Starting phenix.real_space_refine on Thu Mar 14 15:58:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6og1_20049/03_2024/6og1_20049_updated.pdb" } resolution = 3.3 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 32 5.16 5 C 5749 2.51 5 N 1669 2.21 5 O 1748 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F ASP 326": "OD1" <-> "OD2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 358": "OE1" <-> "OE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F GLU 680": "OE1" <-> "OE2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 701": "OD1" <-> "OD2" Residue "F PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 733": "OD1" <-> "OD2" Residue "F GLU 739": "OE1" <-> "OE2" Residue "F GLU 752": "OE1" <-> "OE2" Residue "F ASP 797": "OD1" <-> "OD2" Residue "F TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 819": "NH1" <-> "NH2" Residue "F ASP 851": "OD1" <-> "OD2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ASP 809": "OD1" <-> "OD2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ASP 851": "OD1" <-> "OD2" 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: 9207 Number of models: 1 Model: "" Number of chains: 4 Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4518 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.50, per 1000 atoms: 0.60 Number of scatterers: 9207 At special positions: 0 Unit cell: (108.36, 118.68, 105.264, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 9 15.00 O 1748 8.00 N 1669 7.00 C 5749 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: 3.39 Conformation dependent library (CDL) restraints added in 2.0 seconds 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 6 sheets defined 32.0% alpha, 4.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 189 through 192 No H-bonds generated for 'chain 'F' and resid 189 through 192' Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.958A pdb=" N LEU F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 264 removed outlier: 3.815A pdb=" N LEU F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN F 264 " --> pdb=" O LYS F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 319 through 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 349 through 357 removed outlier: 3.600A pdb=" N LEU F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 370 No H-bonds generated for 'chain 'F' and resid 367 through 370' Processing helix chain 'F' and resid 388 through 395 removed outlier: 3.991A pdb=" N ASP F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 395 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 removed outlier: 4.548A pdb=" N ILE F 401 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG F 402 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N MET F 403 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN F 404 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE F 405 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 542 removed outlier: 3.745A pdb=" N VAL F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 557 through 562 removed outlier: 4.447A pdb=" N ARG F 561 " --> pdb=" O LYS F 558 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET F 562 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 569 No H-bonds generated for 'chain 'F' and resid 566 through 569' Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.628A pdb=" N ALA F 579 " --> pdb=" O ALA F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 623 removed outlier: 3.748A pdb=" N ALA F 619 " --> pdb=" O CYS F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 643 removed outlier: 4.133A pdb=" N VAL F 643 " --> pdb=" O LYS F 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 640 through 643' Processing helix chain 'F' and resid 684 through 690 removed outlier: 3.687A pdb=" N PHE F 687 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ASN F 688 " --> pdb=" O ASP F 685 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE F 689 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU F 690 " --> pdb=" O PHE F 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 684 through 690' Processing helix chain 'F' and resid 737 through 740 No H-bonds generated for 'chain 'F' and resid 737 through 740' Processing helix chain 'F' and resid 769 through 783 removed outlier: 3.729A pdb=" N ILE F 774 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU F 779 " --> pdb=" O ALA F 775 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 801 removed outlier: 3.819A pdb=" N LYS F 801 " --> pdb=" O ASP F 797 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 