Starting phenix.real_space_refine on Sat Feb 17 18:29:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/02_2024/7kc0_22803_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 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: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 Zn 1 6.06 5 P 49 5.49 5 Mg 2 5.21 5 S 95 5.16 5 C 12336 2.51 5 N 3232 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 3": "OE1" <-> "OE2" Residue "F GLU 7": "OE1" <-> "OE2" Residue "F ASP 21": "OD1" <-> "OD2" Residue "F GLU 32": "OE1" <-> "OE2" Residue "F ARG 61": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F ASP 150": "OD1" <-> "OD2" Residue "F GLU 189": "OE1" <-> "OE2" Residue "F GLU 198": "OE1" <-> "OE2" Residue "F PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 99": "NH1" <-> "NH2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A ARG 387": "NH1" <-> "NH2" Residue "A PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "A ARG 449": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 475": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "A ASP 584": "OD1" <-> "OD2" Residue "A ASP 585": "OD1" <-> "OD2" Residue "A GLU 588": "OE1" <-> "OE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A ARG 682": "NH1" <-> "NH2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 732": "NH1" <-> "NH2" Residue "A PHE 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A GLU 802": "OE1" <-> "OE2" Residue "A PHE 806": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 816": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 864": "OD1" <-> "OD2" Residue "A ARG 881": "NH1" <-> "NH2" Residue "A ARG 913": "NH1" <-> "NH2" Residue "A ARG 923": "NH1" <-> "NH2" Residue "A ASP 925": "OD1" <-> "OD2" Residue "A ASP 941": "OD1" <-> "OD2" Residue "A PHE 944": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1007": "OE1" <-> "OE2" Residue "A ARG 1017": "NH1" <-> "NH2" Residue "A ARG 1030": "NH1" <-> "NH2" Residue "A GLU 1046": "OE1" <-> "OE2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A GLU 1086": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 66": "OE1" <-> "OE2" Residue "B ARG 75": "NH1" <-> "NH2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 211": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 243": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "B PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ASP 430": "OD1" <-> "OD2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B GLU 450": "OE1" <-> "OE2" Residue "C TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "E GLU 3": "OE1" <-> "OE2" Residue "E PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 41": "OD1" <-> "OD2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 71": "OD1" <-> "OD2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 109": "OD1" <-> "OD2" Residue "E ASP 120": "OD1" <-> "OD2" Residue "E ASP 122": "OD1" <-> "OD2" Residue "E ASP 124": "OD1" <-> "OD2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 150": "OD1" <-> "OD2" Residue "E ASP 156": "OD1" <-> "OD2" Residue "E PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 214": "OD1" <-> "OD2" Residue "E GLU 232": "OE1" <-> "OE2" Residue "E ASP 240": "OD1" <-> "OD2" Residue "E PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G ASP 41": "OD1" <-> "OD2" Residue "G GLU 51": "OE1" <-> "OE2" Residue "G PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 97": "OD1" <-> "OD2" Residue "G PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 120": "OD1" <-> "OD2" Residue "G ASP 122": "OD1" <-> "OD2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "G ASP 187": "OD1" <-> "OD2" Residue "G GLU 192": "OE1" <-> "OE2" Residue "G ASP 204": "OD1" <-> "OD2" Residue "G GLU 232": "OE1" <-> "OE2" Residue "G PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19553 Number of models: 1 Model: "" Number of chains: 10 Chain: "P" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 430 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "T" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "F" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1995 Classifications: {'peptide': 254} Link IDs: {'PTRANS': 8, 'TRANS': 245} Chain: "A" Number of atoms: 8009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 8009 Classifications: {'peptide': 1004} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 40, 'TRANS': 963} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3705 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 28, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 905 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain breaks: 2 Chain: "E" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1987 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain breaks: 3 Chain: "G" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1971 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 4 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, ' ZN': 1, 'D3T': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10704 SG CYS A1069 66.915 77.611 65.309 1.00 55.37 S ATOM 10741 SG CYS A1074 60.429 76.776 65.411 1.00 57.04 S ATOM 10607 SG CYS A1056 64.716 73.893 61.030 1.00 54.43 S ATOM 10633 SG CYS A1059 62.362 80.162 61.171 1.00 55.72 S ATOM 10237 SG CYS A1009 61.638 35.989 62.186 1.00 88.63 S ATOM 10254 SG CYS A1012 59.853 34.377 65.075 1.00 86.87 S ATOM 10340 SG CYS A1024 61.065 32.444 62.025 1.00 85.29 S ATOM 10360 SG CYS A1027 58.240 34.636 61.146 1.00 83.64 S Time building chain proxies: 10.57, per 1000 atoms: 0.54 Number of scatterers: 19553 At special positions: 0 Unit cell: (109.032, 144.55, 161.