Starting phenix.real_space_refine on Fri Feb 16 00:17:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d99_30617/02_2024/7d99_30617.pdb" } resolution = 2.9 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= 0.006 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 K 2 8.98 5 S 104 5.16 5 Cl 4 4.86 5 C 8904 2.51 5 N 2314 2.21 5 O 2472 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 674": "NH1" <-> "NH2" Residue "A ARG 744": "NH1" <-> "NH2" Residue "A ARG 816": "NH1" <-> "NH2" Residue "A ARG 866": "NH1" <-> "NH2" Residue "A ARG 872": "NH1" <-> "NH2" Residue "A ARG 1076": "NH1" <-> "NH2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 405": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 528": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 608": "NH1" <-> "NH2" Residue "B ARG 610": "NH1" <-> "NH2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 674": "NH1" <-> "NH2" Residue "B ARG 744": "NH1" <-> "NH2" Residue "B ARG 816": "NH1" <-> "NH2" Residue "B ARG 866": "NH1" <-> "NH2" Residue "B ARG 872": "NH1" <-> "NH2" Residue "B ARG 1076": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13800 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6841 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 34, 'TRANS': 856} Chain breaks: 2 Chain: "B" Number of atoms: 6841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 891, 6841 Classifications: {'peptide': 891} Link IDs: {'PTRANS': 34, 'TRANS': 856} Chain breaks: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 1, ' CL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 7.34, per 1000 atoms: 0.53 Number of scatterers: 13800 At special positions: 0 Unit cell: (112.554, 128.778, 149.058, 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) K 2 19.00 Cl 4 17.00 S 104 16.00 O 2472 8.00 N 2314 7.00 C 8904 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 352 " 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=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 360 " " NAG E 1 " - " ASN B 312 " " NAG F 1 " - " ASN B 360 " Time building additional restraints: 5.34 Conformation dependent library (CDL) restraints added in 2.6 seconds 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 6 sheets defined 60.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 85 through 90 removed outlier: 3.862A pdb=" N LEU A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 3.744A pdb=" N GLU A 104 " --> pdb=" O VAL A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 164 removed outlier: 6.563A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 162 " --> pdb=" O ALA A 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 177 removed outlier: 3.613A pdb=" N SER A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 191 removed outlier: 3.580A pdb=" N ARG A 191 " --> pdb=" O TYR A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 228 removed outlier: 4.277A pdb=" N PHE A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 224 " --> pdb=" O THR A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 242 through 269 removed outlier: 3.602A pdb=" N MET A 247 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.637A pdb=" N LYS A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 301 removed outlier: 3.603A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 287 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 removed outlier: 3.705A pdb=" N GLY A 340 " --> pdb=" O SER A 336 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 359 removed outlier: 3.534A pdb=" N ILE A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 353 through 359' Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.717A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 433 through 439 removed outlier: 3.541A pdb=" N ALA A 436 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 439 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 475 Proline residue: A 452 - end of helix removed outlier: 3.556A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 465 " --> pdb=" O THR A 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 3.866A pdb=" N GLY A 487 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 484 through 488' Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.642A pdb=" N LEU A 499 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 500 " --> pdb=" O ILE A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 525 removed outlier: 3.556A pdb=" N THR A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 537 removed outlier: 3.550A pdb=" N LEU A 529 " --> pdb=" O GLY A 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.706A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 removed outlier: 3.556A pdb=" N VAL A 577 " --> pdb=" O SER A 573 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) Proline residue: A 579 - end of helix removed outlier: 3.780A pdb=" N PHE A 584 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.648A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 622 " --> pdb=" O LEU A 618 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 659 Processing helix chain 'A' and resid 663 through 681 removed outlier: 3.795A pdb=" N SER A 669 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG A 679 " --> pdb=" O TYR A 675 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 681 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 719 removed outlier: 3.853A pdb=" N SER A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 