797 through 801' Processing helix chain 'F' and resid 804 through 806 No H-bonds generated for 'chain 'F' and resid 804 through 806' Processing helix chain 'F' and resid 815 through 824 removed outlier: 3.741A pdb=" N LYS F 818 " --> pdb=" O ARG F 815 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG F 819 " --> pdb=" O PRO F 816 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 823 " --> pdb=" O ALA F 820 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN F 824 " --> pdb=" O ILE F 821 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 835 Processing helix chain 'A' and resid 170 through 173 No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 removed outlier: 4.048A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.572A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 300 through 304 removed outlier: 3.500A pdb=" N ALA A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 300 through 304' Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.805A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 332' Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.880A pdb=" N ILE A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.951A pdb=" N HIS A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.604A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 removed outlier: 5.247A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 556 through 559 No H-bonds generated for 'chain 'A' and resid 556 through 559' Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.017A pdb=" N LEU A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 567' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.816A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 removed outlier: 3.606A pdb=" N VAL A 643 " --> pdb=" O LYS A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 679 through 681 No H-bonds generated for 'chain 'A' and resid 679 through 681' Processing helix chain 'A' and resid 684 through 687 No H-bonds generated for 'chain 'A' and resid 684 through 687' Processing helix chain 'A' and resid 689 through 695 removed outlier: 4.008A pdb=" N GLN A 692 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 693 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 694 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 695 " --> pdb=" O GLN A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 695' Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.863A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 removed outlier: 4.135A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 800 through 806 removed outlier: 4.327A pdb=" N ASN A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 removed outlier: 3.713A pdb=" N ILE A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing sheet with id= A, first strand: chain 'F' and resid 333 through 337 removed outlier: 6.901A pdb=" N ASN F 201 " --> pdb=" O GLN F 334 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 336 " --> pdb=" O ASN F 201 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL F 203 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 675 through 677 removed outlier: 7.028A pdb=" N ILE F 715 " --> pdb=" O LEU F 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 202 through 205 removed outlier: 5.989A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 236 through 238 Processing sheet with id= E, first strand: chain 'A' and resid 599 through 604 Processing sheet with id= F, first strand: chain 'A' and resid 698 through 700 126 hydrogen bonds defined for protein. 348 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: 1.96 Time building geometry restraints manager: 3.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3261 1.36 - 1.51: 2480 1.51 - 1.66: 3548 1.66 - 1.80: 47 1.80 - 1.95: 12 Bond restraints: 9348 Sorted by residual: bond pdb=" C ARG A 815 " pdb=" N PRO A 816 " ideal model delta sigma weight residual 1.337 1.397 -0.060 9.80e-03 1.04e+04 3.81e+01 bond pdb=" C ALA A 682 " pdb=" N HIS A 683 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.47e-02 4.63e+03 9.00e+00 bond pdb=" CA ALA F 775 " pdb=" C ALA F 775 " ideal model delta sigma weight residual 1.522 1.487 0.035 1.37e-02 5.33e+03 6.49e+00 bond pdb=" CA HIS A 747 " pdb=" CB HIS A 747 " ideal model delta sigma weight residual 1.524 1.556 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" C ALA A 289 " pdb=" N ASP A 290 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.41e-02 5.03e+03 4.36e+00 ... (remaining 9343 not shown) Histogram of bond angle deviations from ideal: 97.65 - 105.34: 