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 4 26.01 S 95 16.00 P 49 15.00 Mg 2 11.99 O 3834 8.00 N 3232 7.00 C 12336 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 58 " - pdb=" SG CYS C 83 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.63 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1101 " pdb="FE1 SF4 A1101 " - pdb=" SG CYS A1069 " pdb="FE2 SF4 A1101 " - pdb=" SG CYS A1074 " pdb="FE3 SF4 A1101 " - pdb=" SG CYS A1056 " pdb="FE4 SF4 A1101 " - pdb=" SG CYS A1059 " Number of angles added : 12 Zn2+ tetrahedral coordination pdb=" ZN A1104 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1012 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1027 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1024 " pdb="ZN ZN A1104 " - pdb=" SG CYS A1009 " Number of angles added : 6 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 59 helices and 26 sheets defined 27.3% alpha, 18.9% beta 19 base pairs and 35 stacking pairs defined. Time for finding SS restraints: 9.71 Creating SS restraints... Processing helix chain 'F' and resid 9 through 17 Processing helix chain 'F' and resid 72 through 81 removed outlier: 3.669A pdb=" N CYS F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 209 through 219 removed outlier: 4.272A pdb=" N ASP F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LYS F 217 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLY F 218 " --> pdb=" O ASP F 214 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 173 through 187 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.833A pdb=" N ASN A 225 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ARG A 228 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 407 through 417 Processing helix chain 'A' and resid 464 through 471 Processing helix chain 'A' and resid 479 through 485 Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 507 through 530 Proline residue: A 524 - end of helix Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 548 through 553 removed outlier: 3.652A pdb=" N ALA A 553 " --> pdb=" O TYR A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 571 Processing helix chain 'A' and resid 612 through 619 Processing helix chain 'A' and resid 630 through 636 Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.643A pdb=" N ARG A 676 " --> pdb=" O SER A 672 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 712 removed outlier: 3.508A pdb=" N LEU A 700 " --> pdb=" O ARG A 696 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 704 " --> pdb=" O LEU A 700 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N TYR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 745 Processing helix chain 'A' and resid 775 through 792 removed outlier: 3.599A pdb=" N LEU A 792 " --> pdb=" O TYR A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 844 through 858 Processing helix chain 'A' and resid 863 through 878 Processing helix chain 'A' and resid 884 through 887 Processing helix chain 'A' and resid 902 through 913 Processing helix chain 'A' and resid 935 through 937 No H-bonds generated for 'chain 'A' and resid 935 through 937' Processing helix chain 'A' and resid 942 through 948 Processing helix chain 'A' and resid 954 through 959 Processing helix chain 'A' and resid 963 through 974 Proline residue: A 972 - end of helix Processing helix chain 'A' and resid 976 through 983 removed outlier: 4.182A pdb=" N MET A 982 " --> pdb=" O GLN A 978 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE A 983 " --> pdb=" O ALA A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1030 No H-bonds generated for 'chain 'A' and resid 1028 through 1030' Processing helix chain 'A' and resid 1034 through 1060 Processing helix chain 'A' and resid 1080 through 1096 removed outlier: 4.210A pdb=" N LYS A1096 " --> pdb=" O GLU A1092 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 13 removed outlier: 4.096A pdb=" N SER B 13 " --> pdb=" O ASN B 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 9 through 13' Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.980A pdb=" N GLU B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N LYS B 74 " --> pdb=" O LYS B 70 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 75 " --> pdb=" O GLU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 229 through 240 Processing helix chain 'B' and resid 275 through 290 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 358 through 366 Processing helix chain 'B' and resid 394 through 404 Processing helix chain 'C' and resid 6 through 15 removed outlier: 3.516A pdb=" N GLU C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU C 13 " --> pdb=" O ILE C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 29 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'E' and resid 9 through 22 removed outlier: 3.842A pdb=" N LYS E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG E 14 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY E 18 " --> pdb=" O ARG E 14 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ASP E 21 " --> pdb=" O ASP E 17 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N CYS E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 72 through 81 removed outlier: 3.735A pdb=" N CYS E 81 " --> pdb=" O LYS E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 153 removed outlier: 3.934A pdb=" N GLN E 153 " --> pdb=" O ARG E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.502A pdb=" N LYS E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY E 218 " --> pdb=" O ASP E 214 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER E 219 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N SER E 220 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 17 removed outlier: 3.599A pdb=" N LYS G 13 " --> pdb=" O ALA G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 72 through 81 removed outlier: 4.114A pdb=" N CYS G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.822A pdb=" N LYS G 217 " --> pdb=" O LEU G 213 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY G 218 " --> pdb=" O ASP G 214 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'F' and resid 2 through 5 removed outlier: 4.120A pdb=" N GLU F 104 " --> pdb=" O THR F 87 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 66 through 71 removed outlier: 7.126A pdb=" N LEU F 25 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL F 40 " --> pdb=" O LEU F 25 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLN F 38 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLY F 34 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE F 239 " --> pdb=" O LEU F 246 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'F' and resid 203 through 208 removed outlier: 6.470A pdb=" N SER F 157 