Starting phenix.real_space_refine on Sat Feb 17 09:34:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/02_2024/6rwl_10041.pdb" } resolution = 3.36 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= 0.003 sd= 0.231 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 S 74 5.16 5 C 11312 2.51 5 N 3272 2.21 5 O 3522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18272 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2137 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "B" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2014 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "C" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1518 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1641 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "F" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "M" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "S" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "I" Number of atoms: 2137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2137 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 9, 'TRANS': 260} Chain: "J" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2014 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 7, 'TRANS': 244} Chain breaks: 2 Chain: "K" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1518 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 5, 'TRANS': 187} Chain breaks: 2 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1641 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Chain: "N" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 566 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "E" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 378 Classifications: {'peptide': 47} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 44} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "W" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "Q" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 470 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.913 61.881 30.254 1.00 37.53 S ATOM 357 SG CYS A 43 76.936 63.929 31.771 1.00 39.56 S ATOM 2468 SG CYS B 40 71.030 143.477 58.094 1.00 80.15 S ATOM 2490 SG CYS B 43 73.569 141.955 55.534 1.00 83.44 S ATOM 4455 SG CYS C 40 106.176 126.370 21.472 1.00107.25 S ATOM 4477 SG CYS C 43 104.083 128.815 23.704 1.00103.88 S ATOM 8211 SG CYS M 40 37.069 132.725 53.118 1.00 65.37 S ATOM 8233 SG CYS M 43 34.765 130.442 55.342 1.00 72.88 S ATOM 9467 SG CYS I 40 49.756 112.020 30.316 1.00 38.67 S ATOM 9489 SG CYS I 43 52.734 109.975 31.835 1.00 41.63 S ATOM 11600 SG CYS J 40 58.347 30.545 58.243 1.00 79.04 S ATOM 11622 SG CYS J 43 55.847 32.108 55.669 1.00 84.64 S ATOM 13587 SG CYS K 40 23.777 47.848 21.442 1.00102.18 S ATOM 13609 SG CYS K 43 25.862 45.375 23.651 1.00 98.27 S ATOM 17343 SG CYS E 40 92.671 41.176 53.291 1.00 65.46 S ATOM 17365 SG CYS E 43 94.963 43.473 55.514 1.00 73.36 S Time building chain proxies: 9.58, per 1000 atoms: 0.52 Number of scatterers: 18272 At special positions: 0 Unit cell: (131.1, 175.26, 97.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 8 29.99 S 74 16.00 P 84 15.00 O 3522 8.00 N 3272 7.00 C 11312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.47 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 500 " - pdb=" SG CYS B 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb=" ZN E 500 " pdb="ZN ZN E 500 " - pdb=" ND1 HIS E 16 " pdb="ZN ZN E 500 " - pdb=" NE2 HIS E 12 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 43 " pdb="ZN ZN E 500 " - pdb=" SG CYS E 40 " pdb=" ZN I 500 " pdb="ZN ZN I 500 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 500 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 43 " pdb="ZN ZN I 500 " - pdb=" SG CYS I 40 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 43 " pdb="ZN ZN J 500 " - pdb=" SG CYS J 40 " pdb=" ZN K 500 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " pdb="ZN ZN K 500 " - pdb=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 40 " pdb="ZN ZN K 500 " - pdb=" SG CYS K 43 " pdb=" ZN M 500 " pdb="ZN ZN M 500 " - pdb=" ND1 HIS M 16 " pdb="ZN ZN M 500 " - pdb=" NE2 HIS M 12 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 43 " pdb="ZN ZN M 500 " - pdb=" SG CYS M 40 " Number of angles added : 14 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3864 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 16 sheets defined 49.5% alpha, 19.2% beta 30 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 26 removed outlier: 3.640A pdb=" N MET A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 93 through 108 removed outlier: 4.091A pdb=" N THR A 97 " --> pdb=" O THR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 134 Processing helix chain 'A' and resid 148 through 165 removed outlier: 3.735A pdb=" N GLU A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 169 removed outlier: 3.541A pdb=" N ALA A 169 " --> pdb=" O ARG A 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 166 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 4.018A pdb=" N ALA A 175 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 219 Processing helix chain 'B' and resid 2 through 16 Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.544A pdb=" N MET B 22 " --> pdb=" O ASN B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 39 Processing helix chain 'B' and resid 93 through 108 removed outlier: 3.751A pdb=" N THR B 97 " --> pdb=" O THR B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 134 Processing helix chain 'B' and resid 151 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 171 through 186 removed outlier: 4.156A pdb=" N ALA B 175 " --> pdb=" O LYS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 221 removed outlier: 3.649A pdb=" N ARG B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 27 Processing helix chain 'C' and resid 29 through 39 removed outlier: 3.619A pdb=" N ALA C 33 " --> pdb=" O PRO C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 108 removed outlier: 4.033A pdb=" N THR C 97 " --> pdb=" O THR C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 123 through 134 Processing helix chain 'C' and resid 150 through 165 Processing helix chain 'C' and resid 166 through 169 removed outlier: 3.609A pdb=" N ALA C 169 " --> pdb=" O ARG C 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.690A pdb=" N ALA C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 217 Processing helix chain 'D' and resid 93 through 108 removed outlier: 3.638A pdb=" N THR D 97 " --> pdb=" O THR