Starting phenix.real_space_refine on Sat Mar 16 07:34:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g7t_29823/03_2024/8g7t_29823_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 52 5.49 5 S 77 5.16 5 C 8785 2.51 5 N 2400 2.21 5 O 2743 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 249": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 581": "OE1" <-> "OE2" Residue "A GLU 583": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 795": "OE1" <-> "OE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "B ARG 253": "NH1" <-> "NH2" Residue "B ARG 279": "NH1" <-> "NH2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B ARG 296": "NH1" <-> "NH2" Residue "B ARG 342": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "C GLU 249": "OE1" <-> "OE2" Residue "C ARG 316": "NH1" <-> "NH2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "C GLU 422": "OE1" <-> "OE2" Residue "C GLU 448": "OE1" <-> "OE2" Residue "C GLU 450": "OE1" <-> "OE2" Residue "C GLU 464": "OE1" <-> "OE2" Residue "C ARG 502": "NH1" <-> "NH2" Residue "C GLU 530": "OE1" <-> "OE2" Residue "C GLU 531": "OE1" <-> "OE2" Residue "C ARG 533": "NH1" <-> "NH2" Residue "C GLU 556": "OE1" <-> "OE2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "C GLU 591": "OE1" <-> "OE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C ARG 602": "NH1" <-> "NH2" Residue "C GLU 612": "OE1" <-> "OE2" Residue "C GLU 627": "OE1" <-> "OE2" Residue "C GLU 749": "OE1" <-> "OE2" Residue "C GLU 758": "OE1" <-> "OE2" Residue "C GLU 787": "OE1" <-> "OE2" Residue "C PHE 853": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "C GLU 895": "OE1" <-> "OE2" Residue "C GLU 914": "OE1" <-> "OE2" Residue "D ARG 253": "NH1" <-> "NH2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D ARG 279": "NH1" <-> "NH2" Residue "D ARG 291": "NH1" <-> "NH2" Residue "D GLU 295": "OE1" <-> "OE2" Residue "D ARG 296": "NH1" <-> "NH2" Residue "D GLU 316": "OE1" <-> "OE2" Residue "D GLU 333": "OE1" <-> "OE2" Residue "D ARG 342": "NH1" <-> "NH2" Residue "D GLU 350": "OE1" <-> "OE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14059 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5234 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 619} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 616, 5000 Classifications: {'peptide': 616} Link IDs: {'PTRANS': 25, 'TRANS': 590} Chain breaks: 4 Chain: "D" Number of atoms: 1392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1392 Classifications: {'peptide': 178} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 170} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "X" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 523 Unusual residues: {'GTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 12, 'rna3p_pyr': 11} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="GTP X 1 " pdbres=" G X 2 " Chain: "Y" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 516 Unusual residues: {'UTP': 1} Classifications: {'RNA': 23, 'undetermined': 1} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 12} Link IDs: {'rna3p': 22, None: 1} Not linked: pdbres="UTP Y 1 " pdbres=" C Y 2 " Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4302 SG CYS A 810 95.220 82.980 65.658 1.00 24.09 S ATOM 4741 SG CYS A 864 97.097 86.788 66.632 1.00 35.22 S ATOM 4780 SG CYS A 869 93.983 86.644 64.616 1.00 40.34 S ATOM 11150 SG CYS C 864 39.821 27.357 65.024 1.00 81.69 S ATOM 11189 SG CYS C 869 39.334 31.210 66.004 1.00 85.78 S Time building chain proxies: 8.00, per 1000 atoms: 0.57 Number of scatterers: 14059 At special positions: 0 Unit cell: (120.816, 125.011, 136.757, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 77 16.00 P 52 15.00 O 2743 8.00 N 2400 7.00 C 8785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 347 " - pdb=" SG CYS B 402 " distance=2.03 Simple disulfide: pdb=" SG CYS D 347 " - pdb=" SG CYS D 402 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 864 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 869 " 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 15 sheets defined 32.7% alpha, 9.3% beta 13 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 5.97 Creating SS restraints... Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 269 through 283 removed outlier: 3.642A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 removed outlier: 3.735A pdb=" N SER A 308 " --> pdb=" O GLU A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 removed outlier: 3.900A pdb=" N VAL A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 334 through 338' Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 394 removed outlier: 3.761A pdb=" N ILE A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASN A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 393 " --> pdb=" O ASN A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 433 removed outlier: 3.703A pdb=" N ILE A 427 " --> pdb=" O ALA A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 449 No H-bonds generated for 'chain 'A' and resid 446 through 449' Processing helix chain 'A' and resid 470 through 486 removed outlier: 3.704A pdb=" N ILE