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP F 172 " --> pdb=" O SER F 157 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N THR F 163 " --> pdb=" O THR F 166 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 269 through 271 removed outlier: 6.750A pdb=" N PHE A 140 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 120 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG A 138 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 122 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 136 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS A 151 " --> pdb=" O PHE A 139 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 160 through 163 Processing sheet with id= F, first strand: chain 'A' and resid 317 through 319 removed outlier: 6.432A pdb=" N VAL A 397 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N LEU A 460 " --> pdb=" O ILE A 398 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N GLY A 400 " --> pdb=" O LEU A 460 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 462 " --> pdb=" O GLY A 400 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 372 through 375 removed outlier: 6.779A pdb=" N SER A 323 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 342 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER A 321 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 436 through 441 Processing sheet with id= I, first strand: chain 'A' and resid 598 through 600 removed outlier: 3.501A pdb=" N GLY A 598 " --> pdb=" O LEU A 810 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 644 through 646 Processing sheet with id= K, first strand: chain 'A' and resid 816 through 819 Processing sheet with id= L, first strand: chain 'A' and resid 889 through 892 Processing sheet with id= M, first strand: chain 'A' and resid 604 through 609 removed outlier: 3.743A pdb=" N LYS A 803 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ASP A 608 " --> pdb=" O PHE A 801 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N PHE A 801 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'A' and resid 757 through 761 removed outlier: 6.577A pdb=" N MET A 767 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 145 through 149 removed outlier: 4.039A pdb=" N GLY B 106 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 173 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N MET B 178 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL B 187 " --> pdb=" O MET B 178 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 295 through 299 removed outlier: 4.136A pdb=" N ARG B 256 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 343 through 346 removed outlier: 6.407A pdb=" N VAL B 435 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N VAL B 355 " --> pdb=" O VAL B 435 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE B 437 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 8.872A pdb=" N TYR B 436 " --> pdb=" O ASN B 455 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LYS B 457 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL B 438 " --> pdb=" O LYS B 457 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 459 " --> pdb=" O VAL B 438 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 454 " --> pdb=" O ILE B 451 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE B 451 " --> pdb=" O LYS B 454 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 445 " --> pdb=" O SER B 460 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 66 through 68 removed outlier: 3.833A pdb=" N LYS C 66 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS C 58 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL C 56 " --> pdb=" O ILE C 68 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP C 82 " --> pdb=" O CYS C 59 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 111 through 117 removed outlier: 3.643A pdb=" N GLU E 104 " --> pdb=" O THR E 87 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LEU E 88 " --> pdb=" O PHE E 6 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA E 92 " --> pdb=" O LEU E 2 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU E 59 " --> pdb=" O LYS E 5 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 66 through 71 removed outlier: 3.649A pdb=" N VAL E 26 " --> pdb=" O MET E 70 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LEU E 25 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N VAL E 40 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN E 27 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLN E 38 " --> pdb=" O ASN E 27 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 157 through 160 removed outlier: 4.183A pdb=" N LEU E 205 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 167 through 172 Processing sheet with id= W, first strand: chain 'G' and resid 112 through 117 removed outlier: 4.388A pdb=" N LEU G 88 " --> pdb=" O PHE G 6 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLU G 59 " --> pdb=" O LYS G 5 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'G' and resid 66 through 68 removed outlier: 4.698A pdb=" N ASN G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN G 38 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY G 244 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASP G 240 " --> pdb=" O ARG G 224 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ARG G 224 " --> pdb=" O ASP G 240 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 157 through 160 removed outlier: 4.019A pdb=" N LEU G 205 " --> pdb=" O ILE G 160 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 167 through 172 660 hydrogen bonds defined for protein. 1842 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 35 stacking parallelities Total time for adding SS restraints: 7.96 Time building geometry restraints manager: 9.