Starting phenix.real_space_refine on Thu Feb 22 13:23:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wlb_21820/02_2024/6wlb_21820.pdb" } resolution = 3.5 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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 87 5.16 5 C 11421 2.51 5 N 2886 2.21 5 O 3087 1.98 5 H 16960 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 197": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 246": "OE1" <-> "OE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A GLU 302": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 359": "OE1" <-> "OE2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 514": "OD1" <-> "OD2" Residue "A PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 626": "OE1" <-> "OE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 816": "OD1" <-> "OD2" Residue "A PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 197": "OD1" <-> "OD2" Residue "C GLU 231": "OE1" <-> "OE2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 246": "OE1" <-> "OE2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C GLU 302": "OE1" <-> "OE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C GLU 359": "OE1" <-> "OE2" Residue "C GLU 360": "OE1" <-> "OE2" Residue "C ASP 377": "OD1" <-> "OD2" Residue "C GLU 378": "OE1" <-> "OE2" Residue "C PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 486": "OD1" <-> "OD2" Residue "C ASP 514": "OD1" <-> "OD2" Residue "C PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 710": "OD1" <-> "OD2" Residue "C PHE 733": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 821": "OE1" <-> "OE2" Residue "C PHE 893": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 902": "OE1" <-> "OE2" Residue "C PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 924": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 243": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 285": "OD1" <-> "OD2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 350": "OE1" <-> "OE2" Residue "B GLU 359": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B PHE 403": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 480": "OD1" <-> "OD2" Residue "B ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 514": "OD1" <-> "OD2" Residue "B PHE 618": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 658": "OE1" <-> "OE2" Residue "B TYR 735": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 737": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 821": "OE1" <-> "OE2" Residue "B PHE 834": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 901": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 902": "OE1" <-> "OE2" Residue "B PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 931": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34441 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "C" Number of atoms: 11417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11417 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "B" Number of atoms: 11428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 11428 Classifications: {'peptide': 720} Link IDs: {'PCIS': 2, 'PTRANS': 42, 'TRANS': 675} Chain breaks: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 56 Unusual residues: {'BGC': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 14.60, per 1000 atoms: 0.42 Number of scatterers: 34441 At special positions: 0 Unit cell: (136.08, 128.52, 104.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 O 3087 8.00 N 2886 7.00 C 11421 6.00 H 16960 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " BGC D 1 " - " BGC D 2 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " " BGC E 1 " - " BGC E 2 " " BGC E 2 " - " BGC E 3 " " BGC E 3 " - " BGC E 4 " " BGC E 4 " - " BGC E 5 " " BGC F 1 " - " BGC F 2 " " BGC F 2 " - " BGC F 3 " " BGC F 3 " - " BGC F 4 " " BGC F 4 " - " BGC F 5 " Time building additional restraints: 26.51 Conformation dependent library (CDL) restraints added in 3.3 seconds 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4008 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 58.9% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 170 through 194 Processing helix chain 'A' and resid 199 through 222 removed outlier: 3.776A pdb=" N TRP A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 225 No H-bonds generated for 'chain 'A' and resid 223 through 225' Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 266 through 279 removed outlier: 4.053A pdb=" N THR A 270 " --> pdb=" O PRO A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 322 removed outlier: 3.573A pdb=" N PHE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 327 through 333 Processing helix chain 'A' and resid 346 through 373 removed outlier: 3.638A pdb=" N GLU A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.624A pdb=" N ALA A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 