717 " --> pdb=" O SER A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 756 removed outlier: 3.605A pdb=" N GLU A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 755 " --> pdb=" O SER A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 781 removed outlier: 3.691A pdb=" N MET A 774 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 779 " --> pdb=" O SER A 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA A 781 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.994A pdb=" N SER A 807 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 812 " --> pdb=" O TRP A 808 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 815 " --> pdb=" O PHE A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.563A pdb=" N PHE A 834 " --> pdb=" O VAL A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 866 removed outlier: 3.784A pdb=" N LEU A 858 " --> pdb=" O ASP A 854 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 860 " --> pdb=" O GLY A 856 " (cutoff:3.500A) Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 887 through 896 Processing helix chain 'A' and resid 896 through 902 removed outlier: 3.659A pdb=" N TYR A 900 " --> pdb=" O GLN A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1031 removed outlier: 3.661A pdb=" N THR A1019 " --> pdb=" O ARG A1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1029 " --> pdb=" O GLY A1025 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A1030 " --> pdb=" O VAL A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1062 Processing helix chain 'B' and resid 85 through 90 removed outlier: 3.862A pdb=" N LEU B 89 " --> pdb=" O LEU B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 3.744A pdb=" N GLU B 104 " --> pdb=" O VAL B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 164 removed outlier: 6.563A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N LEU B 151 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 177 removed outlier: 3.613A pdb=" N SER B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 191 removed outlier: 3.580A pdb=" N ARG B 191 " --> pdb=" O TYR B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 228 removed outlier: 4.277A pdb=" N PHE B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE B 224 " --> pdb=" O THR B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 242 through 269 removed outlier: 3.602A pdb=" N MET B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N HIS B 249 " --> pdb=" O ALA B 245 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 removed outlier: 3.637A pdb=" N LYS B 275 " --> pdb=" O LYS B 271 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 301 removed outlier: 3.603A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER B 287 " --> pdb=" O CYS B 283 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.705A pdb=" N GLY B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 359 removed outlier: 3.534A pdb=" N ILE B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 353 through 359' Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.717A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 433 through 439 removed outlier: 3.541A pdb=" N ALA B 436 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN B 439 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 475 Proline residue: B 452 - end of helix removed outlier: 3.556A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 3.866A pdb=" N GLY B 487 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 484 through 488' Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.642A pdb=" N LEU B 499 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA B 500 " --> pdb=" O ILE B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 525 removed outlier: 3.556A pdb=" N THR B 515 " --> pdb=" O SER B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 537 removed outlier: 3.550A pdb=" N LEU B 529 " --> pdb=" O GLY B 525 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.706A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 removed outlier: 3.556A pdb=" N VAL B 577 " --> pdb=" O SER B 573 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) Proline residue: B 579 - end of helix removed outlier: 3.780A pdb=" N PHE B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE B 585 " --> pdb=" O LEU B 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.648A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY B 622 " --> pdb=" O LEU B 618 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 659 Processing helix chain 'B' and resid 663 through 681 removed outlier: 3.795A pdb=" N SER B 669 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG B 679 " --> pdb=" O TYR B 675 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N VAL B 680 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU B 681 " --> pdb=" O LEU B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 719 removed outlier: 3.853A pdb=" N SER B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN B 717 " --> pdb=" O SER B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 756 removed outlier: 3.605A pdb=" N GLU B 747 " --> pdb=" O GLN B 743 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 755 " --> pdb=" O SER B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 781 removed outlier: 3.691A pdb=" N MET B 774 " --> pdb=" O LEU B 770 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN B 779 " --> pdb=" O SER B 775 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA B 781 " --> pdb=" O LEU B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 821 removed outlier: 3.994A pdb=" N SER B 807 " --> pdb=" O ASP B 803 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 812 " --> pdb=" O TRP B 808 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 815 " --> pdb=" O PHE B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.563A pdb=" N PHE B 834 " --> pdb=" O VAL B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 866 removed outlier: 3.784A pdb=" N LEU B 858 " --> pdb=" O ASP B 854 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 860 " --> pdb=" O GLY B 856 " (cutoff:3.500A) Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 887 through 896 Processing helix chain 'B' and resid 896 through 902 removed outlier: 3.659A pdb=" N TYR B 900 " --> pdb=" O GLN B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 1012 through 1031 removed outlier: 3.661A pdb=" N THR B1019 " --> pdb=" O ARG B1015 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1029 " --> pdb=" O GLY B1025 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS B1030 " --> pdb=" O VAL B1026 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1062 Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 removed outlier: 3.792A pdb=" N ARG A 313 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 4.298A pdb=" N VAL A 730 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA A 794 " --> pdb=" O MET A 697 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A1068 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL A1037 " --> pdb=" O LEU A1069 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL A1071 " --> pdb=" O VAL A1037 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU A1039 " --> pdb=" O VAL A1071 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS A 845 " --> pdb=" O LEU A1036 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU A1038 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP A 847 " --> pdb=" O LEU A1038 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN A1040 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TRP A 849 " --> pdb=" O ASN A1040 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 313 through 314 removed outlier: 3.792A pdb=" N ARG B 313 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA6, first strand: chain 'B' and resid 761 through 767 removed outlier: 4.298A pdb=" N VAL B 730 " --> pdb=" O LEU B 698 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ALA B 794 " --> pdb=" O MET B 697 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL B1068 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N VAL B1037 " --> pdb=" O LEU B1069 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N VAL B1071 " --> pdb=" O VAL B1037 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N LEU B1039 " --> pdb=" O VAL B1071 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N HIS B 845 " --> pdb=" O LEU B1036 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N LEU B1038 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP B 847 " --> pdb=" O LEU B1038 " (cutoff:3.500A) removed outlier: 8.629A pdb=" N ASN B1040 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N TRP B 849 " --> pdb=" O ASN B1040 " (cutoff:3.500A) 678 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.22 Time building geometry restraints manager: 5.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4368 1.34 - 1.47: 3474 1.47 - 1.60: 6092 1.60 - 1.72: 0 1.72 - 1.85: 164 Bond restraints: 14098 Sorted by residual: bond pdb=" C PHE B 428 " pdb=" N PRO B 429 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.59e+01 bond pdb=" C PHE A 428 " pdb=" N PRO A 429 " ideal model delta sigma weight residual 1.337 1.376 -0.039 9.80e-03 1.04e+04 1.59e+01 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.03e+01 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 97.79 - 105.05: 276 105.05 - 112.31: 7208 112.31 - 119.58: 4542 119.58 - 126.84: 6922 126.84 - 134.11: 196 Bond angle restraints: 19144 Sorted by residual: angle pdb=" N GLY A 664 " pdb=" CA GLY A 664 " pdb=" C GLY A 664 " ideal model delta sigma weight residual 112.73 121.09 -8.36 1.20e+00 6.94e-01 4.85e+01 angle pdb=" N GLY B 664 " pdb=" CA GLY B 664 " pdb=" C GLY B 664 " ideal model delta sigma weight residual 112.73 121.09 -8.36 1.20e+00 6.94e-01 4.85e+01 angle pdb=" N GLU B 391 " pdb=" CA GLU B 391 " pdb=" C GLU B 391 " ideal model delta sigma weight residual 110.42 118.81 -8.39 1.55e+00 4.16e-01 2.93e+01 angle pdb=" N GLU A 391 " pdb=" CA GLU A 391 " pdb=" C GLU A 391 " ideal model delta sigma weight residual 110.42 118.81 -8.39 1.55e+00 4.16e-01 2.93e+01 angle pdb=" N GLY B 784 " pdb=" CA GLY B 784 " pdb=" C GLY B 784 " ideal model delta sigma weight residual 111.02 120.72 -9.70 1.86e+00 2.89e-01 2.72e+01 ... (remaining 19139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.35: 7892 14.35 - 28.70: 382 28.70 - 43.05: 112 43.05 - 57.41: 16 57.41 - 71.76: 6 Dihedral angle restraints: 8408 sinusoidal: 3326 harmonic: 5082 Sorted by residual: dihedral pdb=" CB CYS B 308 " pdb=" SG CYS B 308 " pdb=" SG CYS B 323 " pdb=" CB CYS B 323 " ideal model delta sinusoidal sigma weight residual -86.00 -148.72 62.72 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CB CYS A 308 " pdb=" SG CYS A 308 " pdb=" SG CYS A 323 " pdb=" CB CYS A 323 " ideal model delta sinusoidal sigma weight residual -86.00 -148.72 62.72 1 1.00e+01 1.00e-02 5.20e+01 dihedral