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.43: 8313 1.43 - 1.64: 11553 1.64 - 1.85: 136 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 20014 Sorted by residual: bond pdb=" C4' D3T A1102 " pdb=" C3' D3T A1102 " ideal model delta sigma weight residual 1.287 1.528 -0.241 2.00e-02 2.50e+03 1.46e+02 bond pdb=" O4' D3T A1102 " pdb=" C1' D3T A1102 " ideal model delta sigma weight residual 1.283 1.449 -0.166 2.00e-02 2.50e+03 6.92e+01 bond pdb=" C4' D3T A1102 " pdb=" O4' D3T A1102 " ideal model delta sigma weight residual 1.614 1.457 0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" C5 D3T A1102 " pdb=" C6 D3T A1102 " ideal model delta sigma weight residual 1.486 1.387 0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C2 D3T A1102 " pdb=" N3 D3T A1102 " ideal model delta sigma weight residual 1.493 1.400 0.093 2.00e-02 2.50e+03 2.16e+01 ... (remaining 20009 not shown) Histogram of bond angle deviations from ideal: 73.67 - 87.31: 12 87.31 - 100.95: 47 100.95 - 114.59: 12755 114.59 - 128.23: 14319 128.23 - 141.87: 134 Bond angle restraints: 27267 Sorted by residual: angle pdb=" PB D3T A1102 " pdb=" O3B D3T A1102 " pdb=" PG D3T A1102 " ideal model delta sigma weight residual 123.64 141.87 -18.23 3.00e+00 1.11e-01 3.69e+01 angle pdb=" PA D3T A1102 " pdb=" O3A D3T A1102 " pdb=" PB D3T A1102 " ideal model delta sigma weight residual 123.64 139.75 -16.11 3.00e+00 1.11e-01 2.88e+01 angle pdb=" O3A D3T A1102 " pdb=" PB D3T A1102 " pdb=" O3B D3T A1102 " ideal model delta sigma weight residual 109.47 125.29 -15.82 3.00e+00 1.11e-01 2.78e+01 angle pdb=" N PRO E 184 " pdb=" CA PRO E 184 " pdb=" C PRO E 184 " ideal model delta sigma weight residual 113.47 120.75 -7.28 1.43e+00 4.89e-01 2.59e+01 angle pdb=" O1G D3T A1102 " pdb=" PG D3T A1102 " pdb=" O3B D3T A1102 " ideal model delta sigma weight residual 109.47 124.35 -14.88 3.00e+00 1.11e-01 2.46e+01 ... (remaining 27262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.14: 11389 28.14 - 56.27: 617 56.27 - 84.41: 45 84.41 - 112.55: 7 112.55 - 140.68: 1 Dihedral angle restraints: 12059 sinusoidal: 5223 harmonic: 6836 Sorted by residual: dihedral pdb=" C5' D3T A1102 " pdb=" O5' D3T A1102 " pdb=" PA D3T A1102 " pdb=" O3A D3T A1102 " ideal model delta sinusoidal sigma weight residual 202.07 61.39 140.68 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" CA CYS C 58 " pdb=" CB CYS C 58 " pdb=" SG CYS C 58 " pdb=" SG CYS C 83 " ideal model delta sinusoidal sigma weight residual -73.00 -4.87 -68.13 1 2.00e+01 2.50e-03 1.51e+01 dihedral pdb=" CA TYR C 113 " pdb=" C TYR C 113 " pdb=" N GLU C 114 " pdb=" CA GLU C 114 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 12056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2511 0.052 - 0.104: 472 0.104 - 0.156: 106 0.156 - 0.208: 18 0.208 - 0.260: 6 Chirality restraints: 3113 Sorted by residual: chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ARG A1058 " pdb=" N ARG A1058 " pdb=" C ARG A1058 " pdb=" CB ARG A1058 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA VAL E 186 " pdb=" N VAL E 186 " pdb=" C VAL E 186 " pdb=" CB VAL E 186 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 3110 not shown) Planarity restraints: 3317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO E 184 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.70e+00 pdb=" C PRO E 184 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO E 184 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE E 185 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 182 " -0.011 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ILE E 182 " 0.040 2.00e-02 2.50e+03 pdb=" O ILE E 182 " -0.015 2.00e-02 2.50e+03 pdb=" N LYS E 183 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 179 " -0.009 2.00e-02 2.50e+03 1.91e-02 3.64e+00 pdb=" C SER G 179 " 0.033 2.00e-02 2.50e+03 pdb=" O SER G 179 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL G 180 " -0.011 2.00e-02 2.50e+03 ... (remaining 3314 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2129 2.75 - 3.29: 19832 3.29 - 3.82: 32738 3.82 - 4.36: 39859 4.36 - 4.90: 66996 Nonbonded interactions: 161554 Sorted by model distance: nonbonded pdb=" O PHE E 185 " pdb=" OD2 ASP G 109 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 159 " pdb=" OD2 ASP A 261 " model vdw 2.228 2.440 nonbonded pdb=" O ASP A 337 " pdb=" OH TYR A 410 " model vdw 2.231 2.440 nonbonded pdb=" OP1 DA P 21 " pdb=" OH TYR A 897 " model vdw 2.247 2.440 nonbonded pdb=" OH TYR B 44 " pdb=" OD1 ASP B 307 " model vdw 2.250 2.440 ... (remaining 161549 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 'E' and (resid 1 through 69 or resid 71 through 254)) selection = (chain 'F' and (resid 1 through 69 or resid 71 through 118 or resid 120 through \ 160 or resid 162 through 198 or resid 200 through 254)) selection = (chain 'G' and resid 1 through 254) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.670 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 65.240 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 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 0.241 20014 Z= 0.270 Angle : 0.658 18.234 27267 Z= 0.385 Chirality : 0.046 0.260 3113 Planarity : 0.003 0.038 3317 Dihedral : 16.030 140.682 7626 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.90 % Allowed : 13.03 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.16), residues: 2300 helix: -0.87 (0.18), residues: 654 sheet: -2.17 (0.21), residues: 514 loop : -2.94 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1053 HIS 0.004 0.001 HIS C 28 PHE 0.012 0.001 PHE A 140 TYR 0.028 0.001 TYR A 760 ARG 0.003 0.000 ARG A 597 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 2.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8280 (mt) REVERT: F 124 ASP cc_start: 0.7479 (t0) cc_final: 0.6840 (t0) REVERT: F 199 MET cc_start: 0.4941 (tpp) cc_final: 0.3799 (tpt) REVERT: A 841 ASP cc_start: 0.7553 (p0) cc_final: 0.6938 (t0) REVERT: A 908 GLU cc_start: 0.7692 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 1012 CYS cc_start: 0.7769 (OUTLIER) cc_final: 0.6917 (p) REVERT: B 86 LEU cc_start: 0.6932 (mm) cc_final: 0.6657 (mm) REVERT: B 234 GLU cc_start: 0.8175 (tp30) cc_final: 0.7680 (tm-30) REVERT: B 358 LYS cc_start: 0.9017 (tptt) cc_final: 0.8784 (tptp) REVERT: C 8 PHE cc_start: 0.8311 (t80) cc_final: 0.7995 (t80) REVERT: C 12 LYS cc_start: 0.8987 (mtmt) cc_final: 0.8485 (mtmt) REVERT: C 21 LEU cc_start: 0.8475 (mm) cc_final: 0.8087 (mp) REVERT: C 24 ASP cc_start: 0.8391 (m-30) cc_final: 0.7835 (m-30) REVERT: E 58 GLN cc_start: 0.7499 (tp40) cc_final: 0.6829 (tm-30) REVERT: E 66 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6729 (t) REVERT: G 24 GLN cc_start: 0.7690 (mt0) cc_final: 0.7426 (tp40) REVERT: G 29 GLN cc_start: 0.6067 (OUTLIER) cc_final: 0.5734 (mm-40) REVERT: G 181 ILE cc_start: 0.8179 (tp) cc_final: 0.7840 (tt) REVERT: G 182 ILE cc_start: 0.6593 (OUTLIER) cc_final: 0.6019 (mp) REVERT: G 245 PHE cc_start: 0.7176 (p90) cc_final: 0.5374 (p90) outliers start: 61 outliers final: 29 residues processed: 301 average time/residue: 0.3755 time to fit residues: 167.7815 Evaluate side-chains 199 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 165 time to evaluate : 2.