D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 133 Processing helix chain 'D' and resid 151 through 165 Processing helix chain 'D' and resid 166 through 169 Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 195 through 221 removed outlier: 3.629A pdb=" N ARG D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 221 removed outlier: 4.291A pdb=" N GLN F 221 " --> pdb=" O ILE F 217 " (cutoff:3.500A) Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 29 through 40 removed outlier: 3.772A pdb=" N CYS M 40 " --> pdb=" O ILE M 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 26 removed outlier: 3.640A pdb=" N MET I 22 " --> pdb=" O ASN I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 39 Processing helix chain 'I' and resid 93 through 108 removed outlier: 4.091A pdb=" N THR I 97 " --> pdb=" O THR I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 134 Processing helix chain 'I' and resid 148 through 165 removed outlier: 3.735A pdb=" N GLU I 152 " --> pdb=" O GLN I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 166 through 169 removed outlier: 3.542A pdb=" N ALA I 169 " --> pdb=" O ARG I 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 166 through 169' Processing helix chain 'I' and resid 171 through 186 removed outlier: 4.017A pdb=" N ALA I 175 " --> pdb=" O LYS I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 219 Processing helix chain 'J' and resid 2 through 16 Processing helix chain 'J' and resid 18 through 26 removed outlier: 3.544A pdb=" N MET J 22 " --> pdb=" O ASN J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 39 Processing helix chain 'J' and resid 93 through 108 removed outlier: 3.751A pdb=" N THR J 97 " --> pdb=" O THR J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 123 through 134 Processing helix chain 'J' and resid 151 through 165 Processing helix chain 'J' and resid 166 through 169 Processing helix chain 'J' and resid 171 through 186 removed outlier: 4.157A pdb=" N ALA J 175 " --> pdb=" O LYS J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 221 removed outlier: 3.649A pdb=" N ARG J 199 " --> pdb=" O SER J 195 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 27 Processing helix chain 'K' and resid 29 through 39 removed outlier: 3.620A pdb=" N ALA K 33 " --> pdb=" O PRO K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 108 removed outlier: 4.034A pdb=" N THR K 97 " --> pdb=" O THR K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 134 Processing helix chain 'K' and resid 150 through 165 Processing helix chain 'K' and resid 166 through 169 removed outlier: 3.610A pdb=" N ALA K 169 " --> pdb=" O ARG K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 169' Processing helix chain 'K' and resid 171 through 186 removed outlier: 3.690A pdb=" N ALA K 175 " --> pdb=" O LYS K 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 195 through 217 Processing helix chain 'L' and resid 93 through 108 removed outlier: 3.638A pdb=" N THR L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 151 through 165 Processing helix chain 'L' and resid 166 through 169 Processing helix chain 'L' and resid 172 through 186 Processing helix chain 'L' and resid 195 through 221 removed outlier: 3.629A pdb=" N ARG L 199 " --> pdb=" O SER L 195 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 204 through 221 removed outlier: 4.291A pdb=" N GLN N 221 " --> pdb=" O ILE N 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 26 Processing helix chain 'E' and resid 29 through 40 removed outlier: 3.772A pdb=" N CYS E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.248A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 261 removed outlier: 7.325A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A 250 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.225A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 256 through 261 removed outlier: 7.344A pdb=" N ALA B 248 " --> pdb=" O LYS B 244 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS B 244 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL B 250 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU B 241 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE B 223 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 89 removed outlier: 3.845A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP C 61 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.100A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASP D 116 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N CYS D 65 " --> pdb=" O ASP D 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.962A pdb=" N ALA D 248 " --> pdb=" O LYS D 244 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYS D 244 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL D 250 " --> pdb=" O ILE D 242 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 257 through 261 removed outlier: 7.366A pdb=" N ALA F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS F 244 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL F 250 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE F 227 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL F 225 " --> pdb=" O PRO F 238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.247A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 257 through 261 removed outlier: 7.325A pdb=" N ALA I 248 " --> pdb=" O LYS I 244 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N LYS I 244 " --> pdb=" O ALA I 248 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL I 250 " --> pdb=" O ILE I 242 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.225A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TRP J 61 " --> pdb=" O HIS J 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 256 through 261 removed outlier: 7.344A pdb=" N ALA J 248 " --> pdb=" O LYS J 244 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS J 244 " --> pdb=" O ALA J 248 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL J 250 " --> pdb=" O ILE J 242 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU J 241 " --> pdb=" O PHE J 223 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N PHE J 223 " --> pdb=" O LEU J 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 83 through 89 removed outlier: 3.845A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP K 61 " --> pdb=" O HIS K 114 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N LEU K 113 " --> pdb=" O THR K 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.101A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ASP L 116 " --> pdb=" O