187 105.34 - 113.03: 4912 113.03 - 120.72: 4407 120.72 - 128.42: 3071 128.42 - 136.11: 57 Bond angle restraints: 12634 Sorted by residual: angle pdb=" N VAL F 343 " pdb=" CA VAL F 343 " pdb=" C VAL F 343 " ideal model delta sigma weight residual 113.22 105.79 7.43 1.23e+00 6.61e-01 3.65e+01 angle pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" C ILE A 215 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" C ARG A 852 " pdb=" N ILE A 853 " pdb=" CA ILE A 853 " ideal model delta sigma weight residual 120.49 127.77 -7.28 1.38e+00 5.25e-01 2.79e+01 angle pdb=" N ASN A 297 " pdb=" CA ASN A 297 " pdb=" C ASN A 297 " ideal model delta sigma weight residual 114.75 108.27 6.48 1.26e+00 6.30e-01 2.64e+01 angle pdb=" N ILE A 853 " pdb=" CA ILE A 853 " pdb=" C ILE A 853 " ideal model delta sigma weight residual 109.51 116.53 -7.02 1.43e+00 4.89e-01 2.41e+01 ... (remaining 12629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.03: 5525 33.03 - 66.07: 201 66.07 - 99.10: 18 99.10 - 132.14: 3 132.14 - 165.17: 1 Dihedral angle restraints: 5748 sinusoidal: 2441 harmonic: 3307 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.84 -115.84 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 53.33 -113.33 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N LEU A 386 " pdb=" CA LEU A 386 " ideal model delta harmonic sigma weight residual -180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 5745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1062 0.066 - 0.131: 315 0.131 - 0.196: 41 0.196 - 0.262: 7 0.262 - 0.327: 1 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CB ILE F 571 " pdb=" CA ILE F 571 " pdb=" CG1 ILE F 571 " pdb=" CG2 ILE F 571 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP A 624 " pdb=" N ASP A 624 " pdb=" C ASP A 624 " pdb=" CB ASP A 624 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CG LEU F 280 " pdb=" CB LEU F 280 " pdb=" CD1 LEU F 280 " pdb=" CD2 LEU F 280 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 1423 not shown) Planarity restraints: 1648 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 367 " 0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 368 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 207 " -0.048 5.00e-02 4.00e+02 7.18e-02 8.26e+00 pdb=" N PRO A 208 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A 208 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 208 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 650 " -0.047 5.00e-02 4.00e+02 7.02e-02 7.89e+00 pdb=" N PRO A 651 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO A 651 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 651 " -0.039 5.00e-02 4.00e+02 ... (remaining 1645 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1568 2.77 - 3.30: 7918 3.30 - 3.83: 14539 3.83 - 4.37: 17141 4.37 - 4.90: 28061 Nonbonded interactions: 69227 Sorted by model distance: nonbonded pdb=" O ASP A 241 " pdb=" OD1 ASP A 241 " model vdw 2.234 3.040 nonbonded pdb=" O MET F 629 " pdb=" OH TYR F 661 " model vdw 2.262 2.440 nonbonded pdb=" OD2 ASP F 178 " pdb=" O2' ADP F 901 " model vdw 2.272 2.440 nonbonded pdb=" O SER A 804 " pdb=" OG SER A 804 " model vdw 2.297 2.440 nonbonded pdb=" NH2 ARG F 196 " pdb=" OD1 ASP A 392 " model vdw 2.314 2.520 ... (remaining 69222 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 161 through 283 or resid 294 through 857 or resid 902)) selection = (chain 'F' and (resid 161 through 857 or resid 902)) } 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.830 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 27.600 Find NCS groups from input model: 0.530 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: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5811 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 : 0.007 0.067 9348 Z= 0.467 Angle : 1.216 10.194 12634 Z= 0.682 Chirality : 0.062 0.327 1426 Planarity : 0.008 0.080 1648 Dihedral : 16.868 165.171 3618 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.60 % Favored : 89.32 % Rotamer: Outliers : 0.52 % Allowed : 9.38 % Favored : 90.10 % 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: -5.53 (0.18), residues: 1142 helix: -4.82 (0.11), residues: 401 sheet: -3.29 (0.44), residues: 80 loop : -3.03 (0.20), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 543 HIS 0.016 0.002 HIS A 747 PHE 0.020 0.003 PHE F 687 TYR 0.016 0.003 TYR A 653 ARG 0.012 0.001 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 212 time to evaluate : 1.000 Fit side-chains REVERT: F 199 LYS cc_start: 0.7673 (ttmt) cc_final: 0.7473 (tttm) REVERT: F 298 MET cc_start: 0.4762 (mtm) cc_final: 0.4284 (mtm) REVERT: F 318 GLU cc_start: 0.7347 (tm-30) cc_final: 0.6207 (tt0) REVERT: F 634 MET cc_start: 0.0468 (mmp) cc_final: -0.0560 (mtm) REVERT: F 638 MET cc_start: 0.1410 (mmp) cc_final: 0.0911 (mmt) REVERT: F 737 MET cc_start: 0.2313 (tpt) cc_final: 0.1104 (ppp) REVERT: F 784 LYS cc_start: 0.8138 (mptt) cc_final: 0.7762 (mmtm) REVERT: F 828 PRO cc_start: 0.7942 (Cg_exo) cc_final: 0.7668 (Cg_endo) REVERT: A 184 ASP cc_start: 0.7735 (t0) cc_final: 0.7524 (t70) REVERT: A 533 ASP cc_start: 0.7691 (p0) cc_final: 0.7243 (t0) REVERT: A 562 MET cc_start: 0.5562 (ttm) cc_final: 0.5351 (ttm) REVERT: A 564 GLN cc_start: 0.7440 (tm-30) cc_final: 0.7008 (tm-30) REVERT: A 616 LYS cc_start: 0.8009 (mttt) cc_final: 0.7796 (mtmt) REVERT: A 708 ASP cc_start: 0.7113 (t70) cc_final: 0.6883 (t70) REVERT: A 710 ARG cc_start: 0.8332 (mpt-90) cc_final: 0.7996 (mtt-85) outliers start: 5 outliers final: 2 residues processed: 216 average time/residue: 0.2590 time to fit residues: 73.3685 Evaluate side-chains 129 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 48 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.0070 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 104 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 719 ASN A 174 GLN ** A 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 719 ASN A 794 HIS A 831 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9348 Z= 0.188 Angle : 0.696 6.855 12634 Z= 0.347 Chirality : 0.046 0.197 1426 Planarity : 0.005 0.061 1648 Dihedral : 11.413 175.422 1331 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.27 % Allowed : 14.12 % Favored : 83.61 % 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: -4.67 (0.20), residues: 1142 helix: -4.04 (0.16), residues: 397 sheet: -3.07 (0.52), residues: 74 loop : -2.55 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 543 HIS 0.005 0.001 HIS A 747 PHE 0.010 0.001 PHE A 276 TYR 0.010 0.001 TYR F 661 ARG 0.005 0.000 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 146 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: F 188 ARG cc_start: 0.6471 (ttp80) cc_final: 0.6139 (tpp-160) REVERT: F 242 MET cc_start: 0.3667 (ttm) cc_final: 0.3223 (ttm) REVERT: F 258 ARG cc_start: 0.6550 (mtp-110) cc_final: 0.6104 (mtp180) REVERT: F 276 PHE cc_start: 0.8031 (m-10) cc_final: 0.7539 (m-80) REVERT: F 298 MET cc_start: 0.4505 (mtm) cc_final: 0.3993 (mtm) REVERT: F 318 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6581 (tm-30) REVERT: F 389 LYS cc_start: 0.5464 (mtpt) cc_final: 0.5252 (mtmt) REVERT: F 629 MET cc_start: 0.4878 (tmm) cc_final: 0.3329 (tpt) REVERT: F 634 MET cc_start: 0.0308 (mmp) cc_final: -0.0755 (mtm) REVERT: F 638 MET cc_start: 0.1232 (mmp) cc_final: 0.0650 (mmt) REVERT: F 737 MET cc_start: 0.2910 (tpt) cc_final: 0.1353 (ppp) REVERT: A 164 TYR cc_start: 0.7738 (m-80) cc_final: 0.7259 (m-80) REVERT: A 395 ASP cc_start: 0.8231 (t0) cc_final: 0.7980 (m-30) REVERT: A 533 ASP cc_start: 0.7609 (p0) cc_final: 0.7186 (t0) REVERT: A 562 MET cc_start: 0.5866 (ttm) cc_final: 0.5582 (ttm) REVERT: A 564 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7074 (tm-30) REVERT: A 612 THR cc_start: 0.8561 (m) cc_final: 0.8240 (p) REVERT: A 710 ARG cc_start: 0.8397 (mpt-90) cc_final: 0.8107 (mtt180) outliers start: 22 outliers final: 12 residues processed: 161 average time/residue: 0.2327 time to fit residues: 50.1951 Evaluate side-chains 134 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.0170 chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 0.0770 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 104 optimal weight: 0.0470 chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.3074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS F 770 HIS A 192 GLN A 573 GLN A 641 HIS A 719 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5907 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9348 Z= 0.154 Angle : 0.625 6.619 12634 Z= 0.307 Chirality : 0.044 0.161 1426 Planarity : 0.004 0.048 1648 Dihedral : 10.466 171.793 1329 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 2.16 % Allowed : 16.80 % Favored : 81.03 % 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: -4.20 (0.21), residues: 1142 helix: -3.40 (0.18), residues: 427 sheet: -2.82 (0.50), residues: 84 loop : -2.32 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.010 0.001 PHE A 621 TYR 0.008 0.001 TYR F 661 ARG 0.010 0.000 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 1.065 Fit side-chains REVERT: F 188 ARG