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 16 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1012 CYS Chi-restraints excluded: chain A residue 1056 CYS Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 29 GLN Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 182 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 198 optimal weight: 20.0000 chunk 178 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 213 optimal weight: 7.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 238 GLN ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN A 754 HIS A 851 ASN A 919 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN B 52 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN E 255 ASN G 27 ASN G 153 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20014 Z= 0.241 Angle : 0.573 9.343 27267 Z= 0.297 Chirality : 0.044 0.200 3113 Planarity : 0.004 0.040 3317 Dihedral : 13.969 89.477 3080 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 3.52 % Allowed : 16.74 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.16), residues: 2300 helix: 0.05 (0.20), residues: 656 sheet: -1.66 (0.21), residues: 500 loop : -2.55 (0.17), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1053 HIS 0.006 0.001 HIS G 190 PHE 0.011 0.001 PHE A 140 TYR 0.019 0.001 TYR C 97 ARG 0.007 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 179 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8278 (mt) REVERT: F 161 MET cc_start: 0.8283 (mtt) cc_final: 0.7663 (mtm) REVERT: F 199 MET cc_start: 0.5003 (tpp) cc_final: 0.3787 (tpt) REVERT: A 841 ASP cc_start: 0.7582 (p0) cc_final: 0.7039 (t0) REVERT: A 908 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7307 (tm-30) REVERT: B 358 LYS cc_start: 0.9027 (tptt) cc_final: 0.8827 (tptp) REVERT: C 8 PHE cc_start: 0.8222 (t80) cc_final: 0.7753 (t80) REVERT: C 12 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8623 (mtmt) REVERT: C 21 LEU cc_start: 0.8553 (mm) cc_final: 0.8052 (mp) REVERT: C 24 ASP cc_start: 0.8260 (m-30) cc_final: 0.7842 (m-30) REVERT: C 76 GLN cc_start: 0.7839 (mp10) cc_final: 0.7631 (mp10) REVERT: E 58 GLN cc_start: 0.7651 (tp40) cc_final: 0.7003 (tm-30) REVERT: G 24 GLN cc_start: 0.7710 (mt0) cc_final: 0.7392 (tp40) outliers start: 74 outliers final: 42 residues processed: 241 average time/residue: 0.3095 time to fit residues: 116.5745 Evaluate side-chains 199 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 156 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 64 HIS Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 137 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 83 ASN Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 172 ASP Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 145 optimal weight: 0.0050 chunk 58 optimal weight: 2.9990 chunk 213 optimal weight: 20.0000 chunk 230 optimal weight: 8.9990 chunk 190 optimal weight: 0.9990 chunk 212 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 171 optimal weight: 3.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 153 GLN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20014 Z= 0.201 Angle : 0.544 9.441 27267 Z= 0.282 Chirality : 0.043 0.182 3113 Planarity : 0.004 0.063 3317 Dihedral : 13.818 89.428 3059 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.42 % Allowed : 17.55 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2300 helix: 0.53 (0.21), residues: 655 sheet: -1.34 (0.22), residues: 511 loop : -2.33 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1053 HIS 0.003 0.001 HIS A 903 PHE 0.019 0.001 PHE C 84 TYR 0.013 0.001 TYR A1040 ARG 0.006 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 174 time to evaluate : 2.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8248 (mt) REVERT: F 199 MET cc_start: 0.4966 (tpp) cc_final: 0.3711 (tpt) REVERT: A 132 ASN cc_start: 0.8026 (t0) cc_final: 0.7681 (t0) REVERT: A 540 MET cc_start: 0.7440 (ttm) cc_final: 0.7192 (tpp) REVERT: A 841 ASP cc_start: 0.7570 (p0) cc_final: 0.7079 (t0) REVERT: A 908 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7321 (tm-30) REVERT: B 82 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8190 (tt) REVERT: B 358 LYS cc_start: 0.9036 (tptt) cc_final: 0.8831 (tptm) REVERT: C 8 PHE cc_start: 0.8142 (t80) cc_final: 0.7749 (t80) REVERT: C 12 LYS cc_start: 0.8994 (mtmt) cc_final: 0.8694 (mtmt) REVERT: C 21 LEU cc_start: 0.8511 (mm) cc_final: 0.7967 (mp) REVERT: C 24 ASP cc_start: 0.8290 (m-30) cc_final: 0.7802 (m-30) REVERT: C 76 GLN cc_start: 0.7837 (mp10) cc_final: 0.7577 (mp10) REVERT: E 58 GLN cc_start: 0.7707 (tp40) cc_final: 0.7088 (tm-30) REVERT: G 24 GLN cc_start: 0.7702 (mt0) cc_final: 0.7367 (tp40) REVERT: G 221 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7336 (mt) outliers start: 72 outliers final: 44 residues processed: 234 average time/residue: 0.3010 time to fit residues: 111.7890 Evaluate side-chains 208 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 161 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 651 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 448 VAL Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 221 LEU Chi-restraints excluded: chain G residue 225 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.7980 chunk 160 optimal weight: 0.0770 chunk 110 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 214 optimal weight: 0.0980 chunk 227 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 203 optimal weight: 0.2980 chunk 61 optimal weight: 6.