MET L 63 " (cutoff:3.500A) removed outlier: 9.295A pdb=" N CYS L 65 " --> pdb=" O ASP L 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 257 through 261 removed outlier: 6.961A pdb=" N ALA L 248 " --> pdb=" O LYS L 244 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N LYS L 244 " --> pdb=" O ALA L 248 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL L 250 " --> pdb=" O ILE L 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 257 through 261 removed outlier: 7.366A pdb=" N ALA N 248 " --> pdb=" O LYS N 244 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LYS N 244 " --> pdb=" O ALA N 248 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL N 250 " --> pdb=" O ILE N 242 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N PHE N 227 " --> pdb=" O LYS N 236 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL N 225 " --> pdb=" O PRO N 238 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 74 hydrogen bonds 148 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 5.85 Time building geometry restraints manager: 7.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4519 1.33 - 1.45: 3922 1.45 - 1.57: 10095 1.57 - 1.69: 166 1.69 - 1.81: 108 Bond restraints: 18810 Sorted by residual: bond pdb=" C SER I 57 " pdb=" N PRO I 58 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.64e+00 bond pdb=" C SER A 57 " pdb=" N PRO A 58 " ideal model delta sigma weight residual 1.335 1.353 -0.018 9.40e-03 1.13e+04 3.62e+00 bond pdb=" C TRP A 108 " pdb=" N PRO A 109 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.91e+00 bond pdb=" C TRP I 108 " pdb=" N PRO I 109 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.01e-02 9.80e+03 1.86e+00 bond pdb=" C TRP K 108 " pdb=" N PRO K 109 " ideal model delta sigma weight residual 1.333 1.346 -0.012 1.01e-02 9.80e+03 1.45e+00 ... (remaining 18805 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.88: 976 106.88 - 113.67: 10511 113.67 - 120.46: 7232 120.46 - 127.24: 6668 127.24 - 134.03: 389 Bond angle restraints: 25776 Sorted by residual: angle pdb=" N LYS D 111 " pdb=" CA LYS D 111 " pdb=" C LYS D 111 " ideal model delta sigma weight residual 114.31 110.80 3.51 1.29e+00 6.01e-01 7.39e+00 angle pdb=" N LYS L 111 " pdb=" CA LYS L 111 " pdb=" C LYS L 111 " ideal model delta sigma weight residual 114.31 110.85 3.46 1.29e+00 6.01e-01 7.19e+00 angle pdb=" N VAL A 45 " pdb=" CA VAL A 45 " pdb=" C VAL A 45 " ideal model delta sigma weight residual 106.42 109.96 -3.54 1.51e+00 4.39e-01 5.50e+00 angle pdb=" N VAL I 45 " pdb=" CA VAL I 45 " pdb=" C VAL I 45 " ideal model delta sigma weight residual 106.42 109.92 -3.50 1.51e+00 4.39e-01 5.36e+00 angle pdb=" C GLY F 254 " pdb=" N GLN F 255 " pdb=" CA GLN F 255 " ideal model delta sigma weight residual 122.07 125.33 -3.26 1.43e+00 4.89e-01 5.19e+00 ... (remaining 25771 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.69: 9666 16.69 - 33.38: 824 33.38 - 50.07: 412 50.07 - 66.76: 120 66.76 - 83.45: 10 Dihedral angle restraints: 11032 sinusoidal: 5074 harmonic: 5958 Sorted by residual: dihedral pdb=" CA ILE N 220 " pdb=" C ILE N 220 " pdb=" N GLN N 221 " pdb=" CA GLN N 221 " ideal model delta harmonic sigma weight residual -180.00 -161.45 -18.55 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA ILE F 220 " pdb=" C ILE F 220 " pdb=" N GLN F 221 " pdb=" CA GLN F 221 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL D 77 " pdb=" C VAL D 77 " pdb=" N HIS D 78 " pdb=" CA HIS D 78 " ideal model delta harmonic sigma weight residual 180.00 161.82 18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 11029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1731 0.032 - 0.065: 762 0.065 - 0.097: 207 0.097 - 0.129: 121 0.129 - 0.161: 25 Chirality restraints: 2846 Sorted by residual: chirality pdb=" CB VAL I 151 " pdb=" CA VAL I 151 " pdb=" CG1 VAL I 151 " pdb=" CG2 VAL I 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CB VAL A 151 " pdb=" CA VAL A 151 " pdb=" CG1 VAL A 151 " pdb=" CG2 VAL A 151 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA ILE M 28 " pdb=" N ILE M 28 " pdb=" C ILE M 28 " pdb=" CB ILE M 28 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.84e-01 ... (remaining 2843 not shown) Planarity restraints: 3002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL J 260 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO J 261 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO J 261 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO J 261 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 260 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO B 261 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 260 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO L 261 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 261 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 261 " -0.023 5.00e-02 4.00e+02 ... (remaining 2999 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5777 2.86 - 3.37: 14633 3.37 - 3.88: 28624 3.88 - 4.39: 31916 4.39 - 4.90: 55735 Nonbonded interactions: 136685 Sorted by model distance: nonbonded pdb=" O TRP B 132 " pdb=" OH TYR I 15 " model vdw 2.348 2.440 nonbonded pdb=" NH1 ARG K 107 " pdb=" OE1 GLN L 177 " model vdw 2.366 2.520 nonbonded pdb=" N ASN I 17 " pdb=" OD1 ASN I 17 " model vdw 2.377 2.520 nonbonded pdb=" N ASN A 17 " pdb=" OD1 ASN A 17 " model vdw 2.378 2.520 nonbonded pdb=" OD1 ASP I 207 " pdb=" NZ LYS L 244 " model vdw 2.391 2.520 ... (remaining 136680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 44 or resid 57 through 141 or resid 151 through \ 269 or resid 500)) selection = (chain 'B' and (resid 1 through 269 or resid 500)) selection = (chain 'I' and (resid 1 through 44 or resid 57 through 141 or resid 151 through \ 269 or resid 500)) selection = (chain 'J' and (resid 1 through 269 or resid 500)) } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = chain 'F' selection = chain 'N' } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'T' selection = chain 'W' } 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: 2.430 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: 11.070 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 53.190 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.160 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.003 0.031 18810 Z= 0.180 Angle : 0.558 4.302 25776 Z= 0.348 Chirality : 0.044 0.161 2846 Planarity : 0.005 0.044 3002 Dihedral : 16.129 83.447 7168 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.86 % Allowed : 4.12 % Favored : 93.02 % 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: -3.04 (0.15), residues: 2032 helix: -1.93 (0.11), residues: 950 sheet: -0.14 (0.23), residues: 450 loop : -3.35 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 19 HIS 0.005 0.001 HIS M 12 PHE 0.013 0.001 PHE L 227 TYR 0.010 0.001 TYR J 83 ARG 0.002 0.000 ARG I 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 440 time to evaluate : 2.