cc_start: 0.6547 (ttp80) cc_final: 0.6291 (ttm170) REVERT: F 242 MET cc_start: 0.3688 (ttm) cc_final: 0.3450 (ttm) REVERT: F 298 MET cc_start: 0.4531 (mtm) cc_final: 0.4120 (mtm) REVERT: F 318 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6145 (tt0) REVERT: F 337 PHE cc_start: 0.6007 (t80) cc_final: 0.5674 (t80) REVERT: F 614 LEU cc_start: 0.8247 (tt) cc_final: 0.8017 (tt) REVERT: F 629 MET cc_start: 0.4151 (tmm) cc_final: 0.2890 (tpt) REVERT: F 634 MET cc_start: 0.0125 (mmp) cc_final: -0.0991 (mtt) REVERT: F 737 MET cc_start: 0.2693 (tpt) cc_final: 0.1086 (ppp) REVERT: A 164 TYR cc_start: 0.7635 (m-80) cc_final: 0.7092 (m-80) REVERT: A 395 ASP cc_start: 0.8280 (t0) cc_final: 0.7993 (m-30) REVERT: A 533 ASP cc_start: 0.7486 (p0) cc_final: 0.7220 (t0) REVERT: A 563 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6996 (mt-10) REVERT: A 564 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7293 (tm-30) outliers start: 21 outliers final: 11 residues processed: 146 average time/residue: 0.2229 time to fit residues: 44.5961 Evaluate side-chains 126 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 115 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0970 chunk 78 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 719 ASN A 174 GLN A 641 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9348 Z= 0.176 Angle : 0.615 7.097 12634 Z= 0.297 Chirality : 0.044 0.137 1426 Planarity : 0.004 0.041 1648 Dihedral : 9.960 164.701 1329 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 3.09 % Allowed : 17.22 % Favored : 79.69 % 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: -3.68 (0.22), residues: 1142 helix: -2.89 (0.21), residues: 415 sheet: -2.59 (0.46), residues: 106 loop : -2.05 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.007 0.001 PHE F 276 TYR 0.012 0.001 TYR F 322 ARG 0.012 0.000 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.033 Fit side-chains REVERT: F 188 ARG cc_start: 0.6709 (ttp80) cc_final: 0.6386 (ttm170) REVERT: F 242 MET cc_start: 0.3673 (ttm) cc_final: 0.3446 (ttm) REVERT: F 283 MET cc_start: 0.0253 (ptp) cc_final: -0.0026 (ppp) REVERT: F 298 MET cc_start: 0.4570 (mtm) cc_final: 0.4361 (mtm) REVERT: F 376 LEU cc_start: 0.4044 (OUTLIER) cc_final: 0.3272 (mt) REVERT: F 614 LEU cc_start: 0.8211 (tt) cc_final: 0.8000 (tt) REVERT: F 634 MET cc_start: 0.0377 (mmp) cc_final: -0.1150 (mtt) REVERT: F 716 MET cc_start: 0.5048 (tpt) cc_final: 0.4423 (mpp) REVERT: F 737 MET cc_start: 0.2459 (tpt) cc_final: 0.0944 (ppp) REVERT: F 791 TYR cc_start: 0.7876 (m-80) cc_final: 0.7590 (m-80) REVERT: A 164 TYR cc_start: 0.7733 (m-80) cc_final: 0.7098 (m-80) REVERT: A 321 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8042 (pp30) REVERT: A 395 ASP cc_start: 0.8319 (t0) cc_final: 0.8007 (m-30) REVERT: A 563 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6818 (mt-10) REVERT: A 678 GLU cc_start: 0.6970 (mp0) cc_final: 0.6371 (mp0) REVERT: A 728 ARG cc_start: 0.7162 (mtp85) cc_final: 0.6723 (mtp85) REVERT: A 737 MET cc_start: 0.6940 (mmm) cc_final: 0.6159 (mtt) outliers start: 30 outliers final: 12 residues processed: 145 average time/residue: 0.2390 time to fit residues: 47.0481 Evaluate side-chains 132 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 94 optimal weight: 0.0020 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 56 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 28 optimal weight: 0.3980 chunk 37 optimal weight: 0.4980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5956 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9348 Z= 0.148 Angle : 0.606 7.731 12634 Z= 0.288 Chirality : 0.044 0.159 1426 Planarity : 0.004 0.039 1648 Dihedral : 9.572 154.686 1329 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.09 % Allowed : 17.42 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.23), residues: 1142 helix: -2.48 (0.22), residues: 417 sheet: -2.68 (0.47), residues: 101 loop : -1.79 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.011 0.001 PHE F 276 TYR 0.009 0.001 TYR A 322 ARG 0.011 0.000 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.934 Fit side-chains REVERT: F 242 MET cc_start: 0.3550 (ttm) cc_final: 0.3295 (ttm) REVERT: F 298 MET cc_start: 0.4593 (mtm) cc_final: 0.4329 (mtm) REVERT: F 376 LEU cc_start: 0.3972 (OUTLIER) cc_final: 0.3171 (mt) REVERT: F 552 MET cc_start: 0.0149 (tmm) cc_final: -0.0111 (tmm) REVERT: F 614 LEU cc_start: 0.8143 (tt) cc_final: 0.7912 (tt) REVERT: F 629 MET cc_start: 0.4731 (tmm) cc_final: 0.3400 (tpt) REVERT: F 634 MET cc_start: 0.0194 (mmp) cc_final: -0.1176 (mpp) REVERT: F 716 MET cc_start: 0.5124 (tpt) cc_final: 0.4392 (mpp) REVERT: F 737 MET cc_start: 0.2392 (tpt) cc_final: 0.0910 (ppp) REVERT: F 763 PHE cc_start: 0.1988 (OUTLIER) cc_final: 0.1354 (m-80) REVERT: F 791 TYR cc_start: 0.7921 (m-80) cc_final: 0.7683 (m-80) REVERT: A 184 ASP cc_start: 0.7697 (t0) cc_final: 0.7373 (m-30) REVERT: A 321 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8099 (pp30) REVERT: A 395 ASP cc_start: 0.8192 (t0) cc_final: 0.7869 (m-30) REVERT: A 552 MET cc_start: 0.3655 (OUTLIER) cc_final: 0.3100 (mmm) REVERT: A 563 GLU cc_start: 0.7366 (mt-10) cc_final: 0.7011 (mt-10) REVERT: A 678 GLU cc_start: 0.6968 (mp0) cc_final: 0.6403 (mp0) REVERT: A 737 MET cc_start: 0.7041 (mmm) cc_final: 0.6367 (mtt) REVERT: A 834 LEU cc_start: -0.2374 (OUTLIER) cc_final: -0.2823 (tt) outliers start: 30 outliers final: 20 residues processed: 143 average time/residue: 0.2115 time to fit residues: 41.6435 Evaluate side-chains 140 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 115 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 815 ARG Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 0.1980 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5991 moved from start: 0.3924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9348 Z= 0.174 Angle : 0.607 8.913 12634 Z= 0.288 Chirality : 0.044 0.156 1426 Planarity : 0.004 0.038 1648 Dihedral : 9.351 148.618 1329 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.30 % Allowed : 18.04 % Favored : 78.66 % 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: -3.02 (0.24), residues: 1142 helix: -2.28 (0.23), residues: 412 sheet: -2.69 (0.46), residues: 102 loop : -1.63 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.014 0.001 PHE F 276 TYR 0.010 0.001 TYR A 322 ARG 0.007 0.000 ARG A 561 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.030 Fit side-chains REVERT: F 242 MET cc_start: 0.3605 (ttm) cc_final: 0.3356 (ttm) REVERT: F 322 TYR cc_start: 0.7728 (m-80) cc_final: 0.7335 (m-80) REVERT: F 376 LEU cc_start: 0.4052 (OUTLIER) cc_final: 0.3223 (mt) REVERT: F 552 MET cc_start: 0.0087 (tmm) cc_final: -0.0119 (tmm) REVERT: F 614 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7861 (tt) REVERT: F 629 MET cc_start: 0.4129 (tmm) cc_final: 0.2967 (tpt) REVERT: F 634 MET cc_start: 0.0116 (mmp) cc_final: -0.1406 (mpp) REVERT: F 716 MET cc_start: 0.5259 (tpt) cc_final: 0.4371 (mpp) REVERT: F 737 MET cc_start: 0.2376 (tpt) cc_final: 0.1207 (ppp) REVERT: F 763 PHE cc_start: 0.1940 (OUTLIER) cc_final: 0.1494 (m-80) REVERT: A 170 GLU cc_start: 0.7193 (tt0) cc_final: 0.6771 (tm-30) REVERT: A 184 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7422 (m-30) REVERT: A 321 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8237 (pp30) REVERT: A 395 ASP cc_start: 0.8230 (t0) cc_final: 0.7930 (m-30) REVERT: A 552 MET cc_start: 0.3708 (OUTLIER) cc_final: 0.3198 (mmm) REVERT: A 563 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6908 (mt-10) REVERT: A 678 GLU cc_start: 0.7015 (mp0) cc_final: 0.6546 (mp0) REVERT: A 737 MET cc_start: 0.7057 (mmm) cc_final: 0.6550 (mtt) REVERT: A 834 LEU cc_start: -0.2240 (OUTLIER) cc_final: -0.2663 (tt) outliers start: 32 outliers final: 16 residues processed: 143 average time/residue: 0.2122 time to fit residues: 42.1956 Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 116 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 165 THR Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 614 LEU Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 241 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 723 ASP Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 44 optimal weight: 20.0000 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 794 HIS F 824 GLN F 857 GLN A 641 HIS A 719 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9348 Z= 0.280 Angle : 0.684 7.661 12634 Z= 0.326 Chirality : 0.046 0.163 1426 Planarity : 0.004 0.043 1648 Dihedral : 9.695 151.637 1329 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.51 % Allowed : 19.48 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.24), residues: 1142 helix: -2.29 (0.23), residues: 413 sheet: -2.85 (0.48), residues: 95 loop : -1.64 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 543 HIS 0.007 0.001 HIS A 641 PHE 0.011 0.001 PHE F 276 TYR 0.018 0.001 TYR F 661 ARG 0.007 0.001 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 122 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: F 322 TYR cc_start: 0.7905 (m-80) cc_final: 0.7535 (m-80) REVERT: F 335 LYS cc_start: 0.6960 (tttp) cc_final: 0.6742 (ttpp) REVERT: F 552 MET cc_start: -0.0158 (tmm) cc_final: -0.0380 (tmm) REVERT: F 629 MET cc_start: 0.4765 (tmm) cc_final: 0.3388 (tpt) REVERT: F 737 MET cc_start: 0.2321 (tpt) cc_final: 0.1073 (ppp) REVERT: F 831 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7896 (tt0) REVERT: A 170 GLU cc_start: 0.7177 (tt0) cc_final: 0.6786 (tm-30) REVERT: A 321 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8369 (pp30) REVERT: A 395 ASP cc_start: 0.8465 (t0) cc_final: 0.8109 (m-30) REVERT: A 552 MET cc_start: 0.3899 (OUTLIER) cc_final: 0.3589 (mmm) REVERT: A 563 GLU cc_start: 0.7435 (mt-10) cc_final: 0.7005 (mt-10) REVERT: A 678 GLU cc_start: 0.7225 (mp0) cc_final: 0.6619 (mp0) REVERT: A 737 MET cc_start: 0.7088 (mmm) cc_final: 0.6643 (mtt) REVERT: A 754 ILE cc_start: 0.8234 (mm) cc_final: 0.8022 (mt) REVERT: A 759 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7159 (tt0) REVERT: A 834 LEU cc_start: -0.2277 (OUTLIER) cc_final: -0.2676 (tt) outliers start: 34 outliers final: 20 residues processed: 148 average time/residue: 0.2190 time to fit residues: 44.8209 Evaluate side-chains 142 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 621 PHE Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 674 ILE Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 824 GLN Chi-restraints excluded: chain F residue 831 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 552 MET Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 100 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.4698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9348 Z= 0.170 Angle : 0.621 7.367 12634 Z= 0.295 Chirality : 0.044 0.141 1426 Planarity : 0.004 0.039 1648 Dihedral : 9.412 145.191 1329 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.16 % Allowed : 20.62 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.24), residues: 1142 helix: -1.90 (0.24), residues: 407 sheet: -2.72 (0.48), residues: 95 loop : -1.51 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.008 0.001 HIS A 641 PHE 0.025 0.001 PHE F 276 TYR 0.009 0.001 TYR A 322 ARG 0.007 0.000 ARG F 236 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.929 Fit side-chains REVERT: F 322 TYR cc_start: 0.7833 (m-80) cc_final: 0.7488 (m-80) REVERT: F 629 MET cc_start: 0.4744 (tmm) cc_final: 0.3474 (tpt) REVERT: F 737 MET cc_start: 0.2242 (tpt) cc_final: 0.1027 (ppp) REVERT: A 184 ASP cc_start: 0.7746 (t0) cc_final: 0.7433 (m-30) REVERT: A 316 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7353 (mt) REVERT: A 321 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8369 (pp30) REVERT: A 395 ASP cc_start: 0.8292 (t0) cc_final: 0.7995 (m-30) REVERT: A 552 MET cc_start: 0.3574 (mtp) cc_final: 0.3300 (mmm) REVERT: A 657 GLU cc_start: 0.7617 (tp30) cc_final: 0.7373 (tp30) REVERT: A 678 GLU cc_start: 0.7128 (mp0) cc_final: 0.6558 (mp0) REVERT: A 737 MET cc_start: 0.7115 (mmm) cc_final: 0.6710 (mtt) REVERT: A 754 ILE cc_start: 0.8228 (mm) cc_final: 0.8000 (mt) REVERT: A 759 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7180 (tt0) REVERT: A 834 LEU cc_start: -0.2337 (OUTLIER) cc_final: -0.2730 (tt) outliers start: 21 outliers final: 14 residues processed: 139 average time/residue: 0.2046 time to fit residues: 39.6821 Evaluate side-chains 132 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 769 GLN A 174 GLN A 641 HIS A 719 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6115 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9348 Z= 0.258 Angle : 0.674 8.536 12634 Z= 0.318 Chirality : 0.046 0.142 1426 Planarity : 0.004 0.038 1648 Dihedral : 9.596 149.460 1329 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.47 % Allowed : 20.62 % Favored : 76.91 % 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: -2.70 (0.24), residues: 1142 helix: -1.94 (0.24), residues: 407 sheet: -2.98 (0.49), residues: 85 loop : -1.47 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 543 HIS 0.009 0.001 HIS A 641 PHE 0.023 0.002 PHE A 621 TYR 0.011 0.001 TYR A 322 ARG 0.007 0.000 ARG F 305 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.063 Fit side-chains REVERT: F 322 TYR cc_start: 0.7971 (m-80) cc_final: 0.7586 (m-80) REVERT: F 737 MET cc_start: 0.2181 (tpt) cc_final: 0.1210 (ppp) REVERT: F 831 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 250 LYS cc_start: 0.7862 (mmtm) cc_final: 0.7566 (mtpt) REVERT: A 321 GLN cc_start: 0.9100 (OUTLIER) cc_final: 0.8418 (pp30) REVERT: A 364 GLN cc_start: 0.8056 (tt0) cc_final: 0.7786 (tt0) REVERT: A 395 ASP