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 ASN A 832 GLN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 407 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20014 Z= 0.139 Angle : 0.518 10.558 27267 Z= 0.268 Chirality : 0.042 0.192 3113 Planarity : 0.004 0.061 3317 Dihedral : 13.663 88.809 3054 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.00 % Allowed : 18.78 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.17), residues: 2300 helix: 0.94 (0.21), residues: 647 sheet: -1.10 (0.22), residues: 507 loop : -2.10 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.006 0.001 HIS C 27 PHE 0.016 0.001 PHE C 41 TYR 0.012 0.001 TYR B 109 ARG 0.006 0.000 ARG B 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 174 time to evaluate : 2.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8209 (mt) REVERT: F 120 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7319 (p0) REVERT: F 161 MET cc_start: 0.8713 (mpp) cc_final: 0.8479 (mpp) REVERT: F 199 MET cc_start: 0.5005 (tpp) cc_final: 0.3707 (tpt) REVERT: A 841 ASP cc_start: 0.7565 (p0) cc_final: 0.7349 (t0) REVERT: A 908 GLU cc_start: 0.7683 (tm-30) cc_final: 0.7289 (tm-30) REVERT: B 112 MET cc_start: 0.8510 (mpp) cc_final: 0.8106 (mtm) REVERT: B 358 LYS cc_start: 0.9008 (tptt) cc_final: 0.8798 (tptm) REVERT: C 21 LEU cc_start: 0.8518 (mm) cc_final: 0.7853 (mp) REVERT: C 24 ASP cc_start: 0.8212 (m-30) cc_final: 0.7715 (m-30) REVERT: C 76 GLN cc_start: 0.7863 (mp10) cc_final: 0.7355 (mp10) REVERT: E 14 ARG cc_start: 0.8123 (mpp80) cc_final: 0.7807 (mpp80) REVERT: E 58 GLN cc_start: 0.7691 (tp40) cc_final: 0.7054 (tm-30) REVERT: E 88 LEU cc_start: 0.4258 (OUTLIER) cc_final: 0.3715 (tt) REVERT: G 24 GLN cc_start: 0.7685 (mt0) cc_final: 0.7360 (tp40) REVERT: G 221 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7243 (mt) outliers start: 63 outliers final: 39 residues processed: 224 average time/residue: 0.3119 time to fit residues: 110.1180 Evaluate side-chains 198 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 155 time to evaluate : 2.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 83 ASN Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 615 SER Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 404 LYS Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 115 optimal weight: 0.2980 chunk 203 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN B 52 GLN B 407 ASN C 69 HIS G 190 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20014 Z= 0.167 Angle : 0.519 11.208 27267 Z= 0.269 Chirality : 0.042 0.154 3113 Planarity : 0.003 0.052 3317 Dihedral : 13.618 88.476 3047 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.42 % Allowed : 18.78 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2300 helix: 1.01 (0.21), residues: 647 sheet: -0.90 (0.23), residues: 497 loop : -2.03 (0.17), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS C 27 PHE 0.017 0.001 PHE C 41 TYR 0.021 0.001 TYR C 98 ARG 0.003 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 165 time to evaluate : 2.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8209 (mt) REVERT: F 120 ASP cc_start: 0.7951 (OUTLIER) cc_final: 0.7386 (p0) REVERT: F 161 MET cc_start: 0.8730 (mpp) cc_final: 0.8476 (mpp) REVERT: F 199 MET cc_start: 0.4981 (tpp) cc_final: 0.3650 (tpt) REVERT: A 132 ASN cc_start: 0.8058 (t0) cc_final: 0.7723 (t0) REVERT: A 841 ASP cc_start: 0.7559 (p0) cc_final: 0.7340 (t0) REVERT: A 908 GLU cc_start: 0.7687 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 112 MET cc_start: 0.8476 (mpp) cc_final: 0.8108 (mtm) REVERT: B 358 LYS cc_start: 0.9047 (tptt) cc_final: 0.8823 (tptp) REVERT: C 21 LEU cc_start: 0.8517 (mm) cc_final: 0.7828 (mp) REVERT: C 24 ASP cc_start: 0.8276 (m-30) cc_final: 0.7773 (m-30) REVERT: C 76 GLN cc_start: 0.7869 (mp10) cc_final: 0.7330 (mp10) REVERT: E 58 GLN cc_start: 0.7705 (tp40) cc_final: 0.7011 (tm-30) REVERT: E 88 LEU cc_start: 0.4300 (OUTLIER) cc_final: 0.3791 (tt) REVERT: G 24 GLN cc_start: 0.7718 (mt0) cc_final: 0.7389 (tp40) REVERT: G 80 ARG cc_start: 0.9084 (ptm160) cc_final: 0.8556 (ptm-80) REVERT: G 221 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7254 (mt) outliers start: 72 outliers final: 49 residues processed: 224 average time/residue: 0.3011 time to fit residues: 107.2812 Evaluate side-chains 205 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 152 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 407 ASN Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 133 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 227 optimal weight: 0.6980 chunk 188 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN F 201 GLN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20014 Z= 0.170 Angle : 0.527 9.214 27267 Z= 0.269 Chirality : 0.042 0.176 3113 Planarity : 0.003 0.046 3317 Dihedral : 13.610 88.395 3047 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.47 % Allowed : 19.59 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.17), residues: 2300 helix: 1.03 (0.21), residues: 647 sheet: -0.81 (0.22), residues: 507 loop : -1.95 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 PHE 0.026 0.001 PHE C 8 TYR 0.015 0.001 TYR C 98 ARG 0.003 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 162 time to evaluate : 2.