480 removed outlier: 4.121A pdb=" N ASP A 480 " --> pdb=" O CYS A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 522 removed outlier: 3.925A pdb=" N PHE A 513 " --> pdb=" O ASN A 509 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N MET A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLY A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 542 Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.735A pdb=" N ILE A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 652 Processing helix chain 'A' and resid 653 through 657 removed outlier: 4.250A pdb=" N GLU A 657 " --> pdb=" O CYS A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 685 Processing helix chain 'A' and resid 707 through 728 removed outlier: 3.972A pdb=" N ARG A 711 " --> pdb=" O ASN A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 755 Processing helix chain 'A' and resid 756 through 758 No H-bonds generated for 'chain 'A' and resid 756 through 758' Processing helix chain 'A' and resid 759 through 774 removed outlier: 3.845A pdb=" N ALA A 765 " --> pdb=" O LEU A 761 " (cutoff:3.500A) Proline residue: A 770 - end of helix Processing helix chain 'A' and resid 787 through 811 removed outlier: 3.552A pdb=" N ILE A 800 " --> pdb=" O PHE A 796 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TRP A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 830 removed outlier: 3.661A pdb=" N LEU A 817 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP A 818 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 846 Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 875 through 899 removed outlier: 3.594A pdb=" N LYS A 899 " --> pdb=" O ASP A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 930 removed outlier: 4.163A pdb=" N PHE A 913 " --> pdb=" O GLY A 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 914 " --> pdb=" O LYS A 910 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 3.512A pdb=" N GLY A 927 " --> pdb=" O PRO A 923 " (cutoff:3.500A) Processing helix chain 'A' and resid 938 through 958 Processing helix chain 'C' and resid 170 through 194 Processing helix chain 'C' and resid 199 through 222 removed outlier: 3.813A pdb=" N TRP C 203 " --> pdb=" O ALA C 199 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 225 No H-bonds generated for 'chain 'C' and resid 223 through 225' Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 266 through 279 removed outlier: 4.037A pdb=" N THR C 270 " --> pdb=" O PRO C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 322 removed outlier: 3.608A pdb=" N PHE C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU C 309 " --> pdb=" O VAL C 305 " (cutoff:3.500A) Proline residue: C 316 - end of helix Processing helix chain 'C' and resid 327 through 333 removed outlier: 3.621A pdb=" N SER C 333 " --> pdb=" O GLU C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 373 removed outlier: 3.633A pdb=" N GLU C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 451 removed outlier: 3.572A pdb=" N ALA C 442 " --> pdb=" O GLY C 438 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 480 removed outlier: 4.065A pdb=" N ASP C 480 " --> pdb=" O CYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 522 removed outlier: 3.830A pdb=" N PHE C 513 " --> pdb=" O ASN C 509 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASN C 516 " --> pdb=" O PHE C 512 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N MET C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 611 through 619 Processing helix chain 'C' and resid 621 through 629 removed outlier: 3.715A pdb=" N ILE C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) Processing helix chain 'C' and resid 640 through 652 Processing helix chain 'C' and resid 653 through 657 removed outlier: 4.233A pdb=" N GLU C 657 " --> pdb=" O CYS C 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 685 Processing helix chain 'C' and resid 707 through 728 removed outlier: 3.943A pdb=" N ARG C 711 " --> pdb=" O ASN C 707 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 755 Processing helix chain 'C' and resid 756 through 758 No H-bonds generated for 'chain 'C' and resid 756 through 758' Processing helix chain 'C' and resid 759 through 774 removed outlier: 3.831A pdb=" N ALA C 765 " --> pdb=" O LEU C 761 " (cutoff:3.500A) Proline residue: C 770 - end of helix Processing helix chain 'C' and resid 787 through 811 removed outlier: 3.580A pdb=" N ILE C 800 " --> pdb=" O PHE C 796 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TRP C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 830 removed outlier: 3.592A pdb=" N LEU C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 818 " --> pdb=" O ILE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 830 through 846 Processing helix chain 'C' and resid 870 through 875 Processing