A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 496 No H-bonds generated for 'chain 'A' and resid 494 through 496' Processing helix chain 'A' and resid 507 through 519 Processing helix chain 'A' and resid 531 through 557 removed outlier: 3.753A pdb=" N LYS A 536 " --> pdb=" O SER A 532 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 545 " --> pdb=" O TYR A 541 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 552 " --> pdb=" O TYR A 548 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 577 removed outlier: 3.740A pdb=" N LEU A 564 " --> pdb=" O MET A 560 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 567 " --> pdb=" O ALA A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 600 removed outlier: 3.634A pdb=" N ASP A 585 " --> pdb=" O GLU A 581 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 586 " --> pdb=" O ILE A 582 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 592 " --> pdb=" O GLN A 588 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LYS A 593 " --> pdb=" O ARG A 589 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 624 removed outlier: 3.552A pdb=" N ASP A 613 " --> pdb=" O PRO A 609 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 616 " --> pdb=" O GLU A 612 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A 623 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.763A pdb=" N ILE A 647 " --> pdb=" O LEU A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 653 No H-bonds generated for 'chain 'A' and resid 651 through 653' Processing helix chain 'A' and resid 745 through 770 removed outlier: 3.653A pdb=" N GLU A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 756 " --> pdb=" O GLN A 752 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP A 763 " --> pdb=" O LYS A 759 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 793 removed outlier: 3.527A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU A 778 " --> pdb=" O ALA A 774 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 781 " --> pdb=" O ARG A 777 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE A 783 " --> pdb=" O LYS A 779 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR A 785 " --> pdb=" O LEU A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 840 removed outlier: 3.763A pdb=" N GLU A 840 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 837 through 840' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'C' and resid 245 through 250 removed outlier: 3.713A pdb=" N LEU C 250 " --> pdb=" O TYR C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 255 No H-bonds generated for 'chain 'C' and resid 252 through 255' Processing helix chain 'C' and resid 268 through 283 removed outlier: 3.822A pdb=" N SER C 274 " --> pdb=" O LYS C 270 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU C 276 " --> pdb=" O PHE C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 313 removed outlier: 3.565A pdb=" N SER C 308 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 309 " --> pdb=" O GLN C 305 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE C 310 " --> pdb=" O GLN C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 340 Processing helix chain 'C' and resid 348 through 357 removed outlier: 3.510A pdb=" N LYS C 357 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 374 through 376 No H-bonds generated for 'chain 'C' and resid 374 through 376' Processing helix chain 'C' and resid 382 through 394 removed outlier: 3.622A pdb=" N ILE C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET C 387 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE C 388 " --> pdb=" O ASN C 384 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP C 392 " --> pdb=" O PHE C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 434 removed outlier: 3.847A pdb=" N ASP C 425 " --> pdb=" O ASP C 421 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N TYR C 426 " --> pdb=" O GLU C 422 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE C 427 " --> pdb=" O ALA C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 449 No H-bonds generated for 'chain 'C' and resid 446 through 449' Processing helix chain 'C' and resid 470 through 486 removed outlier: 3.702A pdb=" N ILE C 474 " --> pdb=" O LYS C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 521 removed outlier: 3.610A pdb=" N VAL C 514 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N CYS C 520 " --> pdb=" O VAL C 516 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET C 521 " --> pdb=" O GLN C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 557 removed outlier: 3.582A pdb=" N LYS C 536 " --> pdb=" O SER C 532 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.778A pdb=" N LEU C 564 " --> pdb=" O LYS C 561 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS C 568 " --> pdb=" O ASP C 565 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP C 569 " --> pdb=" O TYR C 566 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE C 571 " --> pdb=" O LYS C 568 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 572 " --> pdb=" O ASP C 569 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C 575 " --> pdb=" O SER C 572 