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8674 (OUTLIER) cc_final: 0.8199 (mt) REVERT: F 120 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7357 (p0) REVERT: F 161 MET cc_start: 0.8729 (mpp) cc_final: 0.8469 (mpp) REVERT: F 199 MET cc_start: 0.5025 (tpp) cc_final: 0.3660 (tpt) REVERT: A 132 ASN cc_start: 0.8041 (t0) cc_final: 0.7665 (t0) REVERT: A 908 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 112 MET cc_start: 0.8481 (mpp) cc_final: 0.8125 (mtm) REVERT: B 234 GLU cc_start: 0.8131 (tp30) cc_final: 0.7789 (tm-30) REVERT: B 358 LYS cc_start: 0.9056 (tptt) cc_final: 0.8821 (tptp) REVERT: C 12 LYS cc_start: 0.9075 (mtmt) cc_final: 0.8713 (mttp) REVERT: C 21 LEU cc_start: 0.8526 (mm) cc_final: 0.7826 (mp) REVERT: C 24 ASP cc_start: 0.8225 (m-30) cc_final: 0.7701 (m-30) REVERT: C 76 GLN cc_start: 0.7899 (mp10) cc_final: 0.7342 (mp10) REVERT: E 58 GLN cc_start: 0.7635 (tp40) cc_final: 0.6935 (tm-30) REVERT: E 175 ILE cc_start: 0.5506 (OUTLIER) cc_final: 0.4909 (mm) REVERT: G 24 GLN cc_start: 0.7730 (mt0) cc_final: 0.7394 (tp40) REVERT: G 80 ARG cc_start: 0.9079 (ptm160) cc_final: 0.8563 (ptm-80) REVERT: G 221 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7251 (mt) outliers start: 73 outliers final: 54 residues processed: 225 average time/residue: 0.3091 time to fit residues: 111.5225 Evaluate side-chains 211 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 153 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 226 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 104 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20014 Z= 0.215 Angle : 0.544 8.935 27267 Z= 0.280 Chirality : 0.042 0.141 3113 Planarity : 0.003 0.043 3317 Dihedral : 13.675 88.788 3047 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.47 % Allowed : 20.02 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.17), residues: 2300 helix: 1.01 (0.21), residues: 648 sheet: -0.72 (0.23), residues: 516 loop : -1.88 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 PHE 0.021 0.001 PHE C 41 TYR 0.014 0.001 TYR A1040 ARG 0.002 0.000 ARG E 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 165 time to evaluate : 2.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8220 (mt) REVERT: F 120 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7395 (p0) REVERT: F 161 MET cc_start: 0.8726 (mpp) cc_final: 0.8446 (mpp) REVERT: F 199 MET cc_start: 0.4979 (tpp) cc_final: 0.3502 (tpt) REVERT: A 132 ASN cc_start: 0.8106 (t0) cc_final: 0.7710 (t0) REVERT: A 908 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 1089 GLU cc_start: 0.7263 (mm-30) cc_final: 0.7058 (mm-30) REVERT: B 112 MET cc_start: 0.8509 (mpp) cc_final: 0.8187 (mtm) REVERT: B 249 ASP cc_start: 0.5575 (t0) cc_final: 0.5283 (t0) REVERT: B 358 LYS cc_start: 0.9072 (tptt) cc_final: 0.8829 (tptp) REVERT: C 21 LEU cc_start: 0.8514 (mm) cc_final: 0.7812 (mp) REVERT: C 24 ASP cc_start: 0.8273 (m-30) cc_final: 0.7760 (m-30) REVERT: C 76 GLN cc_start: 0.7912 (mp10) cc_final: 0.7365 (mp10) REVERT: E 58 GLN cc_start: 0.7654 (tp40) cc_final: 0.6972 (tm-30) REVERT: E 164 LYS cc_start: 0.8143 (mmpt) cc_final: 0.7931 (mmpt) REVERT: G 24 GLN cc_start: 0.7773 (mt0) cc_final: 0.7430 (tp40) REVERT: G 80 ARG cc_start: 0.9086 (ptm160) cc_final: 0.8615 (ptm-80) REVERT: G 221 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7259 (mt) outliers start: 73 outliers final: 60 residues processed: 225 average time/residue: 0.3136 time to fit residues: 111.7170 Evaluate side-chains 216 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 153 time to evaluate : 2.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 188 MET Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.0470 chunk 90 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 144 optimal weight: 0.6980 chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 178 optimal weight: 4.9990 overall best weight: 0.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 HIS F 84 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20014 Z= 0.181 Angle : 0.537 8.510 27267 Z= 0.277 Chirality : 0.042 0.168 3113 Planarity : 0.003 0.046 3317 Dihedral : 13.653 88.833 3047 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.47 % Allowed : 20.40 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.17), residues: 2300 helix: 1.08 (0.21), residues: 646 sheet: -0.66 (0.23), residues: 518 loop : -1.83 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 PHE 0.038 0.001 PHE C 8 TYR 0.024 0.001 TYR C 98 ARG 0.003 0.000 ARG E 14 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 161 time to evaluate : 2.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8212 (mt) REVERT: F 120 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7361 (p0) REVERT: F 161 MET cc_start: 0.8736 (mpp) cc_final: 0.8453 (mpp) REVERT: F 199 MET cc_start: 0.4946 (tpp) cc_final: 0.3467 (tpt) REVERT: A 908 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7294 (tm-30) REVERT: B 112 MET cc_start: 0.8461 (mpp) cc_final: 0.8136 (mtm) REVERT: B 358 LYS cc_start: 0.9066 (tptt) cc_final: 0.8804 (tptp) REVERT: C 21 LEU cc_start: 0.8540 (mm) cc_final: 0.7851 (mp) REVERT: C 24 ASP cc_start: 0.8209 (m-30) cc_final: 0.7693 (m-30) REVERT: C 76 GLN cc_start: 0.7916 (mp10) cc_final: 0.7369 (mp10) REVERT: E 58 GLN cc_start: 0.7648 (tp40) cc_final: 0.6976 (tm-30) REVERT: E 164 LYS cc_start: 0.8162 (mmpt) cc_final: 0.7945 (mmpt) REVERT: G 24 GLN cc_start: 0.7780 (mt0) cc_final: 0.7440 (tp40) REVERT: G 80 ARG cc_start: 0.9104 (ptm160) cc_final: 0.8635 (ptm-80) REVERT: G 221 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.7232 (mt) outliers start: 73 outliers final: 59 residues processed: 220 average time/residue: 0.3053 time to fit residues: 105.8789 Evaluate side-chains 215 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 153 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 783 THR Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 36 ILE Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 203 VAL Chi-restraints excluded: chain G residue 221 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 9.9990 chunk 216 optimal weight: 7.9990 chunk 197 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 91 optimal weight: 0.0970 chunk 165 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 190 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 210 optimal weight: 5.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20014 Z= 0.159 Angle : 0.531 8.579 27267 Z= 0.274 Chirality : 0.042 0.162 3113 Planarity : 0.003 0.060 3317 Dihedral : 13.576 88.554 3047 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.00 % Allowed : 20.83 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2300 helix: 1.17 (0.21), residues: 645 sheet: -0.57 (0.23), residues: 526 loop : -1.79 (0.18), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.004 0.001 HIS G 190 PHE 0.040 0.001 PHE C 8 TYR 0.018 0.001 TYR C 98 ARG 0.004 0.000 ARG A1017 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 163 time to evaluate : 2.