helix chain 'C' and resid 875 through 899 removed outlier: 3.579A pdb=" N LYS C 899 " --> pdb=" O ASP C 895 " (cutoff:3.500A) Processing helix chain 'C' and resid 905 through 930 removed outlier: 4.189A pdb=" N PHE C 913 " --> pdb=" O GLY C 909 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA C 914 " --> pdb=" O LYS C 910 " (cutoff:3.500A) Proline residue: C 923 - end of helix Processing helix chain 'C' and resid 938 through 958 Processing helix chain 'B' and resid 170 through 194 Processing helix chain 'B' and resid 199 through 222 removed outlier: 3.663A pdb=" N TRP B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 225 No H-bonds generated for 'chain 'B' and resid 223 through 225' Processing helix chain 'B' and resid 233 through 242 removed outlier: 3.641A pdb=" N LEU B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 279 removed outlier: 3.971A pdb=" N THR B 270 " --> pdb=" O PRO B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 322 removed outlier: 3.641A pdb=" N PHE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 309 " --> pdb=" O VAL B 305 " (cutoff:3.500A) Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 327 through 333 removed outlier: 3.585A pdb=" N SER B 333 " --> pdb=" O GLU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 373 removed outlier: 3.585A pdb=" N GLN B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 451 removed outlier: 3.742A pdb=" N VAL B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 480 removed outlier: 3.921A pdb=" N ASP B 480 " --> pdb=" O CYS B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 522 removed outlier: 3.687A pdb=" N PHE B 513 " --> pdb=" O ASN B 509 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN B 516 " --> pdb=" O PHE B 512 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N MET B 517 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY B 519 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 542 Processing helix chain 'B' and resid 611 through 619 Processing helix chain 'B' and resid 621 through 629 removed outlier: 3.712A pdb=" N ILE B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 640 through 652 Processing helix chain 'B' and resid 653 through 657 removed outlier: 4.291A pdb=" N GLU B 657 " --> pdb=" O CYS B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 675 through 685 removed outlier: 3.554A pdb=" N GLY B 680 " --> pdb=" O ASP B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 728 removed outlier: 3.995A pdb=" N ARG B 711 " --> pdb=" O ASN B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 755 Processing helix chain 'B' and resid 756 through 758 No H-bonds generated for 'chain 'B' and resid 756 through 758' Processing helix chain 'B' and resid 759 through 776 removed outlier: 3.887A pdb=" N ALA B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) Proline residue: B 770 - end of helix removed outlier: 3.536A pdb=" N LEU B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 809 removed outlier: 3.687A pdb=" N ILE B 800 " --> pdb=" O PHE B 796 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 830 removed outlier: 3.628A pdb=" N LEU B 817 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 846 Processing helix chain 'B' and resid 870 through 875 Processing helix chain 'B' and resid 875 through 899 removed outlier: 3.890A pdb=" N LYS B 899 " --> pdb=" O ASP B 895 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 930 removed outlier: 3.662A pdb=" N GLY B 909 " --> pdb=" O GLY B 905 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE B 913 " --> pdb=" O GLY B 909 " (cutoff:3.500A) Proline residue: B 923 - end of helix removed outlier: 3.576A pdb=" N GLY B 927 " --> pdb=" O PRO B 923 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 928 " --> pdb=" O PHE B 924 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 958 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 164 Processing sheet with id=AA2, first strand: chain 'A' and resid 399 through 403 removed outlier: 6.353A pdb=" N VAL A 253 " --> pdb=" O SER A 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR A 290 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE A 255 " --> pdb=" O TYR A 290 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER A 292 " --> pdb=" O PHE A 255 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL A 257 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 533 " --> pdb=" O ASN A 458 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 491 removed outlier: 7.343A pdb=" N ILE A 691 " --> pdb=" O CYS A 488 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N VAL A 490 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 160 through 164 Processing sheet with id=AA6, first strand: chain 'C' and resid 399 through 403 removed outlier: 6.344A pdb=" N VAL C 253 " --> pdb=" O SER C 288 