pdb=" CA GLU A 703 " pdb=" C GLU A 703 " pdb=" N GLN A 704 " pdb=" CA GLN A 704 " ideal model delta harmonic sigma weight residual 180.00 -150.88 -29.12 0 5.00e+00 4.00e-02 3.39e+01 ... (remaining 8405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1586 0.053 - 0.106: 488 0.106 - 0.159: 130 0.159 - 0.212: 20 0.212 - 0.265: 12 Chirality restraints: 2236 Sorted by residual: chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C4 NAG F 1 " pdb=" C3 NAG F 1 " pdb=" C5 NAG F 1 " pdb=" O4 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2233 not shown) Planarity restraints: 2396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 539 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 540 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 540 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 540 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 539 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO B 540 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 540 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 540 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 804 " -0.044 5.00e-02 4.00e+02 6.56e-02 6.88e+00 pdb=" N PRO B 805 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO B 805 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 805 " -0.037 5.00e-02 4.00e+02 ... (remaining 2393 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.78: 3328 2.78 - 3.37: 13748 3.37 - 3.96: 24558 3.96 - 4.55: 34575 4.55 - 5.14: 52811 Nonbonded interactions: 129020 Sorted by model distance: nonbonded pdb=" O ASN A 331 " pdb=" OD1 ASN A 332 " model vdw 2.187 3.040 nonbonded pdb=" O ASN B 331 " pdb=" OD1 ASN B 332 " model vdw 2.187 3.040 nonbonded pdb=" OE1 GLU A 152 " pdb=" OH TYR A 383 " model vdw 2.277 2.440 nonbonded pdb=" OE1 GLU B 152 " pdb=" OH TYR B 383 " model vdw 2.277 2.440 nonbonded pdb=" OG SER B 713 " pdb=" OE1 GLU B 756 " model vdw 2.293 2.440 ... (remaining 129015 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.780 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 38.060 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.009 0.080 14098 Z= 0.581 Angle : 1.095 10.265 19144 Z= 0.619 Chirality : 0.057 0.265 2236 Planarity : 0.007 0.069 2392 Dihedral : 9.923 71.758 5138 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.75 % Favored : 95.14 % Rotamer: Outliers : 0.41 % Allowed : 2.18 % Favored : 97.41 % 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: -5.36 (0.14), residues: 1770 helix: -4.44 (0.07), residues: 896 sheet: -0.41 (0.42), residues: 140 loop : -2.80 (0.18), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 339 HIS 0.012 0.002 HIS A 853 PHE 0.038 0.004 PHE B 761 TYR 0.021 0.003 TYR A 466 ARG 0.012 0.001 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 309 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 435 MET cc_start: 0.8055 (mmt) cc_final: 0.7683 (mmt) REVERT: B 435 MET cc_start: 0.8054 (mmt) cc_final: 0.7699 (mmt) outliers start: 6 outliers final: 2 residues processed: 311 average time/residue: 1.3945 time to fit residues: 470.6553 Evaluate side-chains 161 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 250 ASN A 330 HIS A 359 ASN A 547 HIS A 615 HIS ** A 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A 868 HIS A1024 ASN B 236 GLN B 250 ASN B 330 HIS B 359 ASN B 547 HIS B 615 HIS ** B 776 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B 868 HIS B1024 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14098 Z= 0.260 Angle : 0.700 12.272 19144 Z= 0.352 Chirality : 0.045 0.215 2236 Planarity : 0.006 0.054 2392 Dihedral : 6.697 57.840 2076 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.86 % Allowed : 12.21 % Favored : 84.92 % 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: -2.87 (0.17), residues: 1770 helix: -1.88 (0.13), residues: 952 sheet: 0.29 (0.46), residues: 130 loop : -2.21 (0.20), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 661 HIS 0.010 0.002 HIS A1018 PHE 0.022 0.002 PHE B 761 TYR 0.013 0.002 TYR B 427 ARG 0.006 0.001 ARG B 877 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 1.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 691 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7209 (tpp80) REVERT: A 747 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: A 774 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7105 (mpp) REVERT: B 583 MET cc_start: 0.8296 (tpp) cc_final: 0.8094 (mmt) REVERT: B 691 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7193 (tpp80) REVERT: B 747 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7230 (mp0) REVERT: B 774 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7098 (mpp) outliers start: 42 outliers final: 10 residues processed: 198 average time/residue: 1.3327 time to fit residues: 288.2843 Evaluate side-chains 165 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 363 GLU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 1018 HIS Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 774 MET Chi-restraints excluded: chain B residue 838 GLN Chi-restraints excluded: chain B residue 1018 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 0.9980 chunk 174 optimal weight: 0.0000 chunk 144 optimal weight: 0.8980 chunk 160 optimal weight: 0.0870 chunk 55 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 overall best weight: 0.