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8140 (m-40) REVERT: A 18 ASN cc_start: 0.8903 (p0) cc_final: 0.8552 (p0) REVERT: A 35 GLU cc_start: 0.7558 (tp30) cc_final: 0.7288 (tp30) REVERT: A 42 LYS cc_start: 0.8726 (mmmt) cc_final: 0.8515 (mmtp) REVERT: A 63 MET cc_start: 0.8377 (ttm) cc_final: 0.8122 (mtp) REVERT: A 107 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7690 (mpt180) REVERT: B 63 MET cc_start: 0.8165 (mmm) cc_final: 0.7924 (ttm) REVERT: B 256 ASP cc_start: 0.6967 (t0) cc_final: 0.6181 (m-30) REVERT: B 267 ILE cc_start: 0.8956 (mp) cc_final: 0.8658 (mt) REVERT: B 270 ASP cc_start: 0.7441 (t70) cc_final: 0.7057 (t0) REVERT: C 155 ASN cc_start: 0.7781 (m-40) cc_final: 0.7457 (t0) REVERT: C 178 MET cc_start: 0.8460 (mtm) cc_final: 0.8226 (mtp) REVERT: D 154 MET cc_start: 0.7137 (mmt) cc_final: 0.6368 (mmt) REVERT: D 215 ASN cc_start: 0.8449 (t0) cc_final: 0.8201 (t0) REVERT: D 268 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7817 (mm) REVERT: F 246 GLU cc_start: 0.7665 (pp20) cc_final: 0.7350 (pp20) REVERT: F 271 TYR cc_start: 0.7330 (t80) cc_final: 0.7043 (t80) REVERT: M 17 ASN cc_start: 0.8843 (m-40) cc_final: 0.8638 (m-40) REVERT: M 34 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8302 (mtpt) REVERT: I 17 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8370 (m-40) REVERT: I 18 ASN cc_start: 0.8766 (p0) cc_final: 0.8414 (p0) REVERT: I 22 MET cc_start: 0.8612 (mtm) cc_final: 0.8330 (mtm) REVERT: I 35 GLU cc_start: 0.7626 (tp30) cc_final: 0.7413 (tp30) REVERT: I 63 MET cc_start: 0.8416 (ttm) cc_final: 0.8162 (mtp) REVERT: I 107 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7478 (mpt180) REVERT: J 63 MET cc_start: 0.8145 (mmm) cc_final: 0.7867 (ttm) REVERT: J 267 ILE cc_start: 0.8842 (mp) cc_final: 0.8500 (mt) REVERT: K 115 THR cc_start: 0.6989 (OUTLIER) cc_final: 0.6624 (p) REVERT: K 155 ASN cc_start: 0.8024 (m-40) cc_final: 0.7673 (t0) REVERT: K 194 TYR cc_start: 0.7596 (m-80) cc_final: 0.7360 (m-10) REVERT: L 88 VAL cc_start: 0.7678 (t) cc_final: 0.7255 (p) REVERT: L 154 MET cc_start: 0.7237 (mmt) cc_final: 0.6070 (mmt) REVERT: L 253 ASP cc_start: 0.7512 (t70) cc_final: 0.7260 (p0) REVERT: N 246 GLU cc_start: 0.7898 (pp20) cc_final: 0.7515 (pp20) REVERT: N 252 GLN cc_start: 0.8582 (OUTLIER) cc_final: 0.8291 (tt0) REVERT: E 15 TYR cc_start: 0.8004 (m-80) cc_final: 0.7793 (m-80) REVERT: E 34 LYS cc_start: 0.8853 (mtmt) cc_final: 0.8443 (mtpt) outliers start: 50 outliers final: 12 residues processed: 479 average time/residue: 0.3380 time to fit residues: 231.5179 Evaluate side-chains 301 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 282 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 148 GLN Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 3.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 0.3980 chunk 54 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 190 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 144 ASN A 148 GLN A 183 HIS B 44 GLN B 157 GLN B 183 HIS B 216 GLN C 216 GLN D 114 HIS D 214 GLN D 216 GLN D 222 ASN M 9 GLN M 17 ASN I 144 ASN I 148 GLN I 183 HIS J 44 GLN J 157 GLN J 183 HIS K 114 HIS ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 GLN L 214 GLN L 216 GLN L 222 ASN E 9 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18810 Z= 0.234 Angle : 0.501 8.552 25776 Z= 0.288 Chirality : 0.041 0.177 2846 Planarity : 0.004 0.042 3002 Dihedral : 18.652 81.937 3175 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.46 % Allowed : 11.38 % Favored : 86.16 % 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: -0.58 (0.18), residues: 2032 helix: 0.97 (0.16), residues: 958 sheet: 0.16 (0.24), residues: 446 loop : -3.00 (0.20), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 PHE 0.016 0.001 PHE K 121 TYR 0.011 0.001 TYR M 15 ARG 0.004 0.000 ARG D 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 299 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: A 42 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8565 (mmtp) REVERT: A 63 MET cc_start: 0.8442 (ttm) cc_final: 0.8171 (mtp) REVERT: A 107 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.6947 (mpt180) REVERT: B 63 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.7984 (ttm) REVERT: B 224 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7258 (tpp80) REVERT: B 256 ASP cc_start: 0.7014 (t0) cc_final: 0.5293 (m-30) REVERT: B 267 ILE cc_start: 0.8968 (mp) cc_final: 0.8617 (mt) REVERT: B 270 ASP cc_start: 0.7485 (t70) cc_final: 0.7257 (t70) REVERT: B 271 TYR cc_start: 0.8659 (m-80) cc_final: 0.7565 (m-80) REVERT: C 120 ASN cc_start: 0.7230 (m-40) cc_final: 0.6911 (m-40) REVERT: C 155 ASN cc_start: 0.8164 (m-40) cc_final: 0.7543 (t0) REVERT: C 178 MET cc_start: 0.8642 (mtm) cc_final: 0.8426 (mtp) REVERT: D 154 MET cc_start: 0.7046 (mmt) cc_final: 0.6271 (mmt) REVERT: F 246 GLU cc_start: 0.7751 (pp20) cc_final: 0.7381 (pp20) REVERT: F 271 TYR cc_start: 0.7329 (t80) cc_final: 0.7122 (t80) REVERT: M 6 GLU cc_start: 0.7675 (tp30) cc_final: 0.7470 (tp30) REVERT: I 17 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8323 (m-40) REVERT: I 63 MET cc_start: 0.8477 (ttm) cc_final: 0.8187 (mtp) REVERT: J 63 MET cc_start: 0.8251 (mmm) cc_final: 0.7913 (ttm) REVERT: J 224 ARG cc_start: 0.7927 (tpp80) cc_final: 0.7406 (tpt-90) REVERT: J 256 ASP cc_start: 0.7261 (t0) cc_final: 0.6822 (m-30) REVERT: J 267 ILE cc_start: 0.8913 (mp) cc_final: 0.8598 (mt) REVERT: K 115 THR cc_start: 0.6710 (OUTLIER) cc_final: 0.6309 (p) REVERT: K 155 ASN cc_start: 0.8275 (m-40) cc_final: 0.7864 (t0) REVERT: L 154 MET cc_start: 0.7314 (mmt) cc_final: 0.6758 (mmt) REVERT: N 246 GLU cc_start: 0.7936 (pp20) cc_final: 0.7515 (pp20) REVERT: E 31 VAL cc_start: 0.8394 (OUTLIER) cc_final: 0.8178 (p) REVERT: E 34 LYS cc_start: 0.8875 (mtmt) cc_final: 0.8475 (mtpt) outliers start: 43 outliers final: 33 residues processed: 327 average time/residue: 0.3508 time to fit residues: 165.2440 Evaluate side-chains 300 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 261 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 31 VAL Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 