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N TYR C 290 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N PHE C 255 " --> pdb=" O TYR C 290 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N SER C 292 " --> pdb=" O PHE C 255 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N VAL C 257 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS C 533 " --> pdb=" O ASN C 458 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 463 through 464 removed outlier: 6.551A pdb=" N ARG C 495 " --> pdb=" O GLY C 702 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 487 through 491 removed outlier: 7.354A pdb=" N ILE C 691 " --> pdb=" O CYS C 488 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL C 490 " --> pdb=" O ILE C 691 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 160 through 164 removed outlier: 3.702A pdb=" N ILE B 161 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 399 through 403 removed outlier: 6.107A pdb=" N ASP B 254 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU B 459 " --> pdb=" O ASP B 254 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N PHE B 256 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS B 533 " --> pdb=" O ASN B 458 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 463 through 464 removed outlier: 6.574A pdb=" N ARG B 495 " --> pdb=" O GLY B 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 487 through 491 removed outlier: 7.534A pdb=" N ILE B 691 " --> pdb=" O CYS B 488 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VAL B 490 " --> pdb=" O ILE B 691 " (cutoff:3.500A) 910 hydrogen bonds defined for protein. 2694 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: 12.35 Time building geometry restraints manager: 27.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16921 1.03 - 1.23: 41 1.23 - 1.42: 7631 1.42 - 1.62: 10217 1.62 - 1.82: 135 Bond restraints: 34945 Sorted by residual: bond pdb=" C1 BGC D 5 " pdb=" O5 BGC D 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 BGC F 5 " pdb=" O5 BGC F 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.27e+01 bond pdb=" C1 BGC E 5 " pdb=" O5 BGC E 5 " ideal model delta sigma weight residual 1.408 1.503 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C1 BGC D 4 " pdb=" O5 BGC D 4 " ideal model delta sigma weight residual 1.408 1.502 -0.094 2.00e-02 2.50e+03 2.23e+01 bond pdb=" C1 BGC E 4 " pdb=" O5 BGC E 4 " ideal model delta sigma weight residual 1.408 1.502 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 34940 not shown) Histogram of bond angle deviations from ideal: 74.10 - 86.10: 50 86.10 - 98.09: 0 98.09 - 110.09: 30932 110.09 - 122.09: 26546 122.09 - 134.09: 5449 Bond angle restraints: 62977 Sorted by residual: angle pdb=" C LEU B 921 " pdb=" CA LEU B 921 " pdb=" HA LEU B 921 " ideal model delta sigma weight residual 109.00 74.10 34.90 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 109.00 74.22 34.78 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 110.00 75.24 34.76 3.00e+00 1.11e-01 1.34e+02 angle pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" HA LEU C 921 " ideal model delta sigma weight residual 110.00 75.25 34.75 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LEU A 921 " pdb=" CA LEU A 921 " pdb=" HA LEU A 921 " ideal model delta sigma weight residual 109.00 74.25 34.75 3.00e+00 1.11e-01 1.34e+02 ... (remaining 62972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 15243 17.62 - 35.24: 1134 35.24 - 52.86: 291 52.86 - 70.48: 106 70.48 - 88.10: 6 Dihedral angle restraints: 16780 sinusoidal: 9073 harmonic: 7707 Sorted by residual: dihedral pdb=" C LEU A 921 " pdb=" N LEU A 921 " pdb=" CA LEU A 921 " pdb=" CB LEU A 921 " ideal model delta harmonic sigma weight residual -122.60 -131.85 9.25 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C LEU C 921 " pdb=" N LEU C 921 " pdb=" CA LEU C 921 " pdb=" CB LEU C 921 " ideal model delta harmonic sigma weight residual -122.60 -131.81 9.21 0 2.50e+00 1.60e-01 1.36e+01 dihedral pdb=" C LEU B 921 " pdb=" N LEU B 921 " pdb=" CA LEU B 921 " pdb=" CB LEU B 921 " ideal model delta harmonic sigma weight residual -122.60 -131.79 9.19 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 16777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 2718 0.295 - 0.590: 3 0.590 - 0.884: 0 0.884 - 1.179: 0 1.179 - 1.474: 3 Chirality restraints: 2724 Sorted by residual: chirality pdb=" CB THR C 872 " pdb=" CA THR C 872 " pdb=" OG1 THR C 872 " pdb=" CG2 THR C 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.43e+01 chirality pdb=" CB THR B 872 " pdb=" CA THR B 872 " pdb=" OG1 THR B 872 " pdb=" CG2 THR B 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.41e+01 chirality pdb=" CB THR A 872 " pdb=" CA THR A 872 " pdb=" OG1 THR A 872 " pdb=" CG2 THR A 872 " both_signs ideal model delta sigma weight residual False 2.55 1.08 1.47 2.00e-01 