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 599 GLN A 776 HIS B 94 ASN B 599 GLN B 776 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14098 Z= 0.148 Angle : 0.574 12.734 19144 Z= 0.282 Chirality : 0.042 0.191 2236 Planarity : 0.004 0.055 2392 Dihedral : 5.610 51.253 2072 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.86 % Allowed : 13.64 % Favored : 83.49 % 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: -1.23 (0.19), residues: 1770 helix: -0.20 (0.16), residues: 958 sheet: 0.52 (0.46), residues: 130 loop : -1.92 (0.22), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 661 HIS 0.008 0.001 HIS A1018 PHE 0.011 0.001 PHE B 541 TYR 0.008 0.001 TYR B 427 ARG 0.003 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 182 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (pp) REVERT: A 747 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7353 (mp0) REVERT: A 783 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8107 (pp) REVERT: A 813 ASP cc_start: 0.7716 (OUTLIER) cc_final: 0.7466 (m-30) REVERT: A 1017 MET cc_start: 0.7945 (mpp) cc_final: 0.7714 (tpp) REVERT: B 315 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 747 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7359 (mp0) REVERT: B 783 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8087 (pp) REVERT: B 1017 MET cc_start: 0.7969 (mpp) cc_final: 0.7747 (tpp) REVERT: B 1060 VAL cc_start: 0.8788 (t) cc_final: 0.8507 (t) outliers start: 42 outliers final: 8 residues processed: 201 average time/residue: 1.1818 time to fit residues: 262.3846 Evaluate side-chains 175 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 160 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 154 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14098 Z= 0.282 Angle : 0.631 16.509 19144 Z= 0.307 Chirality : 0.044 0.190 2236 Planarity : 0.004 0.059 2392 Dihedral : 5.293 45.440 2072 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.62 % Allowed : 13.85 % Favored : 82.54 % 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: -0.80 (0.19), residues: 1770 helix: 0.28 (0.17), residues: 936 sheet: 0.59 (0.46), residues: 130 loop : -1.86 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 380 HIS 0.010 0.001 HIS B1018 PHE 0.021 0.002 PHE B 761 TYR 0.012 0.001 TYR B 636 ARG 0.004 0.000 ARG B 872 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 168 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8393 (pp) REVERT: A 691 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7147 (tpp80) REVERT: A 747 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7559 (mp0) REVERT: A 783 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8550 (pp) REVERT: A 1060 VAL cc_start: 0.8828 (t) cc_final: 0.8560 (t) REVERT: B 315 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8415 (pp) REVERT: B 691 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7134 (tpp80) REVERT: B 747 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: B 783 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8520 (pp) REVERT: B 1016 ARG cc_start: 0.6402 (mtt180) cc_final: 0.6158 (mtt180) REVERT: B 1060 VAL cc_start: 0.8808 (t) cc_final: 0.8542 (t) outliers start: 53 outliers final: 19 residues processed: 209 average time/residue: 1.2108 time to fit residues: 278.0327 Evaluate side-chains 180 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 808 TRP Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1077 GLU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 747 GLU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1077 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.6980 chunk 2 optimal weight: 0.0050 chunk 128 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 0.5980 chunk 118 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 87 optimal weight: 5.9990 chunk 154 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14098 Z= 0.137 Angle : 0.552 15.206 19144 Z= 0.268 Chirality : 0.041 0.180 2236 Planarity : 0.004 0.060 2392 Dihedral : 4.776 34.588 2072 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.07 % Allowed : 14.60 % Favored : 82.33 % 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: -0.29 (0.20), residues: 1770 helix: 0.74 (0.17), residues: 948 sheet: 0.84 (0.47), residues: 130 loop : -1.73 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 661 HIS 0.012 0.001 HIS A1018 PHE 0.011 0.001 PHE B 541 TYR 0.008 0.001 TYR B 636 ARG 0.005 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 170 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 691 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.6807 (tpp80) REVERT: A 783 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8135 (pp) REVERT: B 315 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8302 (pp) REVERT: B 691 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6796 (tpp80) REVERT: B 783 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8159 (pp) outliers start: 45 outliers final: 12 residues processed: 197 average time/residue: 1.2154 time to fit residues: 263.6145 Evaluate side-chains 178 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 813 ASP Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1060 VAL Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 101 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 142 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 chunk 90 optimal weight: 0.0270 chunk 166 optimal weight: 6.9990 overall best weight: 0.7050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS B 236 