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8657 (OUTLIER) cc_final: 0.8212 (mt) REVERT: F 120 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7287 (p0) REVERT: F 161 MET cc_start: 0.8721 (mpp) cc_final: 0.8444 (mpp) REVERT: F 199 MET cc_start: 0.4960 (tpp) cc_final: 0.3401 (tpt) REVERT: A 908 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7286 (tm-30) REVERT: B 112 MET cc_start: 0.8408 (mpp) cc_final: 0.8114 (mtm) REVERT: B 234 GLU cc_start: 0.8081 (tp30) cc_final: 0.7732 (tm-30) REVERT: B 358 LYS cc_start: 0.9043 (tptt) cc_final: 0.8781 (tptp) REVERT: B 403 MET cc_start: 0.7712 (mmt) cc_final: 0.7400 (mmt) REVERT: C 21 LEU cc_start: 0.8540 (mm) cc_final: 0.7846 (mp) REVERT: C 24 ASP cc_start: 0.8192 (m-30) cc_final: 0.7706 (m-30) REVERT: C 76 GLN cc_start: 0.7906 (mp10) cc_final: 0.7350 (mp10) REVERT: E 58 GLN cc_start: 0.7612 (tp40) cc_final: 0.6944 (tm-30) REVERT: E 164 LYS cc_start: 0.8136 (mmpt) cc_final: 0.7905 (mmpt) REVERT: E 190 HIS cc_start: 0.7464 (m90) cc_final: 0.7070 (m170) REVERT: G 24 GLN cc_start: 0.7854 (mt0) cc_final: 0.7449 (tp40) REVERT: G 80 ARG cc_start: 0.9139 (ptm160) cc_final: 0.8592 (ptt-90) outliers start: 63 outliers final: 55 residues processed: 215 average time/residue: 0.3085 time to fit residues: 104.7824 Evaluate side-chains 213 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 156 time to evaluate : 2.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 16 ASP Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 0.7980 chunk 223 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 155 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 144 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN F 201 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 85 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20014 Z= 0.187 Angle : 0.542 8.481 27267 Z= 0.279 Chirality : 0.042 0.172 3113 Planarity : 0.004 0.059 3317 Dihedral : 13.600 88.557 3047 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.81 % Allowed : 21.07 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.18), residues: 2300 helix: 1.17 (0.21), residues: 645 sheet: -0.56 (0.23), residues: 528 loop : -1.77 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 103 HIS 0.003 0.001 HIS E 64 PHE 0.039 0.001 PHE C 8 TYR 0.019 0.001 TYR C 98 ARG 0.014 0.000 ARG E 14 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4600 Ramachandran restraints generated. 2300 Oldfield, 0 Emsley, 2300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 157 time to evaluate : 2.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 15 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8210 (mt) REVERT: F 199 MET cc_start: 0.4944 (tpp) cc_final: 0.3300 (tpt) REVERT: A 908 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7284 (tm-30) REVERT: A 1089 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6984 (mm-30) REVERT: B 112 MET cc_start: 0.8450 (mpp) cc_final: 0.8202 (mtm) REVERT: B 234 GLU cc_start: 0.8092 (tp30) cc_final: 0.7727 (tm-30) REVERT: B 358 LYS cc_start: 0.9053 (tptt) cc_final: 0.8785 (tptp) REVERT: B 403 MET cc_start: 0.7750 (mmt) cc_final: 0.7422 (mmt) REVERT: C 21 LEU cc_start: 0.8512 (mm) cc_final: 0.7972 (mp) REVERT: C 24 ASP cc_start: 0.8210 (m-30) cc_final: 0.7779 (m-30) REVERT: C 76 GLN cc_start: 0.7919 (mp10) cc_final: 0.7367 (mp10) REVERT: E 58 GLN cc_start: 0.7650 (tp40) cc_final: 0.6933 (tm-30) REVERT: E 164 LYS cc_start: 0.8159 (mmpt) cc_final: 0.7931 (mmpt) REVERT: E 188 MET cc_start: 0.3601 (ppp) cc_final: -0.0216 (mtt) REVERT: G 24 GLN cc_start: 0.7884 (mt0) cc_final: 0.7461 (tp40) REVERT: G 80 ARG cc_start: 0.9132 (ptm160) cc_final: 0.8578 (ptt-90) outliers start: 59 outliers final: 54 residues processed: 206 average time/residue: 0.3042 time to fit residues: 99.7729 Evaluate side-chains 207 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 152 time to evaluate : 2.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 15 ILE Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 166 THR Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 223 ASP Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 379 GLU Chi-restraints excluded: chain A residue 422 ASP Chi-restraints excluded: chain A residue 558 ILE Chi-restraints excluded: chain A residue 654 VAL Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 810 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 210 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 391 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 398 LEU Chi-restraints excluded: chain B residue 416 LEU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 461 VAL Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 7 TYR Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 97 TYR Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 12 PHE Chi-restraints excluded: chain E residue 70 MET Chi-restraints excluded: chain E residue 156 ASP Chi-restraints excluded: chain E residue 163 THR Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 186 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 64 HIS F 84 ASN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 ASN A 798 ASN ** A 832 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 190 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.100526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.076965 restraints weight = 58139.765| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.67 r_work: 0.3260 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20014 Z= 0.288 Angle : 0.597 8.717 27267 Z= 0.306 Chirality : 0.044 0.188 3113 Planarity : 0.004 0.055 3317 Dihedral : 13.826 89.643 3047 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 3.00 % Allowed : 21.21 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2300 helix: 0.97 (0.21), residues: 647 sheet: -0.71 (0.23), residues: 535 loop : -1.76 (0.18), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 103 HIS 0.004 0.001 HIS A 903 PHE 0.039 0.001 PHE C 8 TYR 0.019 0.002 TYR C 98 ARG 0.013 0.000 ARG E 14 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3986.43 seconds wall clock time: 74 minutes 16.96 seconds (4456.96 seconds total)