50 MET Chi-restraints excluded: chain I residue 107 ARG Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 265 CYS Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 126 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 158 optimal weight: 5.9990 chunk 129 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 189 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 153 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 ASN D 222 ASN ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 ASN L 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18810 Z= 0.152 Angle : 0.445 7.786 25776 Z= 0.256 Chirality : 0.040 0.219 2846 Planarity : 0.003 0.034 3002 Dihedral : 18.349 81.502 3162 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.52 % Allowed : 13.27 % Favored : 84.21 % 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: 0.32 (0.19), residues: 2032 helix: 1.93 (0.17), residues: 960 sheet: 0.34 (0.24), residues: 446 loop : -2.76 (0.21), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 PHE 0.024 0.001 PHE K 121 TYR 0.012 0.001 TYR E 15 ARG 0.003 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 288 time to evaluate : 2.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8131 (m-40) REVERT: A 42 LYS cc_start: 0.8779 (mmmt) cc_final: 0.8531 (mmtp) REVERT: A 107 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.7394 (mpt180) REVERT: B 63 MET cc_start: 0.8314 (mmm) cc_final: 0.7927 (ttm) REVERT: B 224 ARG cc_start: 0.7639 (tpp80) cc_final: 0.7184 (tpp80) REVERT: B 256 ASP cc_start: 0.6678 (t0) cc_final: 0.5869 (m-30) REVERT: B 266 LYS cc_start: 0.7446 (ttpt) cc_final: 0.7137 (ptmt) REVERT: B 267 ILE cc_start: 0.8983 (mp) cc_final: 0.8582 (mt) REVERT: B 270 ASP cc_start: 0.7579 (t70) cc_final: 0.7338 (t70) REVERT: B 271 TYR cc_start: 0.8682 (m-80) cc_final: 0.7602 (m-80) REVERT: C 155 ASN cc_start: 0.8048 (m-40) cc_final: 0.7547 (t0) REVERT: F 246 GLU cc_start: 0.7694 (pp20) cc_final: 0.7325 (pp20) REVERT: M 6 GLU cc_start: 0.7637 (tp30) cc_final: 0.7404 (tp30) REVERT: M 22 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8131 (ttm) REVERT: M 34 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8396 (mtpt) REVERT: M 35 GLU cc_start: 0.8385 (tp30) cc_final: 0.8066 (tp30) REVERT: I 24 GLU cc_start: 0.7375 (tt0) cc_final: 0.7088 (mt-10) REVERT: I 154 MET cc_start: 0.8787 (mmt) cc_final: 0.8441 (mmm) REVERT: J 63 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7868 (ttm) REVERT: J 224 ARG cc_start: 0.8011 (tpp80) cc_final: 0.7538 (tpt-90) REVERT: J 266 LYS cc_start: 0.7569 (ttpt) cc_final: 0.7104 (pttt) REVERT: J 267 ILE cc_start: 0.9013 (mp) cc_final: 0.8686 (mt) REVERT: K 155 ASN cc_start: 0.8123 (m-40) cc_final: 0.7697 (t0) REVERT: K 178 MET cc_start: 0.8838 (mtm) cc_final: 0.8360 (mtt) REVERT: L 154 MET cc_start: 0.7281 (mmt) cc_final: 0.6450 (mmt) REVERT: N 246 GLU cc_start: 0.7847 (pp20) cc_final: 0.7200 (pp20) REVERT: N 271 TYR cc_start: 0.7536 (t80) cc_final: 0.7253 (t80) REVERT: E 34 LYS cc_start: 0.8882 (mtmt) cc_final: 0.8483 (mtpt) REVERT: E 35 GLU cc_start: 0.8290 (tp30) cc_final: 0.7883 (tp30) outliers start: 44 outliers final: 27 residues processed: 317 average time/residue: 0.3600 time to fit residues: 163.2984 Evaluate side-chains 290 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 259 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 107 ARG Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 207 ASP Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain E residue 3 ASP Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.0050 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 181 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN D 222 ASN L 222 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18810 Z= 0.200 Angle : 0.466 7.223 25776 Z= 0.267 Chirality : 0.040 0.163 2846 Planarity : 0.003 0.032 3002 Dihedral : 18.387 81.377 3155 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.57 % Allowed : 14.70 % Favored : 82.72 % 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: 0.61 (0.19), residues: 2032 helix: 2.20 (0.17), residues: 962 sheet: 0.42 (0.24), residues: 446 loop : -2.65 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 235 HIS 0.005 0.001 HIS J 12 PHE 0.014 0.001 PHE K 26 TYR 0.009 0.001 TYR A 83 ARG 0.007 0.000 ARG J 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 269 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.8214 (m-40) REVERT: A 42 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8612 (mmtp) REVERT: B 63 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7927 (ttm) REVERT: B 224 ARG cc_start: 0.7657 (tpp80) cc_final: 0.7400 (tpp80) REVERT: B 256 ASP cc_start: 0.6639 (t0) cc_final: 0.5839 (m-30) REVERT: B 267 ILE cc_start: 0.9014 (mp) cc_final: 0.8663 (mt) REVERT: C 155 ASN cc_start: 0.8061 (m-40) cc_final: 0.7523 (t0) REVERT: D 178 MET cc_start: 0.8120 (mtt) cc_final: 0.7473 (mtt) REVERT: D 222 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8738 (t0) REVERT: M 6 GLU cc_start: 0.7721 (tp30) cc_final: 0.7472 (tp30) REVERT: M 22 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8201 (ttm) REVERT: M 34 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8519 (mtpt) REVERT: M 35 GLU cc_start: 0.8410 (tp30) cc_final: 0.8014 (tp30) REVERT: I 17 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: I 24 GLU cc_start: 0.7467 (tt0) cc_final: 0.7107 (mt-10) REVERT: I 154 MET cc_start: 0.8793 (mmt) cc_final: 0.8451 (mmm) REVERT: J 63 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7865 (ttm) REVERT: J 256 ASP cc_start: 0.7177 (t0) cc_final: 0.6630 (m-30) REVERT: J 266 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7130 (pttt) REVERT: J 267 ILE cc_start: 0.9024 (mp) cc_final: 0.8692 (mt) REVERT: K 11 GLU cc_start: 0.7284 (tp30) cc_final: 0.6660 (mt-10) REVERT: K 155 ASN cc_start: 0.8041 (m-40) cc_final: 0.7686 (t0) REVERT: K 178 MET cc_start: 0.8849 (mtm) cc_final: 0.8370 (mtt) REVERT: L 154 MET cc_start: 0.7092 (mmt) cc_final: 0.6559 (mmt) REVERT: L 178 MET cc_start: 0.7987 (mtt) cc_final: 0.7759 (mtt) REVERT: N 246 GLU cc_start: 0.7881 (pp20) cc_final: 0.7235 (pp20) REVERT: N 271 TYR cc_start: 0.7625 (t80) cc_final: 0.7322 (t80) REVERT: E 34 LYS cc_start: 0.8959 (mtmt) cc_final: 0.8576 (mtpt) REVERT: E 35 GLU cc_start: 0.8265 (tp30) cc_final: 0.8061 (tp30) outliers start: 45 outliers final: 31 residues processed: 295 average time/residue: 0.3354 time to fit residues: 144.3639 Evaluate side-chains 290 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 