2.50e+01 5.40e+01 ... (remaining 2721 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 194 " -0.077 5.00e-02 4.00e+02 1.13e-01 2.03e+01 pdb=" N PRO B 195 " 0.194 5.00e-02 4.00e+02 pdb=" CA PRO B 195 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO B 195 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 194 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO C 195 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 480 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO B 481 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 481 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 481 " -0.031 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.92: 91 1.92 - 2.59: 34213 2.59 - 3.26: 104125 3.26 - 3.93: 124404 3.93 - 4.60: 198179 Nonbonded interactions: 461012 Sorted by model distance: nonbonded pdb=" H ASN B 707 " pdb="HD22 ASN B 707 " model vdw 1.250 2.100 nonbonded pdb=" HA LEU B 921 " pdb=" HB3 LEU B 921 " model vdw 1.610 1.952 nonbonded pdb=" HA LEU C 921 " pdb=" HB3 LEU C 921 " model vdw 1.625 1.952 nonbonded pdb=" HA LEU A 921 " pdb=" HB3 LEU A 921 " model vdw 1.626 1.952 nonbonded pdb=" H LEU A 921 " pdb=" HA LEU A 921 " model vdw 1.641 1.816 ... (remaining 461007 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 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = (chain 'B' and (resid 157 through 424 or (resid 425 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name NE or name CZ or name NH \ 1 or name NH2 or name H or name HA )) or resid 426 through 958)) selection = chain 'C' } ncs_group { reference = 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 group one per residue 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: 2.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.490 Extract box with map and model: 10.090 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 99.210 Find NCS groups from input model: 1.400 Set up NCS constraints: 0.130 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 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 : 0.005 0.095 17985 Z= 0.300 Angle : 0.568 11.704 24465 Z= 0.292 Chirality : 0.063 1.474 2724 Planarity : 0.004 0.113 3054 Dihedral : 12.885 88.098 6720 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.16 % Allowed : 0.27 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.33 (0.19), residues: 2142 helix: 2.31 (0.16), residues: 1179 sheet: -0.81 (0.38), residues: 162 loop : -0.96 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 954 HIS 0.003 0.000 HIS C 920 PHE 0.023 0.001 PHE C 840 TYR 0.010 0.001 TYR A 173 ARG 0.012 0.001 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 297 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 294 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 669 ILE cc_start: 0.7896 (mm) cc_final: 0.7631 (mm) outliers start: 3 outliers final: 0 residues processed: 297 average time/residue: 0.5932 time to fit residues: 273.5221 Evaluate side-chains 256 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 163 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 chunk 126 optimal weight: 0.6980 chunk 196 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 714 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17985 Z= 0.197 Angle : 0.536 11.578 24465 Z= 0.284 Chirality : 0.062 1.454 2724 Planarity : 0.004 0.055 3054 Dihedral : 3.395 27.078 2646 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.91 % Allowed : 5.02 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.19), residues: 2142 helix: 2.22 (0.16), residues: 1188 sheet: -1.16 (0.34), residues: 192 loop : -0.97 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.011 0.001 HIS C 434 PHE 0.018 0.001 PHE A 924 TYR 0.015 0.001 TYR A 670 ARG 0.003 0.000 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 281 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 264 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 215 PHE cc_start: 0.7899 (OUTLIER) cc_final: 0.7463 (t80) outliers start: 17 outliers final: 14 residues processed: 273 average time/residue: 0.6005 time to fit residues: 256.3925 Evaluate side-chains 261 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 793 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 790 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 66 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 640 ASN C 640 ASN B 640 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17985 Z= 0.207 Angle : 0.527 11.641 24465 Z= 0.277 Chirality : 0.062 1.470 2724 Planarity : 0.004 0.056 3054 Dihedral : 3.387 18.392 2646 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.23 % Allowed : 5.93 % Favored : 92.