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 592 removed outlier: 3.520A pdb=" N ASP C 585 " --> pdb=" O GLU C 581 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 602 removed outlier: 3.538A pdb=" N VAL C 600 " --> pdb=" O GLU C 596 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG C 602 " --> pdb=" O GLU C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 624 removed outlier: 3.647A pdb=" N LEU C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN C 619 " --> pdb=" O CYS C 615 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 620 " --> pdb=" O PHE C 616 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU C 621 " --> pdb=" O ILE C 617 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C 622 " --> pdb=" O LEU C 618 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS C 623 " --> pdb=" O GLN C 619 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 624 " --> pdb=" O GLU C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 637 through 647 removed outlier: 3.757A pdb=" N ASP C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS C 644 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ASN C 645 " --> pdb=" O ASP C 641 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP C 646 " --> pdb=" O ALA C 642 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 770 removed outlier: 3.567A pdb=" N ASN C 754 " --> pdb=" O LYS C 750 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR C 756 " --> pdb=" O GLN C 752 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU C 766 " --> pdb=" O ASN C 762 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 792 removed outlier: 3.650A pdb=" N HIS C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE C 783 " --> pdb=" O LYS C 779 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 789 " --> pdb=" O THR C 785 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ILE C 790 " --> pdb=" O HIS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing sheet with id= A, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= B, first strand: chain 'A' and resid 457 through 462 removed outlier: 3.687A pdb=" N PHE A 459 " --> pdb=" O CYS A 738 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A 740 " --> pdb=" O PHE A 459 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N THR A 742 " --> pdb=" O ARG A 461 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL A 712 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU A 741 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU A 714 " --> pdb=" O LEU A 741 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 631 " --> pdb=" O ILE A 713 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR A 715 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N PHE A 633 " --> pdb=" O TYR A 715 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 892 through 895 removed outlier: 3.786A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N CYS A 810 " --> pdb=" O LEU A 816 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N LEU A 816 " --> pdb=" O CYS A 810 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 883 through 887 removed outlier: 7.031A pdb=" N LYS A 878 " --> pdb=" O LYS A 858 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LYS A 858 " --> pdb=" O LYS A 878 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 280 through 282 Processing sheet with id= G, first strand: chain 'B' and resid 313 through 318 removed outlier: 3.784A pdb=" N HIS B 313 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP B 315 " --> pdb=" O ILE B 378 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 378 " --> pdb=" O TRP B 315 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 317 " --> pdb=" O VAL B 376 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 376 " --> pdb=" O VAL B 317 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 412 through 416 removed outlier: 4.087A pdb=" N TRP B 325 " --> pdb=" O TRP B 351 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 349 " --> pdb=" O VAL B 327 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 294 through 296 Processing sheet with id= J, first strand: chain 'C' and resid 460 through 462 removed outlier: 7.614A pdb=" N ARG C 461 " --> pdb=" O CYS C 738 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N LEU C 740 " --> pdb=" O ARG C 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 631 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 633 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 715 " --> pdb=" O PHE C 633 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 893 through 896 removed outlier: 3.770A pdb=" N CYS C 818 " --> pdb=" O LEU C 808 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 823 through 825 removed outlier: 4.618A pdb=" N TYR C 831 " --> pdb=" O ILE C 887 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL C 833 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 842 through 846 removed outlier: 3.518A pdb=" N ARG C 859 " --> pdb=" O HIS C 876 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N HIS C 876 " --> pdb=" O ARG C 859 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS C 861 " --> pdb=" O