Starting phenix.real_space_refine on Fri Nov 17 14:55:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_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_22803/11_2023/7kc0_22803_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_22803_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kc0_22803/11_2023/7kc0_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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 10.66, per 1000 atoms: 0.55 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: 8.56 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: 9.11 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: 8.26 Time building geometry restraints manager: 9.07 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: 11347 28.14 - 56.27: 599 56.27 - 84.41: 45 84.41 - 112.55: 7 112.55 - 140.68: 1 Dihedral angle restraints: 11999 sinusoidal: 5163 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 11996 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: 4.420 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: 0.030 Extract box with map and model: 16.090 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 65.900 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.760 ------------------------------------------------------------------------------- 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 : 15.940 140.682 7566 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 *********************** 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 : 2.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 29 residues processed: 301 average time/residue: 0.3785 time to fit residues: 169.3524 Evaluate side-chains 190 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 2.294 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1819 time to fit residues: 13.1275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 137 optimal weight: 1.9990 chunk 213 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 G 27 ASN G 153 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20014 Z= 0.268 Angle : 0.593 9.550 27267 Z= 0.308 Chirality : 0.044 0.198 3113 Planarity : 0.004 0.040 3317 Dihedral : 13.407 89.711 2966 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.47 % Allowed : 17.69 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.16), residues: 2300 helix: 0.02 (0.20), residues: 654 sheet: -1.67 (0.22), residues: 500 loop : -2.57 (0.17), residues: 1146 *********************** 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 222 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 170 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 213 average time/residue: 0.3115 time to fit residues: 104.3083 Evaluate side-chains 174 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 2.315 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1980 time to fit residues: 11.3022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 145 optimal weight: 0.0020 chunk 58 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 230 optimal weight: 7.9990 chunk 190 optimal weight: 0.8980 chunk 212 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20014 Z= 0.202 Angle : 0.547 9.725 27267 Z= 0.285 Chirality : 0.043 0.184 3113 Planarity : 0.004 0.065 3317 Dihedral : 13.421 89.766 2966 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.09 % Allowed : 18.74 % Favored : 79.17 % 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: -1.91 (0.17), residues: 2300 helix: 0.51 (0.21), residues: 652 sheet: -1.40 (0.22), residues: 516 loop : -2.34 (0.17), residues: 1132 *********************** 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 218 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 174 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 212 average time/residue: 0.3248 time to fit residues: 108.4945 Evaluate side-chains 167 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 149 time to evaluate : 2.312 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1858 time to fit residues: 9.4334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 211 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 143 optimal weight: 5.9990 chunk 214 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 203 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 83 ASN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN C 27 HIS C 69 HIS E 153 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 20014 Z= 0.350 Angle : 0.627 11.616 27267 Z= 0.322 Chirality : 0.045 0.176 3113 Planarity : 0.004 0.064 3317 Dihedral : 13.644 89.373 2966 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.52 % Allowed : 19.31 % Favored : 78.17 % 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: -1.79 (0.17), residues: 2300 helix: 0.46 (0.20), residues: 647 sheet: -1.22 (0.22), residues: 491 loop : -2.19 (0.17), residues: 1162 *********************** 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 207 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 154 time to evaluate : 2.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 32 residues processed: 200 average time/residue: 0.3217 time to fit residues: 101.2923 Evaluate side-chains 169 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 2.283 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.1979 time to fit residues: 14.6304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 189 optimal weight: 9.9990 chunk 128 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 203 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20014 Z= 0.186 Angle : 0.561 10.652 27267 Z= 0.287 Chirality : 0.043 0.195 3113 Planarity : 0.004 0.061 3317 Dihedral : 13.541 89.544 2966 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.43 % Allowed : 21.16 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2300 helix: 0.73 (0.21), residues: 644 sheet: -1.10 (0.22), residues: 521 loop : -2.06 (0.18), residues: 1135 *********************** 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 190 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 160 time to evaluate : 2.