125 residues out of total 1067 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 107 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 501 CYS Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 613 LEU Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 684 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0030 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 675 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.102361 restraints weight = 15932.729| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.45 r_work: 0.3175 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9995 Z= 0.168 Angle : 0.543 10.476 13488 Z= 0.270 Chirality : 0.041 0.167 1519 Planarity : 0.003 0.036 1714 Dihedral : 5.360 49.284 1398 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.69 % Allowed : 21.47 % Favored : 76.84 % 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: -0.54 (0.24), residues: 1206 helix: 0.21 (0.23), residues: 521 sheet: -0.12 (0.37), residues: 190 loop : -0.96 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 231 HIS 0.002 0.000 HIS B 72 PHE 0.009 0.001 PHE A 112 TYR 0.009 0.001 TYR B 206 ARG 0.004 0.000 ARG B 623 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2111.50 seconds wall clock time: 39 minutes 16.52 seconds (2356.52 seconds total)