cc_start: 0.8418 (t0) cc_final: 0.8068 (m-30) REVERT: A 607 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8564 (t) REVERT: A 678 GLU cc_start: 0.7185 (mp0) cc_final: 0.6598 (mp0) REVERT: A 737 MET cc_start: 0.7283 (mmm) cc_final: 0.6796 (mtt) REVERT: A 754 ILE cc_start: 0.8309 (mm) cc_final: 0.8080 (mt) REVERT: A 759 GLU cc_start: 0.7498 (mt-10) cc_final: 0.7179 (tt0) REVERT: A 834 LEU cc_start: -0.2391 (OUTLIER) cc_final: -0.2768 (tt) outliers start: 24 outliers final: 16 residues processed: 139 average time/residue: 0.1982 time to fit residues: 38.8450 Evaluate side-chains 135 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 831 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 70 optimal weight: 0.0370 chunk 55 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 97 optimal weight: 0.5980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 641 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6068 moved from start: 0.5106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9348 Z= 0.172 Angle : 0.618 8.153 12634 Z= 0.291 Chirality : 0.044 0.137 1426 Planarity : 0.004 0.038 1648 Dihedral : 9.324 143.537 1329 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.27 % Allowed : 20.72 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.25), residues: 1142 helix: -1.69 (0.25), residues: 403 sheet: -2.82 (0.50), residues: 85 loop : -1.34 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 PHE 0.010 0.001 PHE A 621 TYR 0.008 0.001 TYR A 322 ARG 0.006 0.000 ARG F 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2284 Ramachandran restraints generated. 1142 Oldfield, 0 Emsley, 1142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.044 Fit side-chains REVERT: F 322 TYR cc_start: 0.7902 (m-80) cc_final: 0.7495 (m-80) REVERT: F 376 LEU cc_start: 0.4471 (OUTLIER) cc_final: 0.3691 (mt) REVERT: F 629 MET cc_start: 0.4743 (tmm) cc_final: 0.3507 (tpt) REVERT: F 737 MET cc_start: 0.2194 (tpt) cc_final: 0.1379 (ppp) REVERT: F 831 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 170 GLU cc_start: 0.7270 (tt0) cc_final: 0.7037 (tm-30) REVERT: A 184 ASP cc_start: 0.7840 (t0) cc_final: 0.7495 (m-30) REVERT: A 321 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8335 (pp30) REVERT: A 364 GLN cc_start: 0.8078 (tt0) cc_final: 0.7828 (tt0) REVERT: A 395 ASP cc_start: 0.8252 (t0) cc_final: 0.7932 (m-30) REVERT: A 607 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8513 (t) REVERT: A 678 GLU cc_start: 0.7208 (mp0) cc_final: 0.6643 (mp0) REVERT: A 737 MET cc_start: 0.7261 (mmm) cc_final: 0.6813 (mtt) REVERT: A 754 ILE cc_start: 0.8216 (mm) cc_final: 0.7978 (mt) REVERT: A 759 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7204 (tt0) REVERT: A 834 LEU cc_start: -0.2273 (OUTLIER) cc_final: -0.2624 (tt) outliers start: 22 outliers final: 17 residues processed: 141 average time/residue: 0.2012 time to fit residues: 40.3151 Evaluate side-chains 139 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 203 VAL Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 315 THR Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 532 THR Chi-restraints excluded: chain F residue 577 VAL Chi-restraints excluded: chain F residue 673 VAL Chi-restraints excluded: chain F residue 763 PHE Chi-restraints excluded: chain F residue 831 GLN Chi-restraints excluded: chain F residue 846 LEU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 321 GLN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 607 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 8.9990 chunk 84 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS A 719 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.258348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.212391 restraints weight = 10717.289| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 2.91 r_work: 0.4012 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9348 Z= 0.182 Angle : 0.618 7.953 12634 Z= 0.292 Chirality : 0.044 0.155 1426 Planarity : 0.004 0.038 1648 Dihedral : 9.219 141.395 1329 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.27 % Allowed : 20.93 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.25), residues: 1142 helix: -1.59 (0.25), residues: 406 sheet: -2.72 (0.50), residues: 85 loop : -1.26 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 543 HIS 0.009 0.001 HIS A 641 PHE 0.010 0.001 PHE A 621 TYR 0.010 0.001 TYR F 319 ARG 0.006 0.000 ARG A 728 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2121.70 seconds wall clock time: 38 minutes 34.20 seconds (2314.20 seconds total)