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.14 (0.19), residues: 2142 helix: 2.10 (0.15), residues: 1197 sheet: -0.80 (0.35), residues: 165 loop : -1.06 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 314 HIS 0.006 0.001 HIS B 434 PHE 0.010 0.001 PHE A 893 TYR 0.012 0.001 TYR B 756 ARG 0.003 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 264 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7849 (pt) cc_final: 0.7211 (tp) REVERT: A 647 GLU cc_start: 0.7919 (tp30) cc_final: 0.7668 (tp30) REVERT: C 215 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7536 (t80) REVERT: C 647 GLU cc_start: 0.7766 (tp30) cc_final: 0.7565 (tp30) REVERT: B 215 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7611 (t80) REVERT: B 329 GLU cc_start: 0.8401 (tp30) cc_final: 0.8121 (tp30) outliers start: 23 outliers final: 18 residues processed: 277 average time/residue: 0.6276 time to fit residues: 267.2741 Evaluate side-chains 260 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 240 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 925 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 101 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 131 optimal weight: 0.0270 chunk 197 optimal weight: 0.9980 chunk 208 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 186 optimal weight: 0.0970 chunk 56 optimal weight: 0.5980 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17985 Z= 0.146 Angle : 0.505 11.559 24465 Z= 0.262 Chirality : 0.061 1.449 2724 Planarity : 0.004 0.049 3054 Dihedral : 3.223 16.998 2646 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.12 % Allowed : 7.26 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.35 (0.19), residues: 2142 helix: 2.28 (0.16), residues: 1194 sheet: -0.92 (0.33), residues: 195 loop : -0.91 (0.23), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 314 HIS 0.003 0.001 HIS C 434 PHE 0.016 0.001 PHE B 893 TYR 0.010 0.001 TYR B 756 ARG 0.005 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 257 time to evaluate : 2.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7786 (pt) cc_final: 0.7193 (tp) REVERT: C 215 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7558 (t80) REVERT: C 647 GLU cc_start: 0.7710 (tp30) cc_final: 0.7497 (tp30) REVERT: C 878 PRO cc_start: 0.8225 (Cg_exo) cc_final: 0.7708 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 329 GLU cc_start: 0.8370 (tp30) cc_final: 0.8130 (tp30) outliers start: 21 outliers final: 15 residues processed: 268 average time/residue: 0.6597 time to fit residues: 272.2816 Evaluate side-chains 260 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 243 time to evaluate : 2.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 86 optimal weight: 0.8980 chunk 178 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 187 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17985 Z= 0.244 Angle : 0.532 11.591 24465 Z= 0.279 Chirality : 0.062 1.469 2724 Planarity : 0.004 0.059 3054 Dihedral : 3.470 17.006 2646 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.50 % Allowed : 7.43 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.27 (0.19), residues: 2142 helix: 2.26 (0.16), residues: 1191 sheet: -0.76 (0.36), residues: 165 loop : -1.08 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 314 HIS 0.005 0.001 HIS A 434 PHE 0.013 0.001 PHE C 893 TYR 0.016 0.001 TYR B 422 ARG 0.004 0.000 ARG B 508 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 254 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8009 (pt) cc_final: 0.7428 (tp) REVERT: A 647 GLU cc_start: 0.7913 (tp30) cc_final: 0.7666 (tp30) REVERT: C 215 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7600 (t80) REVERT: C 840 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.6824 (m-80) REVERT: C 878 PRO cc_start: 0.8178 (Cg_exo) cc_final: 0.7600 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7518 (t80) REVERT: B 329 GLU cc_start: 0.8419 (tp30) cc_final: 0.8169 (tp30) REVERT: B 517 MET cc_start: 0.8203 (tpt) cc_final: 0.7972 (mmm) outliers start: 28 outliers final: 18 residues processed: 270 average time/residue: 0.6536 time to fit residues: 269.1993 Evaluate side-chains 266 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 245 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 921 LEU Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 0.5980 chunk 188 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 208 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17985 Z= 0.149 Angle : 0.508 11.540 24465 Z= 0.264 Chirality : 0.061 1.450 2724 Planarity : 0.004 0.050 3054 Dihedral : 3.277 16.340 2646 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.39 % Allowed : 7.75 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.42 (0.19), residues: 2142 helix: 2.35 (0.16), residues: 1194 sheet: -0.62 (0.37), residues: 165 loop : -0.98 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 314 HIS 0.003 0.001 HIS B 920 PHE 0.013 0.001 PHE B 893 TYR 0.016 0.001 TYR A 422 ARG 0.005 0.000 ARG C 508 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 271 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 2.