173 optimal weight: 7.9990 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN C 114 HIS D 222 ASN I 252 GLN L 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18810 Z= 0.332 Angle : 0.550 8.871 25776 Z= 0.311 Chirality : 0.043 0.142 2846 Planarity : 0.004 0.039 3002 Dihedral : 18.656 81.624 3151 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.20 % Allowed : 14.82 % Favored : 81.98 % 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: 0.52 (0.19), residues: 2032 helix: 2.09 (0.17), residues: 962 sheet: 0.34 (0.24), residues: 456 loop : -2.65 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP J 235 HIS 0.006 0.001 HIS J 12 PHE 0.016 0.002 PHE K 26 TYR 0.013 0.002 TYR A 83 ARG 0.004 0.000 ARG L 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 261 time to evaluate : 2.060 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASN cc_start: 0.8824 (OUTLIER) cc_final: 0.8364 (m-40) REVERT: A 35 GLU cc_start: 0.7689 (tp30) cc_final: 0.7328 (tp30) REVERT: B 63 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8024 (ttm) REVERT: B 68 LEU cc_start: 0.8253 (tp) cc_final: 0.7991 (tp) REVERT: B 224 ARG cc_start: 0.7789 (tpp80) cc_final: 0.7285 (tpt-90) REVERT: B 256 ASP cc_start: 0.6700 (t0) cc_final: 0.5884 (m-30) REVERT: B 267 ILE cc_start: 0.8997 (mp) cc_final: 0.8691 (mt) REVERT: C 11 GLU cc_start: 0.7392 (tp30) cc_final: 0.6701 (mt-10) REVERT: C 155 ASN cc_start: 0.8103 (m-40) cc_final: 0.7584 (t0) REVERT: C 194 TYR cc_start: 0.7639 (OUTLIER) cc_final: 0.6851 (m-80) REVERT: D 178 MET cc_start: 0.8102 (mtt) cc_final: 0.7553 (mtt) REVERT: M 6 GLU cc_start: 0.7844 (tp30) cc_final: 0.7550 (tp30) REVERT: M 22 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8191 (ttm) REVERT: M 27 GLN cc_start: 0.8912 (mm-40) cc_final: 0.8678 (mm-40) REVERT: M 34 LYS cc_start: 0.8913 (mtmt) cc_final: 0.8531 (mtpt) REVERT: I 17 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8340 (m-40) REVERT: I 24 GLU cc_start: 0.7517 (tt0) cc_final: 0.7142 (mt-10) REVERT: J 63 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7938 (ttm) REVERT: J 235 TRP cc_start: 0.6264 (m100) cc_final: 0.5735 (m100) REVERT: J 256 ASP cc_start: 0.7270 (t0) cc_final: 0.6566 (m-30) REVERT: J 267 ILE cc_start: 0.8989 (mp) cc_final: 0.8660 (mt) REVERT: K 11 GLU cc_start: 0.7371 (tp30) cc_final: 0.6724 (mt-10) REVERT: K 155 ASN cc_start: 0.8245 (m-40) cc_final: 0.7791 (t0) REVERT: K 178 MET cc_start: 0.8872 (mtm) cc_final: 0.8282 (mtp) REVERT: L 154 MET cc_start: 0.7305 (mmt) cc_final: 0.6745 (mmt) REVERT: L 178 MET cc_start: 0.7943 (mtt) cc_final: 0.7688 (mtt) REVERT: L 222 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8820 (t0) REVERT: N 246 GLU cc_start: 0.7942 (pp20) cc_final: 0.7620 (pp20) REVERT: N 252 GLN cc_start: 0.8572 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: N 271 TYR cc_start: 0.7596 (t80) cc_final: 0.7273 (t80) REVERT: E 34 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8556 (mtpt) outliers start: 56 outliers final: 39 residues processed: 295 average time/residue: 0.3371 time to fit residues: 144.7543 Evaluate side-chains 290 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 243 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain D residue 65 CYS Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 219 LYS Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 40 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 203 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 ASN I 117 ASN J 17 ASN K 168 GLN L 222 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 18810 Z= 0.308 Angle : 0.531 6.603 25776 Z= 0.301 Chirality : 0.042 0.136 2846 Planarity : 0.004 0.038 3002 Dihedral : 18.622 81.320 3151 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.97 % Allowed : 16.30 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2032 helix: 2.15 (0.17), residues: 960 sheet: 0.30 (0.24), residues: 456 loop : -2.58 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 131 HIS 0.006 0.001 HIS B 12 PHE 0.015 0.002 PHE M 1 TYR 0.012 0.001 TYR A 83 ARG 0.003 0.000 ARG J 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 255 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.8015 (ttm) REVERT: B 224 ARG cc_start: 0.7765 (tpp80) cc_final: 0.7291 (tpt-90) REVERT: C 11 GLU cc_start: 0.7430 (tp30) cc_final: 0.6693 (mt-10) REVERT: C 155 ASN cc_start: 0.8092 (m-40) cc_final: 0.7577 (t0) REVERT: C 194 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6815 (m-80) REVERT: D 63 MET cc_start: 0.7789 (mtp) cc_final: 0.7518 (mtp) REVERT: D 117 ASN cc_start: 0.6004 (m-40) cc_final: 0.5579 (p0) REVERT: D 178 MET cc_start: 0.8079 (mtt) cc_final: 0.7637 (mtt) REVERT: M 6 GLU cc_start: 0.7860 (tp30) cc_final: 0.7522 (tp30) REVERT: M 22 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8204 (ttm) REVERT: M 34 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8540 (mtpt) REVERT: I 24 GLU cc_start: 0.7441 (tt0) cc_final: 0.7129 (mt-10) REVERT: J 63 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7933 (ttm) REVERT: J 235 TRP cc_start: 0.6350 (m100) cc_final: 0.5770 (m100) REVERT: J 267 ILE cc_start: 0.8983 (mp) cc_final: 0.8690 (mt) REVERT: K 155 ASN cc_start: 0.8235 (m-40) cc_final: 0.7814 (t0) REVERT: K 178 MET cc_start: 0.8861 (mtm) cc_final: 0.8252 (mtp) REVERT: K 210 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7633 (t) REVERT: L 154 MET cc_start: 0.7321 (mmt) cc_final: 0.6748 (mmt) REVERT: L 178 MET cc_start: 0.7895 (mtt) cc_final: 0.7661 (mtt) REVERT: N 246 GLU cc_start: 0.7971 (pp20) cc_final: 0.7667 (pp20) REVERT: N 252 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: N 271 TYR cc_start: 0.7571 (t80) cc_final: 0.7280 (t80) REVERT: E 27 GLN cc_start: 0.8906 (mm-40) cc_final: 0.8692 (mm-40) REVERT: E 34 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8564 (mtpt) REVERT: E 35 GLU cc_start: 0.8295 (tp30) cc_final: 0.7912 (tp30) outliers start: 52 outliers final: 37 residues processed: 288 average time/residue: 0.3406 time to fit residues: 142.8297 Evaluate side-chains 296 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 24 GLU Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 232 ASP Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 203 ILE Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 210 THR Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 chunk 171 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 202 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18810 Z= 0.142 Angle : 0.452 8.353 25776 Z= 0.255 