GLY C 874 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N GLY C 874 " --> pdb=" O LYS C 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 313 through 318 removed outlier: 3.803A pdb=" N HIS D 313 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N TRP D 315 " --> pdb=" O ILE D 378 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE D 378 " --> pdb=" O TRP D 315 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA D 388 " --> pdb=" O TRP D 379 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 412 through 416 removed outlier: 3.651A pdb=" N ALA D 413 " --> pdb=" O GLY D 328 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY D 328 " --> pdb=" O ALA D 413 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N TRP D 325 " --> pdb=" O TRP D 351 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL D 327 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N CYS D 348 " --> pdb=" O TRP D 360 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 32 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2190 1.29 - 1.42: 4030 1.42 - 1.55: 8036 1.55 - 1.69: 107 1.69 - 1.82: 103 Bond restraints: 14466 Sorted by residual: bond pdb=" C3' UTP Y 1 " pdb=" C4' UTP Y 1 " ideal model delta sigma weight residual 1.654 1.300 0.354 2.00e-02 2.50e+03 3.14e+02 bond pdb=" C2' UTP Y 1 " pdb=" C3' UTP Y 1 " ideal model delta sigma weight residual 1.301 1.619 -0.318 2.00e-02 2.50e+03 2.52e+02 bond pdb=" C4' UTP Y 1 " pdb=" O4' UTP Y 1 " ideal model delta sigma weight residual 1.320 1.575 -0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C1' UTP Y 1 " pdb=" C2' UTP Y 1 " ideal model delta sigma weight residual 1.585 1.343 0.242 2.00e-02 2.50e+03 1.46e+02 bond pdb=" C1' GTP X 1 " pdb=" C2' GTP X 1 " ideal model delta sigma weight residual 1.524 1.292 0.232 2.00e-02 2.50e+03 1.35e+02 ... (remaining 14461 not shown) Histogram of bond angle deviations from ideal: 100.74 - 107.38: 732 107.38 - 114.03: 8228 114.03 - 120.68: 5609 120.68 - 127.32: 4991 127.32 - 133.97: 223 Bond angle restraints: 19783 Sorted by residual: angle pdb=" C ASN D 394 " pdb=" N GLN D 395 " pdb=" CA GLN D 395 " ideal model delta sigma weight residual 121.54 128.92 -7.38 1.91e+00 2.74e-01 1.49e+01 angle pdb=" C GLU A 330 " pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 123.91 129.44 -5.53 1.66e+00 3.63e-01 1.11e+01 angle pdb=" C PHE A 853 " pdb=" N SER A 854 " pdb=" CA SER A 854 " ideal model delta sigma weight residual 121.54 127.61 -6.07 1.91e+00 2.74e-01 1.01e+01 angle pdb=" CA GLN D 395 " pdb=" CB GLN D 395 " pdb=" CG GLN D 395 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.64e+00 angle pdb=" C GLY A 659 " pdb=" N ILE A 660 " pdb=" CA ILE A 660 " ideal model delta sigma weight residual 120.77 125.21 -4.44 1.46e+00 4.69e-01 9.25e+00 ... (remaining 19778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.61: 8320 28.61 - 57.21: 368 57.21 - 85.82: 83 85.82 - 114.42: 9 114.42 - 143.03: 3 Dihedral angle restraints: 8783 sinusoidal: 4019 harmonic: 4764 Sorted by residual: dihedral pdb=" O3A GTP X 1 " pdb=" O3B GTP X 1 " pdb=" PB GTP X 1 " pdb=" PG GTP X 1 " ideal model delta sinusoidal sigma weight residual 303.79 160.76 143.03 1 2.00e+01 2.50e-03 4.32e+01 dihedral pdb=" O5' GTP X 1 " pdb=" O3A GTP X 1 " pdb=" PA GTP X 1 " pdb=" PB GTP X 1 " ideal model delta sinusoidal sigma weight residual 274.12 155.49 118.63 1 2.00e+01 2.50e-03 3.55e+01 dihedral pdb=" CA VAL B 392 " pdb=" C VAL B 392 " pdb=" N ASP B 393 " pdb=" CA ASP B 393 " ideal model delta harmonic sigma weight residual 180.00 150.25 29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8780 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1783 0.049 - 0.097: 326 0.097 - 0.146: 92 0.146 - 0.194: 18 0.194 - 0.243: 5 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CB ILE C 343 " pdb=" CA ILE C 343 " pdb=" CG1 ILE C 343 " pdb=" CG2 ILE C 343 " both_signs ideal model delta sigma weight residual False 2.64 2.89 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB ILE A 343 " pdb=" CA ILE A 343 " pdb=" CG1 ILE A 343 " pdb=" CG2 ILE A 343 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 345 " pdb=" CA ILE A 345 " pdb=" CG1 ILE A 345 " pdb=" CG2 ILE A 345 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2221 not shown) Planarity restraints: 2333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 261 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.89e+00 pdb=" C ILE A 261 " 0.038 2.00e-02 2.50e+03 pdb=" O ILE A 261 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE A 262 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 343 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ILE A 343 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE A 343 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE A 344 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 261 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ILE C 261 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE C 261 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 262 " 0.011 2.00e-02 2.50e+03 ... (remaining 2330 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1502 2.75 - 3.29: 12291 3.29 - 3.83: 22982 3.83 - 4.36: 27003 4.36 - 4.90: 44613 Nonbonded interactions: 108391 Sorted by model distance: nonbonded pdb=" O ASP C 469 " pdb=" OD1 ASP C 469 " model vdw 2.218 3.040 nonbonded pdb=" O SER D 407 " pdb=" OG SER D 407 " model vdw 2.322 2.440 nonbonded pdb=" O SER D 278 " pdb=" OG SER D 278 " model vdw 2.326 2.440 nonbonded pdb=" O SER B 278 " pdb=" OG SER B 278 " model vdw 2.330 2.440 nonbonded pdb=" OG SER D 335 " pdb=" OD1 ASP D 337 " model vdw 2.340 2.440 ... (remaining 108386 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 241 through 658 or resid 691 through 699 or resid 710 thro \ ugh 718 or resid 736 through 793 or resid 800 through 921 or resid 1001)) selection = chain 'C' } ncs_group { reference = (chain 'B' and (resid 252 through 382 or (resid 383 through 384 and (name N or n \ ame CA or name C or name O or name CB )) or resid 385 through 430)) selection = (chain 'D' and (resid 252 through 394 or (resid 395 through 399 and (name N or n \ ame CA or name C or name O or name CB )) or resid 400 through 430)) } 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.670 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 45.360 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 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 0.354 14466 Z= 0.473 Angle : 0.585 8.878 19783 Z= 0.320 Chirality : 0.045 0.243 2224 Planarity : 0.004 0.048 2333 Dihedral : 16.310 143.030 5675 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.29 % Allowed : 12.76 % Favored : 84.95 % 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: -5.23 (0.15), residues: 1593 helix: -4.62 (0.06), residues: 536 sheet: -2.31 (0.33), residues: 250 loop : -2.99 (0.17), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP D 379 HIS 0.002 0.000 HIS D 324 PHE 0.014 0.001 PHE C 853 TYR 0.011 0.001 TYR C 879 ARG 0.002 0.000 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 272 time to evaluate : 1.733 Fit side-chains REVERT: A 272 PHE cc_start: 0.8137 (t80) cc_final: 0.7779 (t80) REVERT: A 405 VAL cc_start: 0.8804 (t) cc_final: 0.8567 (t) REVERT: A 579 PHE cc_start: 0.8481 (OUTLIER) cc_final: 0.7644 (m-10) REVERT: B 348 CYS cc_start: 0.5952 (p) cc_final: 0.5745 (p) REVERT: B 402 CYS cc_start: 0.1746 (t) cc_final: 0.1270 (t) REVERT: C 579 PHE cc_start: 0.5205 (m-80) cc_final: 0.4612 (m-80) outliers start: 33 outliers final: 21 residues processed: 297 average time/residue: 0.2827 time to fit residues: 120.4509 Evaluate side-chains 196 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 706 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 747 VAL Chi-restraints excluded: chain A residue 785 THR Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 515 THR Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 884 ILE Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 83 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 49 optimal weight: 0.0970 chunk 77 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 393 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 595 GLN A 726 GLN A 762 ASN A 782 HIS A 805 ASN A 830 HIS B 256 GLN ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN C 299 GLN C 305 GLN C 317 HIS C 354 ASN C 380 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 517 GLN C 606 ASN C 691 HIS C 710 ASN C 769 GLN C 786 HIS D 313 HIS D 321 ASN D 356 GLN D 429 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14466 Z= 0.249 Angle : 0.537 8.708 19783 Z= 0.273 Chirality : 0.041 0.251 2224 Planarity : 0.004 0.046 2333 Dihedral : 12.967 100.602 2496 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.47 % Allowed : 16.09 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.18), residues: 1593 helix: -1.90 (0.18), residues: 538 sheet: -2.17 (0.35), residues: 220 loop : -2.59 (0.18), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.009 0.001 HIS A 782 PHE 0.014 0.001 PHE A 388 TYR 0.014 0.001 TYR C 383 ARG 0.005 0.001 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 169 time to evaluate : 1.628 Fit side-chains REVERT: A 579 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: B 348 CYS cc_start: 0.6413 (p) cc_final: 0.6203 (p) REVERT: C 579 PHE cc_start: 0.5367 (m-80) cc_final: 0.4662 (m-10) REVERT: C 622 TYR cc_start: 0.7062 (m-80) cc_final: 0.6656 (m-10) outliers start: 50 outliers final: 39 residues processed: 204 average time/residue: 0.2486 time to fit residues: 76.0953 Evaluate side-chains 189 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 317 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 629 ILE Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 691 HIS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 274 VAL Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 321 ASN Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 123 optimal weight: 0.5980 chunk 100 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 148 optimal weight: 7.9990 chunk 160 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 HIS B 313 HIS ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14466 Z= 0.125 Angle : 0.446 10.607 19783 Z= 0.226 Chirality : 0.038 0.150 2224 