GLN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14098 Z= 0.149 Angle : 0.550 15.022 19144 Z= 0.266 Chirality : 0.041 0.184 2236 Planarity : 0.004 0.061 2392 Dihedral : 4.480 22.387 2072 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.14 % Allowed : 14.32 % Favored : 82.54 % 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: -0.03 (0.20), residues: 1770 helix: 1.00 (0.17), residues: 950 sheet: 0.91 (0.47), residues: 130 loop : -1.69 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 850 HIS 0.012 0.001 HIS A1018 PHE 0.010 0.001 PHE B 428 TYR 0.009 0.001 TYR B 636 ARG 0.004 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8300 (pp) REVERT: A 691 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6758 (tpp80) REVERT: A 783 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8222 (pp) REVERT: A 1060 VAL cc_start: 0.8740 (t) cc_final: 0.8481 (t) REVERT: B 315 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8296 (pp) REVERT: B 691 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6769 (tpp80) REVERT: B 783 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8196 (pp) REVERT: B 1060 VAL cc_start: 0.8752 (t) cc_final: 0.8497 (t) outliers start: 46 outliers final: 12 residues processed: 201 average time/residue: 1.1127 time to fit residues: 247.5726 Evaluate side-chains 188 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 170 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1047 ASN Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 125 optimal weight: 0.5980 chunk 97 optimal weight: 0.1980 chunk 144 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS B 236 GLN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14098 Z= 0.169 Angle : 0.559 14.676 19144 Z= 0.270 Chirality : 0.041 0.187 2236 Planarity : 0.004 0.061 2392 Dihedral : 4.385 21.997 2072 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.73 % Allowed : 15.14 % Favored : 82.13 % 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: 0.19 (0.20), residues: 1770 helix: 1.20 (0.17), residues: 950 sheet: 0.99 (0.47), residues: 134 loop : -1.63 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 850 HIS 0.010 0.001 HIS A1018 PHE 0.011 0.001 PHE B 541 TYR 0.010 0.001 TYR A 636 ARG 0.005 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 177 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8300 (pp) REVERT: A 691 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.6794 (tpp80) REVERT: A 783 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8309 (pp) REVERT: A 1060 VAL cc_start: 0.8745 (t) cc_final: 0.8474 (t) REVERT: B 315 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8317 (pp) REVERT: B 691 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.6739 (tpp80) REVERT: B 731 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8237 (pt) REVERT: B 783 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 1060 VAL cc_start: 0.8736 (t) cc_final: 0.8469 (t) outliers start: 40 outliers final: 14 residues processed: 203 average time/residue: 1.1930 time to fit residues: 267.7272 Evaluate side-chains 190 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain A residue 1049 GLN Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 1033 ASP Chi-restraints excluded: chain B residue 1049 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 134 optimal weight: 4.9990 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS B 236 GLN B 699 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14098 Z= 0.160 Angle : 0.560 14.877 19144 Z= 0.271 Chirality : 0.042 0.198 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.316 21.689 2072 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.66 % Allowed : 15.08 % Favored : 82.26 % 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: 0.36 (0.20), residues: 1770 helix: 1.36 (0.17), residues: 948 sheet: 1.01 (0.47), residues: 134 loop : -1.58 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 850 HIS 0.011 0.001 HIS B1018 PHE 0.011 0.001 PHE B 541 TYR 0.010 0.001 TYR B 636 ARG 0.006 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 181 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8293 (pp) REVERT: A 691 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6756 (tpp80) REVERT: A 783 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8263 (pp) REVERT: A 1060 VAL cc_start: 0.8755 (t) cc_final: 0.8458 (t) REVERT: B 315 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 691 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6752 (tpp80) REVERT: B 731 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8174 (pt) REVERT: B 783 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8270 (pp) REVERT: B 1060 VAL cc_start: 0.8736 (t) cc_final: 0.8453 (t) outliers start: 39 outliers final: 14 residues processed: 207 average time/residue: 1.1649 time to fit residues: 266.7595 Evaluate side-chains 199 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 731 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 144 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1018 HIS B 236 GLN B 699 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1018 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14098 Z= 0.163 Angle : 0.569 14.627 19144 Z= 0.273 Chirality : 0.042 0.220 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.296 21.729 2072 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.80 % Allowed : 15.01 % Favored : 82.20 % 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: 0.50 (0.20), residues: 