Chirality : 0.039 0.133 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.202 79.597 3150 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.12 % Allowed : 17.39 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 2032 helix: 2.60 (0.17), residues: 960 sheet: 0.45 (0.24), residues: 456 loop : -2.51 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 131 HIS 0.004 0.001 HIS K 12 PHE 0.010 0.001 PHE M 1 TYR 0.007 0.001 TYR J 83 ARG 0.003 0.000 ARG I 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 266 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8264 (mmm) cc_final: 0.7925 (ttm) REVERT: B 224 ARG cc_start: 0.7731 (tpp80) cc_final: 0.7265 (tpt-90) REVERT: B 267 ILE cc_start: 0.9026 (mp) cc_final: 0.8724 (mt) REVERT: B 271 TYR cc_start: 0.8762 (m-80) cc_final: 0.8238 (m-80) REVERT: C 11 GLU cc_start: 0.7307 (tp30) cc_final: 0.6608 (mt-10) REVERT: C 155 ASN cc_start: 0.8039 (m-40) cc_final: 0.7489 (t0) REVERT: C 194 TYR cc_start: 0.7220 (OUTLIER) cc_final: 0.6625 (m-80) REVERT: D 117 ASN cc_start: 0.5725 (m-40) cc_final: 0.5316 (p0) REVERT: D 178 MET cc_start: 0.7976 (mtt) cc_final: 0.7543 (mtt) REVERT: M 6 GLU cc_start: 0.7669 (tp30) cc_final: 0.7384 (tp30) REVERT: M 22 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8292 (ttm) REVERT: M 34 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8508 (mtpt) REVERT: I 24 GLU cc_start: 0.7247 (tt0) cc_final: 0.6978 (mt-10) REVERT: I 154 MET cc_start: 0.8724 (mmt) cc_final: 0.8488 (mmm) REVERT: J 63 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7939 (ttm) REVERT: J 235 TRP cc_start: 0.6211 (m100) cc_final: 0.5476 (m100) REVERT: J 266 LYS cc_start: 0.7346 (ttpt) cc_final: 0.6989 (pttt) REVERT: J 267 ILE cc_start: 0.8997 (mp) cc_final: 0.8687 (mt) REVERT: K 11 GLU cc_start: 0.7276 (tp30) cc_final: 0.6630 (mt-10) REVERT: K 155 ASN cc_start: 0.8179 (m-40) cc_final: 0.7748 (t0) REVERT: K 178 MET cc_start: 0.8768 (mtm) cc_final: 0.7937 (mtt) REVERT: L 154 MET cc_start: 0.7110 (mmt) cc_final: 0.6652 (mmt) REVERT: L 178 MET cc_start: 0.7768 (mtt) cc_final: 0.7540 (mtt) REVERT: N 271 TYR cc_start: 0.7502 (t80) cc_final: 0.7280 (t80) REVERT: E 27 GLN cc_start: 0.8876 (mm-40) cc_final: 0.8646 (mm-40) REVERT: E 34 LYS cc_start: 0.8888 (mtmt) cc_final: 0.8549 (mtpt) outliers start: 37 outliers final: 29 residues processed: 284 average time/residue: 0.3486 time to fit residues: 144.0577 Evaluate side-chains 280 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 248 time to evaluate : 2.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain E residue 18 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18810 Z= 0.170 Angle : 0.464 8.461 25776 Z= 0.263 Chirality : 0.040 0.130 2846 Planarity : 0.003 0.045 3002 Dihedral : 18.278 79.126 3150 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.17 % Allowed : 18.36 % Favored : 79.46 % 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: 1.02 (0.19), residues: 2032 helix: 2.59 (0.17), residues: 964 sheet: 0.49 (0.24), residues: 456 loop : -2.50 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 131 HIS 0.004 0.001 HIS I 51 PHE 0.012 0.001 PHE M 1 TYR 0.009 0.001 TYR K 194 ARG 0.005 0.000 ARG L 231 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 244 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8298 (mmm) cc_final: 0.7972 (ttm) REVERT: B 224 ARG cc_start: 0.7734 (tpp80) cc_final: 0.7263 (tpt-90) REVERT: B 266 LYS cc_start: 0.7328 (ttpt) cc_final: 0.7105 (ttpp) REVERT: B 267 ILE cc_start: 0.9020 (mp) cc_final: 0.8729 (mt) REVERT: B 271 TYR cc_start: 0.8921 (m-80) cc_final: 0.8472 (m-80) REVERT: C 11 GLU cc_start: 0.7343 (tp30) cc_final: 0.6647 (mt-10) REVERT: C 155 ASN cc_start: 0.8043 (m-40) cc_final: 0.7500 (t0) REVERT: C 194 TYR cc_start: 0.7334 (OUTLIER) cc_final: 0.6753 (m-80) REVERT: D 117 ASN cc_start: 0.6013 (m-40) cc_final: 0.5601 (p0) REVERT: D 178 MET cc_start: 0.8013 (mtt) cc_final: 0.7624 (mtt) REVERT: M 6 GLU cc_start: 0.7698 (tp30) cc_final: 0.7425 (tp30) REVERT: M 22 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8132 (ttm) REVERT: M 34 LYS cc_start: 0.8936 (mtmt) cc_final: 0.8566 (mtpt) REVERT: I 24 GLU cc_start: 0.7185 (tt0) cc_final: 0.6942 (mt-10) REVERT: I 154 MET cc_start: 0.8732 (mmt) cc_final: 0.8503 (mmm) REVERT: J 63 MET cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: J 235 TRP cc_start: 0.6197 (m100) cc_final: 0.5468 (m100) REVERT: J 266 LYS cc_start: 0.7252 (ttpt) cc_final: 0.6912 (pttt) REVERT: J 267 ILE cc_start: 0.8999 (mp) cc_final: 0.8690 (mt) REVERT: J 273 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7589 (mmt90) REVERT: K 11 GLU cc_start: 0.7286 (tp30) cc_final: 0.6642 (mt-10) REVERT: K 155 ASN cc_start: 0.8080 (m-40) cc_final: 0.7720 (t0) REVERT: K 178 MET cc_start: 0.8782 (mtm) cc_final: 0.8003 (mtt) REVERT: L 154 MET cc_start: 0.7124 (mmt) cc_final: 0.6673 (mmt) REVERT: L 231 ARG cc_start: 0.8455 (ttm110) cc_final: 0.8227 (mmm-85) REVERT: E 34 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8586 (mtpt) outliers start: 38 outliers final: 34 residues processed: 263 average time/residue: 0.3407 time to fit residues: 131.5362 Evaluate side-chains 286 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain E residue 18 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 113 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 187 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18810 Z= 0.199 Angle : 0.477 8.178 25776 Z= 0.270 Chirality : 0.040 0.129 2846 Planarity : 0.003 0.039 3002 Dihedral : 18.334 78.905 3150 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.69 % Allowed : 17.96 % Favored : 79.35 % 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: 1.04 (0.19), residues: 2032 helix: 2.61 (0.17), residues: 962 sheet: 0.48 (0.24), residues: 450 loop : -2.44 (0.23), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 131 HIS 0.004 0.001 HIS J 12 PHE 0.014 0.001 PHE M 1 TYR 0.010 0.001 TYR B 83 ARG 0.005 0.000 ARG J 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 248 time to evaluate : 2.