Planarity : 0.003 0.041 2333 Dihedral : 12.646 97.716 2479 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.47 % Allowed : 16.85 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1593 helix: -0.44 (0.21), residues: 539 sheet: -1.92 (0.35), residues: 220 loop : -2.34 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 351 HIS 0.008 0.001 HIS A 782 PHE 0.009 0.001 PHE A 471 TYR 0.011 0.001 TYR B 400 ARG 0.006 0.000 ARG A 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 156 time to evaluate : 1.555 Fit side-chains REVERT: A 579 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.8168 (m-80) REVERT: A 811 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8562 (ttt180) REVERT: B 348 CYS cc_start: 0.6300 (p) cc_final: 0.6075 (p) REVERT: C 579 PHE cc_start: 0.5444 (m-80) cc_final: 0.4738 (m-10) REVERT: C 595 GLN cc_start: 0.8375 (pm20) cc_final: 0.8113 (pm20) REVERT: C 622 TYR cc_start: 0.6978 (m-80) cc_final: 0.6659 (m-10) REVERT: C 623 HIS cc_start: 0.6880 (t70) cc_final: 0.6655 (t-170) REVERT: D 324 HIS cc_start: 0.8008 (m90) cc_final: 0.7806 (m90) outliers start: 50 outliers final: 33 residues processed: 192 average time/residue: 0.2448 time to fit residues: 70.8845 Evaluate side-chains 184 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 149 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 3.9990 chunk 70 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 157 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 141 optimal weight: 0.2980 chunk 42 optimal weight: 0.1980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 710 ASN ** D 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14466 Z= 0.132 Angle : 0.441 11.616 19783 Z= 0.223 Chirality : 0.039 0.147 2224 Planarity : 0.003 0.038 2333 Dihedral : 12.497 97.449 2479 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.74 % Allowed : 16.71 % Favored : 79.54 % 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: -1.76 (0.21), residues: 1593 helix: 0.38 (0.23), residues: 540 sheet: -1.70 (0.36), residues: 226 loop : -2.12 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 351 HIS 0.006 0.001 HIS C 786 PHE 0.010 0.001 PHE A 471 TYR 0.023 0.001 TYR D 424 ARG 0.004 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 163 time to evaluate : 1.789 Fit side-chains REVERT: A 470 LYS cc_start: 0.8243 (mmmt) cc_final: 0.8020 (mmmm) REVERT: A 923 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6429 (ppp) REVERT: B 308 LEU cc_start: 0.1628 (OUTLIER) cc_final: 0.1371 (pp) REVERT: B 348 CYS cc_start: 0.6188 (p) cc_final: 0.5942 (p) REVERT: C 595 GLN cc_start: 0.8378 (pm20) cc_final: 0.8084 (pm20) REVERT: C 622 TYR cc_start: 0.6922 (m-80) cc_final: 0.6523 (m-10) REVERT: C 789 PHE cc_start: 0.7783 (t80) cc_final: 0.7479 (t80) outliers start: 54 outliers final: 39 residues processed: 200 average time/residue: 0.2406 time to fit residues: 72.9103 Evaluate side-chains 190 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 149 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 7.9990 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 117 optimal weight: 0.2980 chunk 65 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 317 HIS A 375 HIS A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 769 GLN A 782 HIS A 876 HIS B 321 ASN C 280 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS C 786 HIS D 256 GLN D 285 HIS D 288 GLN D 321 ASN D 394 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14466 Z= 0.356 Angle : 0.585 10.568 19783 Z= 0.295 Chirality : 0.043 0.215 2224 Planarity : 0.004 0.042 2333 Dihedral : 12.760 105.059 2478 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 4.51 % Allowed : 17.41 % Favored : 78.09 % 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: -1.65 (0.21), residues: 1593 helix: 0.36 (0.23), residues: 548 sheet: -1.79 (0.32), residues: 276 loop : -1.92 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 351 HIS 0.009 0.001 HIS C 280 PHE 0.015 0.002 PHE A 776 TYR 0.013 0.002 TYR A 566 ARG 0.006 0.001 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 139 time to evaluate : 1.566 Fit side-chains REVERT: A 255 MET cc_start: 0.8308 (mtt) cc_final: 0.7953 (mtt) REVERT: A 470 LYS cc_start: 0.8280 (mmmt) cc_final: 0.8066 (mmmm) REVERT: A 811 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8683 (ttt180) REVERT: A 923 MET cc_start: 0.7365 (OUTLIER) cc_final: 0.6555 (ppp) REVERT: B 308 LEU cc_start: 0.2284 (OUTLIER) cc_final: 0.1990 (pp) REVERT: B 371 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7357 (p0) REVERT: C 622 TYR cc_start: 0.7147 (m-80) cc_final: 0.6704 (m-10) outliers start: 65 outliers final: 47 residues processed: 189 average time/residue: 0.2628 time to fit residues: 73.8496 Evaluate side-chains 179 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 128 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 262 THR Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 587 THR Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 691 HIS Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 92 optimal weight: 0.0470 chunk 38 optimal weight: 5.9990 chunk 157 optimal weight: 10.0000 chunk 130 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.0670 chunk 82 optimal weight: 8.