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.7981 (pt) cc_final: 0.7389 (tp) REVERT: C 215 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7594 (t80) REVERT: C 840 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.6788 (m-80) REVERT: B 215 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7473 (t80) REVERT: B 329 GLU cc_start: 0.8378 (tp30) cc_final: 0.8141 (tp30) REVERT: B 517 MET cc_start: 0.8150 (tpt) cc_final: 0.7948 (mmm) outliers start: 26 outliers final: 15 residues processed: 258 average time/residue: 0.6402 time to fit residues: 251.3404 Evaluate side-chains 257 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 239 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 879 THR Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 152 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 116 optimal weight: 2.9990 chunk 208 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 714 GLN C 714 GLN B 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17985 Z= 0.262 Angle : 0.541 11.546 24465 Z= 0.283 Chirality : 0.062 1.458 2724 Planarity : 0.005 0.059 3054 Dihedral : 3.550 16.762 2646 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.39 % Allowed : 8.49 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.29 (0.19), residues: 2142 helix: 2.26 (0.15), residues: 1197 sheet: -0.28 (0.38), residues: 150 loop : -1.17 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 314 HIS 0.005 0.001 HIS A 434 PHE 0.011 0.001 PHE C 310 TYR 0.011 0.001 TYR B 173 ARG 0.006 0.000 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 2.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8129 (pt) cc_final: 0.7572 (tp) REVERT: C 215 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7648 (t80) REVERT: C 840 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.6839 (m-80) REVERT: C 878 PRO cc_start: 0.8107 (Cg_exo) cc_final: 0.7537 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7870 (OUTLIER) cc_final: 0.7486 (t80) REVERT: B 329 GLU cc_start: 0.8440 (tp30) cc_final: 0.8191 (tp30) outliers start: 26 outliers final: 17 residues processed: 257 average time/residue: 0.6261 time to fit residues: 246.8229 Evaluate side-chains 254 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 234 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 9.9990 chunk 83 optimal weight: 0.4980 chunk 124 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 141 optimal weight: 0.0870 chunk 102 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 189 optimal weight: 1.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 17985 Z= 0.165 Angle : 0.516 11.544 24465 Z= 0.267 Chirality : 0.061 1.451 2724 Planarity : 0.004 0.056 3054 Dihedral : 3.384 16.418 2646 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.34 % Allowed : 8.71 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.40 (0.19), residues: 2142 helix: 2.36 (0.16), residues: 1194 sheet: -0.26 (0.38), residues: 150 loop : -1.11 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 314 HIS 0.003 0.001 HIS C 920 PHE 0.008 0.001 PHE C 317 TYR 0.012 0.001 TYR A 422 ARG 0.006 0.000 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 238 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8168 (pt) cc_final: 0.7644 (tp) REVERT: C 215 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7627 (t80) REVERT: C 329 GLU cc_start: 0.8383 (tp30) cc_final: 0.8140 (tp30) REVERT: C 840 PHE cc_start: 0.7985 (OUTLIER) cc_final: 0.6800 (m-80) REVERT: C 878 PRO cc_start: 0.8034 (Cg_exo) cc_final: 0.7487 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 329 GLU cc_start: 0.8399 (tp30) cc_final: 0.8162 (tp30) REVERT: B 787 LEU cc_start: 0.7312 (pt) cc_final: 0.6694 (tp) outliers start: 25 outliers final: 18 residues processed: 253 average time/residue: 0.6539 time to fit residues: 251.5692 Evaluate side-chains 254 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 2.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN A 820 ASN C 509 ASN B 221 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17985 Z= 0.313 Angle : 0.570 11.551 24465 Z= 0.300 Chirality : 0.062 1.463 2724 Planarity : 0.005 0.063 3054 Dihedral : 3.817 19.801 2646 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 1.34 % Allowed : 9.08 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.11 (0.19), residues: 2142 helix: 2.13 (0.15), residues: 1206 sheet: -0.58 (0.39), residues: 150 loop : -1.28 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 314 HIS 0.005 0.001 HIS A 434 PHE 0.016 0.001 PHE B 893 TYR 0.012 0.002 TYR A 331 ARG 0.006 0.001 ARG C 717 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 261 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 2.