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8300 (mmm) cc_final: 0.7991 (ttm) REVERT: B 224 ARG cc_start: 0.7737 (tpp80) cc_final: 0.7261 (tpt-90) REVERT: B 266 LYS cc_start: 0.7331 (ttpt) cc_final: 0.7110 (ttpp) REVERT: B 267 ILE cc_start: 0.9012 (mp) cc_final: 0.8724 (mt) REVERT: B 271 TYR cc_start: 0.8937 (m-80) cc_final: 0.8519 (m-80) REVERT: C 11 GLU cc_start: 0.7380 (tp30) cc_final: 0.6649 (mt-10) REVERT: C 155 ASN cc_start: 0.8058 (m-40) cc_final: 0.7499 (t0) REVERT: C 194 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6695 (m-80) REVERT: D 117 ASN cc_start: 0.6073 (m-40) cc_final: 0.5625 (p0) REVERT: D 178 MET cc_start: 0.8028 (mtt) cc_final: 0.7664 (mtt) REVERT: M 6 GLU cc_start: 0.7698 (tp30) cc_final: 0.7425 (tp30) REVERT: M 22 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8208 (ttm) REVERT: M 34 LYS cc_start: 0.8928 (mtmt) cc_final: 0.8561 (mtpt) REVERT: I 24 GLU cc_start: 0.7207 (tt0) cc_final: 0.6844 (mt-10) REVERT: I 154 MET cc_start: 0.8730 (mmt) cc_final: 0.8505 (mmm) REVERT: J 63 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7832 (ttm) REVERT: J 235 TRP cc_start: 0.6095 (m100) cc_final: 0.5295 (m100) REVERT: J 266 LYS cc_start: 0.7219 (ttpt) cc_final: 0.6869 (pttt) REVERT: J 267 ILE cc_start: 0.8998 (mp) cc_final: 0.8695 (mt) REVERT: K 11 GLU cc_start: 0.7285 (tp30) cc_final: 0.6648 (mt-10) REVERT: K 155 ASN cc_start: 0.8091 (m-40) cc_final: 0.7729 (t0) REVERT: K 178 MET cc_start: 0.8815 (mtm) cc_final: 0.8066 (mtt) REVERT: L 117 ASN cc_start: 0.6353 (m-40) cc_final: 0.5665 (p0) REVERT: L 154 MET cc_start: 0.7145 (mmt) cc_final: 0.6664 (mmt) REVERT: E 34 LYS cc_start: 0.8922 (mtmt) cc_final: 0.8562 (mtpt) outliers start: 47 outliers final: 40 residues processed: 270 average time/residue: 0.3485 time to fit residues: 136.0884 Evaluate side-chains 297 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 254 time to evaluate : 1.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 251 ILE Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 234 GLN Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 229 GLU Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 2.9990 chunk 121 optimal weight: 0.0870 chunk 94 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 0.8980 chunk 166 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 128 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18810 Z= 0.137 Angle : 0.453 10.104 25776 Z= 0.256 Chirality : 0.039 0.131 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.103 78.681 3150 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.00 % Allowed : 18.76 % Favored : 79.23 % 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: 1.17 (0.20), residues: 2032 helix: 2.74 (0.17), residues: 964 sheet: 0.45 (0.25), residues: 430 loop : -2.26 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 131 HIS 0.003 0.001 HIS D 114 PHE 0.010 0.001 PHE M 1 TYR 0.007 0.001 TYR J 83 ARG 0.006 0.000 ARG A 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4064 Ramachandran restraints generated. 2032 Oldfield, 0 Emsley, 2032 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 264 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 MET cc_start: 0.8279 (mmm) cc_final: 0.7928 (ttm) REVERT: B 224 ARG cc_start: 0.7715 (tpp80) cc_final: 0.7218 (tpt-90) REVERT: B 266 LYS cc_start: 0.7305 (ttpt) cc_final: 0.7076 (ttpp) REVERT: B 267 ILE cc_start: 0.8988 (mp) cc_final: 0.8672 (mt) REVERT: B 271 TYR cc_start: 0.8763 (m-80) cc_final: 0.8463 (m-80) REVERT: B 273 ARG cc_start: 0.7413 (mpp80) cc_final: 0.6776 (mpp80) REVERT: C 11 GLU cc_start: 0.7322 (tp30) cc_final: 0.6626 (mt-10) REVERT: C 155 ASN cc_start: 0.8028 (m-40) cc_final: 0.7473 (t0) REVERT: D 117 ASN cc_start: 0.6065 (m-40) cc_final: 0.5613 (p0) REVERT: D 178 MET cc_start: 0.7980 (mtt) cc_final: 0.7603 (mtt) REVERT: M 6 GLU cc_start: 0.7623 (tp30) cc_final: 0.7366 (tp30) REVERT: M 22 MET cc_start: 0.8676 (OUTLIER) cc_final: 0.8320 (ttm) REVERT: M 34 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8676 (mtpt) REVERT: I 24 GLU cc_start: 0.7216 (tt0) cc_final: 0.7008 (mt-10) REVERT: I 154 MET cc_start: 0.8758 (mmt) cc_final: 0.8501 (mmm) REVERT: J 63 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7818 (ttm) REVERT: J 253 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6592 (t0) REVERT: J 266 LYS cc_start: 0.7190 (ttpt) cc_final: 0.6834 (pttt) REVERT: J 267 ILE cc_start: 0.8918 (mp) cc_final: 0.8579 (mt) REVERT: K 11 GLU cc_start: 0.7268 (tp30) cc_final: 0.6586 (mt-10) REVERT: K 155 ASN cc_start: 0.8061 (m-40) cc_final: 0.7679 (t0) REVERT: K 178 MET cc_start: 0.8764 (mtm) cc_final: 0.8097 (mtt) REVERT: L 154 MET cc_start: 0.7112 (mmt) cc_final: 0.6721 (mmt) REVERT: E 34 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8571 (mtpt) outliers start: 35 outliers final: 28 residues processed: 284 average time/residue: 0.3345 time to fit residues: 140.0126 Evaluate side-chains 283 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 252 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 259 VAL Chi-restraints excluded: chain B residue 17 ASN Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 234 GLN Chi-restraints excluded: chain C residue 18 ASN Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain F residue 203 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain M residue 22 MET Chi-restraints excluded: chain I residue 17 ASN Chi-restraints excluded: chain I residue 218 SER Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 260 VAL Chi-restraints excluded: chain J residue 63 MET Chi-restraints excluded: chain J residue 253 ASP Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 24 GLU Chi-restraints excluded: chain K residue 68 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 211 THR Chi-restraints excluded: chain L residue 207 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain N residue 240 THR Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 18 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 146 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 214 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.150484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.111545 restraints weight = 26149.131| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 2.56 r_work: 0.3287 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18810 Z= 0.197 Angle : 0.476 8.069 25776 Z= 0.269 Chirality : 0.040 0.127 2846 Planarity : 0.003 0.037 3002 Dihedral : 18.292 79.094 3147 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.06 % Allowed : 19.11 % Favored : 78.83 % 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: 1.14 (0.20), residues: 2032 helix: 2.70 (0.17), residues: 962 sheet: 0.44 (0.25), residues: 430 loop : -2.23 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 131 HIS 0.004 0.001 HIS I 51 PHE 0.013 0.001 PHE M 1 TYR 0.010 0.001 TYR J 83 ARG 0.007 0.000 ARG I 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.69 seconds wall clock time: 75 minutes 36.74 seconds (4536.74 seconds total)