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 457 GLN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 782 HIS ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14466 Z= 0.120 Angle : 0.455 9.323 19783 Z= 0.231 Chirality : 0.039 0.129 2224 Planarity : 0.003 0.035 2333 Dihedral : 12.562 92.880 2476 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.05 % Allowed : 19.69 % Favored : 77.25 % 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: -1.28 (0.22), residues: 1593 helix: 0.87 (0.23), residues: 546 sheet: -1.64 (0.32), residues: 263 loop : -1.85 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 351 HIS 0.008 0.001 HIS A 782 PHE 0.008 0.001 PHE A 471 TYR 0.010 0.001 TYR D 390 ARG 0.006 0.000 ARG B 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 144 time to evaluate : 1.781 Fit side-chains REVERT: A 255 MET cc_start: 0.8253 (mtt) cc_final: 0.7864 (mtt) REVERT: A 811 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8679 (ttt180) REVERT: A 890 GLU cc_start: 0.7586 (tt0) cc_final: 0.7334 (tt0) REVERT: A 923 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6445 (ppp) REVERT: B 308 LEU cc_start: 0.2224 (OUTLIER) cc_final: 0.1916 (pp) REVERT: B 352 LYS cc_start: 0.8068 (ptpt) cc_final: 0.7798 (ptpt) REVERT: B 371 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7332 (p0) REVERT: C 622 TYR cc_start: 0.7036 (m-80) cc_final: 0.6571 (m-10) outliers start: 44 outliers final: 34 residues processed: 174 average time/residue: 0.2472 time to fit residues: 64.9406 Evaluate side-chains 179 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 647 ILE Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 9.9990 chunk 17 optimal weight: 0.0060 chunk 89 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 98 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14466 Z= 0.233 Angle : 0.494 9.215 19783 Z= 0.249 Chirality : 0.040 0.196 2224 Planarity : 0.003 0.039 2333 Dihedral : 12.587 101.998 2474 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.88 % Allowed : 19.00 % 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: -1.22 (0.22), residues: 1593 helix: 0.95 (0.23), residues: 550 sheet: -1.67 (0.32), residues: 272 loop : -1.82 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 351 HIS 0.004 0.001 HIS A 381 PHE 0.008 0.001 PHE A 776 TYR 0.011 0.001 TYR C 715 ARG 0.005 0.000 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 134 time to evaluate : 1.591 Fit side-chains REVERT: A 811 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8600 (ttt180) REVERT: A 890 GLU cc_start: 0.7710 (tt0) cc_final: 0.7418 (tt0) REVERT: A 923 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6401 (ppp) REVERT: B 308 LEU cc_start: 0.2392 (OUTLIER) cc_final: 0.2090 (pp) REVERT: B 334 MET cc_start: 0.6305 (tpt) cc_final: 0.6063 (tpp) REVERT: B 371 ASP cc_start: 0.7421 (OUTLIER) cc_final: 0.7117 (p0) REVERT: C 622 TYR cc_start: 0.7158 (m-80) cc_final: 0.6686 (m-10) outliers start: 56 outliers final: 43 residues processed: 178 average time/residue: 0.2374 time to fit residues: 64.2743 Evaluate side-chains 174 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 150 optimal weight: 30.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 HIS A 794 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 524 GLN C 557 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14466 Z= 0.227 Angle : 0.492 8.789 19783 Z= 0.249 Chirality : 0.040 0.179 2224 Planarity : 0.004 0.077 2333 Dihedral : 12.586 99.134 2474 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.54 % Allowed : 19.63 % 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: -1.18 (0.22), residues: 1593 helix: 0.97 (0.23), residues: 553 sheet: -1.70 (0.32), residues: 274 loop : -1.75 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 351 HIS 0.005 0.001 HIS A 381 PHE 0.023 0.001 PHE D 389 TYR 0.011 0.001 TYR C 715 ARG 0.004 0.000 ARG C 811 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 129 time to evaluate : 1.590 Fit side-chains REVERT: A 255 MET cc_start: 0.8267 (mtt) cc_final: 0.7858 (mtt) REVERT: A 811 ARG cc_start: 0.9125 (OUTLIER) cc_final: 0.8768 (ttt180) REVERT: A 923 MET cc_start: 0.7274 (OUTLIER) cc_final: 0.6392 (ppp) REVERT: B 308 LEU cc_start: 0.2669 (OUTLIER) cc_final: 0.2369 (pp) REVERT: B 371 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7098 (p0) REVERT: C 256 LYS cc_start: 0.8339 (mmtt) cc_final: 0.8132 (mmtm) REVERT: C 622 TYR cc_start: 0.7122 (m-80) cc_final: 0.6552 (m-10) outliers start: 51 outliers final: 42 residues processed: 169 average time/residue: 0.2361 time to fit residues: 61.4874 Evaluate side-chains 172 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 811 ARG Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 344 ILE Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 562 ASP Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 132 optimal weight: 0.0870 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN B 260 HIS C 298 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14466 Z= 