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 187 average time/residue: 0.3268 time to fit residues: 96.2274 Evaluate side-chains 160 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 2.343 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1901 time to fit residues: 7.7045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 76 optimal weight: 0.7980 chunk 204 optimal weight: 20.0000 chunk 44 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 56 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 119 optimal weight: 0.0170 overall best weight: 0.8022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 964 ASN E 190 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20014 Z= 0.174 Angle : 0.538 9.360 27267 Z= 0.278 Chirality : 0.042 0.158 3113 Planarity : 0.004 0.050 3317 Dihedral : 13.418 89.838 2966 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.09 % Allowed : 21.64 % Favored : 77.27 % 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: -1.33 (0.17), residues: 2300 helix: 0.92 (0.21), residues: 643 sheet: -0.95 (0.22), residues: 513 loop : -1.95 (0.18), residues: 1144 *********************** 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 181 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 2.448 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 172 average time/residue: 0.3200 time to fit residues: 85.9330 Evaluate side-chains 151 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1659 time to fit residues: 5.9997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 219 optimal weight: 20.0000 chunk 25 optimal weight: 4.9990 chunk 129 optimal weight: 8.9990 chunk 166 optimal weight: 0.8980 chunk 128 optimal weight: 0.9990 chunk 191 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 226 optimal weight: 0.0370 chunk 141 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 201 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 20014 Z= 0.192 Angle : 0.549 9.240 27267 Z= 0.283 Chirality : 0.042 0.170 3113 Planarity : 0.004 0.047 3317 Dihedral : 13.405 89.867 2966 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.14 % Allowed : 22.06 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.17), residues: 2300 helix: 0.94 (0.21), residues: 644 sheet: -0.92 (0.22), residues: 517 loop : -1.88 (0.18), residues: 1139 *********************** 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 174 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 2.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 11 residues processed: 173 average time/residue: 0.3189 time to fit residues: 87.9558 Evaluate side-chains 154 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 143 time to evaluate : 2.174 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1811 time to fit residues: 6.6599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 140 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 68 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 144 optimal weight: 2.9990 chunk 154 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 20014 Z= 0.274 Angle : 0.582 9.202 27267 Z= 0.299 Chirality : 0.043 0.165 3113 Planarity : 0.004 0.050 3317 Dihedral : 13.504 89.841 2966 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.95 % Allowed : 22.06 % Favored : 76.99 % 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: -1.25 (0.17), residues: 2300 helix: 0.85 (0.21), residues: 645 sheet: -0.83 (0.23), residues: 514 loop : -1.85 (0.18), residues: 1141 *********************** 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 168 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 148 time to evaluate : 2.302 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 9 residues processed: 164 average time/residue: 0.3204 time to fit residues: 82.8529 Evaluate side-chains 152 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 2.216 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1811 time to fit residues: 6.0672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 206 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 211 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 165 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 190 optimal weight: 3.9990 chunk 199 optimal weight: 6.9990 chunk 210 optimal weight: 5.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20014 Z= 0.318 Angle : 0.614 9.025 27267 Z= 0.316 Chirality : 0.044 0.177 3113 Planarity : 0.004 0.069 3317 Dihedral : 13.623 89.294 2966 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.33 % Allowed : 22.73 % 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: -1.27 (0.17), residues: 2300 helix: 0.77 (0.21), residues: 645 sheet: -0.86 (0.22), residues: 517 loop : -1.81 (0.18), residues: 1138 *********************** 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 150 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 143 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 0.3323 time to fit residues: 77.4781 Evaluate side-chains 143 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 139 time to evaluate : 2.362 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1857 time to fit residues: 4.5392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 138 optimal weight: 4.9990 chunk 223 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 234 optimal weight: 6.9990 chunk 215 optimal weight: 0.0270 chunk 186 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- 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 A 798 ASN ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN E 190 HIS ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20014 Z= 0.245 Angle : 0.587 12.609 27267 Z= 0.301 Chirality : 0.043 0.160 3113 Planarity : 0.004 0.063 3317 Dihedral : 13.570 89.192 2966 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 0.19 % Allowed : 23.11 % Favored : 76.70 % 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: -1.19 (0.17), residues: 2300 helix: 0.84 (0.21), residues: 647 sheet: -0.85 (0.22), residues: 533 loop : -1.76 (0.18), residues: 1120 ********************** 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 151 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 147 time to evaluate : 2.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 149 average time/residue: 0.3240 time to fit residues: 75.5180 Evaluate side-chains 145 residues out of total 2104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 2.273 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1739 time to fit residues: 3.9865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 235 random chunks: chunk 148 optimal weight: 0.9990 chunk 198 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 191 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 84 ASN A 184 ASN ** A 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 948 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN ** E 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.099491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.075946 restraints weight = 57965.298| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.66 r_work: 0.3238 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 20014 Z= 0.360 Angle : 0.652 12.504 27267 Z= 0.333 Chirality : 0.045 0.189 3113 Planarity : 0.004 0.061 3317 Dihedral : 13.724 88.868 2966 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 0.33 % Allowed : 23.25 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.17), residues: 2300 helix: 0.66 (0.20), residues: 647 sheet: -0.96 (0.22), residues: 521 loop : -1.79 (0.18), residues: 1132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3890.92 seconds wall clock time: 75 minutes 20.69 seconds (4520.69 seconds total)