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8348 (pt) cc_final: 0.7923 (tp) REVERT: C 215 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7659 (t80) REVERT: C 840 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6818 (m-80) REVERT: C 878 PRO cc_start: 0.8004 (Cg_exo) cc_final: 0.7527 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7526 (t80) REVERT: B 787 LEU cc_start: 0.7318 (pt) cc_final: 0.6790 (tp) outliers start: 25 outliers final: 20 residues processed: 252 average time/residue: 0.6457 time to fit residues: 245.0952 Evaluate side-chains 255 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 232 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 872 THR Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 198 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 132 optimal weight: 0.2980 chunk 105 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17985 Z= 0.174 Angle : 0.530 11.532 24465 Z= 0.276 Chirality : 0.062 1.448 2724 Planarity : 0.004 0.060 3054 Dihedral : 3.537 16.521 2646 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.28 % Allowed : 9.29 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.31 (0.19), residues: 2142 helix: 2.31 (0.16), residues: 1200 sheet: -0.53 (0.38), residues: 150 loop : -1.19 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 314 HIS 0.003 0.001 HIS A 434 PHE 0.015 0.001 PHE C 893 TYR 0.012 0.001 TYR B 756 ARG 0.008 0.000 ARG C 717 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4284 Ramachandran restraints generated. 2142 Oldfield, 0 Emsley, 2142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Residue VAL 196 is missing expected H atoms. Skipping. Residue TYR 431 is missing expected H atoms. Skipping. Residue ALA 765 is missing expected H atoms. Skipping. Residue LYS 778 is missing expected H atoms. Skipping. Residue ILE 780 is missing expected H atoms. Skipping. Residue ILE 781 is missing expected H atoms. Skipping. Residue LEU 784 is missing expected H atoms. Skipping. Residue TYR 901 is missing expected H atoms. Skipping. Residue MET 929 is missing expected H atoms. Skipping. Evaluate side-chains 250 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 2.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 510 ILE cc_start: 0.8298 (pt) cc_final: 0.7797 (tp) REVERT: C 215 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7680 (t80) REVERT: C 840 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.6794 (m-80) REVERT: C 878 PRO cc_start: 0.8001 (Cg_exo) cc_final: 0.7571 (Cg_endo) REVERT: B 215 PHE cc_start: 0.7887 (OUTLIER) cc_final: 0.7500 (t80) REVERT: B 329 GLU cc_start: 0.8418 (tp30) cc_final: 0.8185 (tp30) REVERT: B 787 LEU cc_start: 0.7262 (pt) cc_final: 0.6739 (tp) outliers start: 24 outliers final: 19 residues processed: 242 average time/residue: 0.6525 time to fit residues: 242.3050 Evaluate side-chains 246 residues out of total 1872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 224 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 665 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain C residue 194 ASN Chi-restraints excluded: chain C residue 215 PHE Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 805 LEU Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 840 PHE Chi-restraints excluded: chain C residue 872 THR Chi-restraints excluded: chain C residue 937 THR Chi-restraints excluded: chain B residue 215 PHE Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain B residue 433 HIS Chi-restraints excluded: chain B residue 769 ILE Chi-restraints excluded: chain B residue 790 MET Chi-restraints excluded: chain B residue 840 PHE Chi-restraints excluded: chain B residue 921 LEU Chi-restraints excluded: chain B residue 937 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 158 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 176 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.180212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.135427 restraints weight = 72345.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.141568 restraints weight = 32221.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.145355 restraints weight = 20161.101| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17985 Z= 0.203 Angle : 0.532 11.576 24465 Z= 0.277 Chirality : 0.062 1.452 2724 Planarity : 0.004 0.062 3054 Dihedral : 3.510 16.118 2646 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.23 % Allowed : 9.51 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.32 (0.19), residues: 2142 helix: 2.33 (0.16), residues: 1203 sheet: -0.55 (0.38), residues: 150 loop : -1.20 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 314 HIS 0.003 0.001 HIS A 434 PHE 0.014 0.001 PHE B 893 TYR 0.010 0.001 TYR B 756 ARG 0.006 0.000 ARG B 508 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6512.02 seconds wall clock time: 116 minutes 39.87 seconds (6999.87 seconds total)