0.121 Angle : 0.466 14.921 19783 Z= 0.232 Chirality : 0.039 0.126 2224 Planarity : 0.003 0.065 2333 Dihedral : 12.515 94.066 2474 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.12 % Allowed : 20.32 % Favored : 76.56 % 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: -0.96 (0.22), residues: 1593 helix: 1.21 (0.24), residues: 548 sheet: -1.48 (0.33), residues: 264 loop : -1.72 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 351 HIS 0.015 0.001 HIS C 557 PHE 0.010 0.001 PHE C 504 TYR 0.014 0.001 TYR C 509 ARG 0.003 0.000 ARG A 859 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 138 time to evaluate : 1.636 Fit side-chains REVERT: A 763 ASP cc_start: 0.7951 (m-30) cc_final: 0.7726 (m-30) REVERT: A 923 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6322 (ppp) REVERT: B 308 LEU cc_start: 0.2585 (OUTLIER) cc_final: 0.2300 (pp) REVERT: B 371 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7069 (p0) REVERT: C 622 TYR cc_start: 0.7102 (m-80) cc_final: 0.6564 (m-10) outliers start: 45 outliers final: 35 residues processed: 172 average time/residue: 0.2350 time to fit residues: 62.2489 Evaluate side-chains 171 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 133 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 760 MET Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 260 HIS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 20.0000 chunk 94 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 149 optimal weight: 30.0000 chunk 129 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN ** B 260 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14466 Z= 0.185 Angle : 0.487 13.722 19783 Z= 0.243 Chirality : 0.039 0.168 2224 Planarity : 0.003 0.064 2333 Dihedral : 12.507 97.923 2474 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.33 % Allowed : 20.11 % Favored : 76.56 % 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: -0.95 (0.22), residues: 1593 helix: 1.24 (0.23), residues: 551 sheet: -1.57 (0.32), residues: 274 loop : -1.69 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 351 HIS 0.004 0.001 HIS A 623 PHE 0.023 0.001 PHE D 389 TYR 0.015 0.001 TYR C 548 ARG 0.003 0.000 ARG D 320 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 134 time to evaluate : 1.418 Fit side-chains REVERT: A 923 MET cc_start: 0.7173 (OUTLIER) cc_final: 0.6302 (ppp) REVERT: B 308 LEU cc_start: 0.2634 (OUTLIER) cc_final: 0.2342 (pp) REVERT: B 334 MET cc_start: 0.6777 (tpt) cc_final: 0.6339 (tpp) REVERT: B 371 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6962 (p0) REVERT: C 622 TYR cc_start: 0.7116 (m-80) cc_final: 0.6639 (m-10) outliers start: 48 outliers final: 39 residues processed: 169 average time/residue: 0.2298 time to fit residues: 60.2902 Evaluate side-chains 173 residues out of total 1463 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 131 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 THR Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 PHE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 630 THR Chi-restraints excluded: chain A residue 725 ILE Chi-restraints excluded: chain A residue 751 GLU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 882 PHE Chi-restraints excluded: chain A residue 903 THR Chi-restraints excluded: chain A residue 923 MET Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 281 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 371 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 392 VAL Chi-restraints excluded: chain C residue 259 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 359 THR Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 441 THR Chi-restraints excluded: chain C residue 454 TYR Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 513 ILE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 557 HIS Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 641 ASP Chi-restraints excluded: chain C residue 711 LEU Chi-restraints excluded: chain C residue 852 GLN Chi-restraints excluded: chain C residue 903 THR Chi-restraints excluded: chain D residue 371 ASP Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 54 optimal weight: 0.0370 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 794 GLN C 298 ASN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.108665 restraints weight = 22340.400| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.65 r_work: 0.3111 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14466 Z= 0.135 Angle : 0.469 12.837 19783 Z= 0.235 Chirality : 0.039 0.139 2224 Planarity : 0.003 0.061 2333 Dihedral : 12.429 94.851 2472 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 3.05 % Allowed : 20.53 % Favored : 76.42 % 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: -0.89 (0.22), residues: 1593 helix: 1.32 (0.24), residues: 545 sheet: -1.37 (0.33), residues: 264 loop : -1.73 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 351 HIS 0.006 0.001 HIS B 260 PHE 0.019 0.001 PHE C 504 TYR 0.020 0.001 TYR C 548 ARG 0.004 0.000 ARG C 559 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3372.05 seconds wall clock time: 61 minutes 23.09 seconds (3683.09 seconds total)