1770 helix: 1.48 (0.17), residues: 950 sheet: 1.11 (0.47), residues: 134 loop : -1.54 (0.22), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 850 HIS 0.010 0.001 HIS B1018 PHE 0.011 0.001 PHE B 541 TYR 0.010 0.001 TYR A 636 ARG 0.005 0.000 ARG A 872 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8314 (pp) REVERT: A 691 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6727 (tpp80) REVERT: A 774 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.6716 (mpp) REVERT: A 783 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8275 (pp) REVERT: A 1060 VAL cc_start: 0.8782 (t) cc_final: 0.8481 (t) REVERT: B 315 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8338 (pp) REVERT: B 691 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6725 (tpp80) REVERT: B 783 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 1016 ARG cc_start: 0.6318 (mtt180) cc_final: 0.6046 (mtt180) REVERT: B 1060 VAL cc_start: 0.8775 (t) cc_final: 0.8471 (t) outliers start: 41 outliers final: 14 residues processed: 207 average time/residue: 1.1487 time to fit residues: 263.1798 Evaluate side-chains 194 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 173 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 117 optimal weight: 0.0270 chunk 177 optimal weight: 8.9990 chunk 163 optimal weight: 2.9990 chunk 141 optimal weight: 0.0770 chunk 14 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 150 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 699 ASN ** A 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 853 HIS A1018 HIS B 236 GLN B 699 ASN ** B 789 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 853 HIS B1018 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14098 Z= 0.171 Angle : 0.575 14.648 19144 Z= 0.279 Chirality : 0.042 0.271 2236 Planarity : 0.004 0.062 2392 Dihedral : 4.303 21.725 2072 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.91 % Allowed : 15.96 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.20), residues: 1770 helix: 1.55 (0.17), residues: 948 sheet: 1.11 (0.48), residues: 134 loop : -1.56 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 850 HIS 0.009 0.001 HIS A1018 PHE 0.011 0.001 PHE A 541 TYR 0.010 0.001 TYR B 636 ARG 0.006 0.000 ARG A 872 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3540 Ramachandran restraints generated. 1770 Oldfield, 0 Emsley, 1770 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 173 time to evaluate : 1.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8319 (pp) REVERT: A 691 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.6739 (tpp80) REVERT: A 747 GLU cc_start: 0.7447 (mp0) cc_final: 0.7138 (mp0) REVERT: A 774 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.6723 (mpp) REVERT: A 783 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8271 (pp) REVERT: A 1060 VAL cc_start: 0.8793 (t) cc_final: 0.8480 (t) REVERT: B 91 ASN cc_start: 0.7959 (t0) cc_final: 0.7667 (m-40) REVERT: B 315 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8344 (pp) REVERT: B 691 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.6721 (tpp80) REVERT: B 783 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8261 (pp) REVERT: B 1016 ARG cc_start: 0.6437 (mtt180) cc_final: 0.6185 (mtt180) REVERT: B 1048 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7748 (ttm-80) REVERT: B 1060 VAL cc_start: 0.8789 (t) cc_final: 0.8473 (t) outliers start: 28 outliers final: 14 residues processed: 194 average time/residue: 1.1772 time to fit residues: 252.6429 Evaluate side-chains 193 residues out of total 1466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 172 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 480 VAL Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 691 ARG Chi-restraints excluded: chain A residue 696 VAL Chi-restraints excluded: chain A residue 774 MET Chi-restraints excluded: chain A residue 783 LEU Chi-restraints excluded: chain A residue 818 THR Chi-restraints excluded: chain A residue 1033 ASP Chi-restraints excluded: chain B residue 308 CYS Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 574 LEU Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain B residue 696 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 818 THR Chi-restraints excluded: chain B residue 1033 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 26 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 GLN A 365 GLN A 699 ASN A 853 HIS A1018 HIS B 365 GLN B 699 ASN B 853 HIS B1018 HIS ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.148410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.106174 restraints weight = 16291.984| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.15 r_work: 0.2957 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14098 Z= 0.174 Angle : 0.578 14.575 19144 Z= 0.279 Chirality : 0.043 0.261 2236 Planarity : 0.004 0.061 2392 Dihedral : 4.309 21.733 2072 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.32 % Allowed : 15.83 % Favored : 81.86 % 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: 0.57 (0.20), residues: 1770 helix: 1.58 (0.17), residues: 948 sheet: 1.10 (0.48), residues: 134 loop : -1.55 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 850 HIS 0.010 0.001 HIS B1018 PHE 0.011 0.001 PHE A 541 TYR 0.010 0.001 TYR B 636 ARG 0.006 0.000 ARG A 872 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.63 seconds wall clock time: 91 minutes 39.18 seconds (5499.18 seconds total)