Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 17:59:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/04_2023/6rwl_10041.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/04_2023/6rwl_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_10041/04_2023/6rwl_10041.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/04_2023/6rwl_10041.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/04_2023/6rwl_10041.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwl_10041/04_2023/6rwl_10041.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 9.97, per 1000 atoms: 0.55 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: 7.22 Conformation dependent library (CDL) restraints added in 2.6 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: 4.65 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: 5.82 Time building geometry restraints manager: 7.70 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: 9624 16.69 - 33.38: 754 33.38 - 50.07: 408 50.07 - 66.76: 120 66.76 - 83.45: 10 Dihedral angle restraints: 10916 sinusoidal: 4958 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 10913 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: 3.020 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: 0.020 Extract box with map and model: 12.270 Check model and map are aligned: 0.290 Set scattering table: 0.160 Process input model: 52.670 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.130 ------------------------------------------------------------------------------- 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 : 16.018 83.447 7052 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 % 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 *********************** 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 : 2.237 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 outliers start: 50 outliers final: 12 residues processed: 479 average time/residue: 0.3489 time to fit residues: 239.1322 Evaluate side-chains 287 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 275 time to evaluate : 2.264 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1660 time to fit residues: 6.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 88 optimal weight: 6.9990 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: 0.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 183 HIS B 44 GLN B 157 GLN B 183 HIS B 216 GLN C 216 GLN D 114 HIS D 216 GLN D 222 ASN M 9 GLN I 144 ASN I 183 HIS J 44 GLN J 157 GLN J 183 HIS ** K 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN K 216 GLN L 214 GLN L 216 GLN L 222 ASN E 9 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 18810 Z= 0.231 Angle : 0.505 8.510 25776 Z= 0.290 Chirality : 0.041 0.175 2846 Planarity : 0.004 0.043 3002 Dihedral : 18.289 80.873 3022 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 1.60 % 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: 0.99 (0.16), residues: 958 sheet: 0.14 (0.24), residues: 442 loop : -3.01 (0.20), residues: 632 *********************** 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 324 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 296 time to evaluate : 2.051 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 outliers start: 28 outliers final: 22 residues processed: 309 average time/residue: 0.3379 time to fit residues: 152.4831 Evaluate side-chains 277 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 255 time to evaluate : 2.083 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1804 time to fit residues: 10.0704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 0.6980 chunk 59 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 153 optimal weight: 0.0020 overall best weight: 2.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN C 114 HIS D 155 ASN D 214 GLN D 222 ASN K 114 HIS L 155 ASN L 222 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.058 18810 Z= 0.331 Angle : 0.553 8.492 25776 Z= 0.315 Chirality : 0.043 0.204 2846 Planarity : 0.004 0.037 3002 Dihedral : 18.494 79.022 3022 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.89 % 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: 0.04 (0.19), residues: 2032 helix: 1.66 (0.17), residues: 962 sheet: 0.22 (0.24), residues: 442 loop : -2.85 (0.21), residues: 628 *********************** 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 308 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 275 time to evaluate : 2.246 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 outliers start: 33 outliers final: 17 residues processed: 296 average time/residue: 0.3448 time to fit residues: 148.3473 Evaluate side-chains 259 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 242 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1703 time to fit residues: 8.0833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 0.8980 chunk 143 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 128 optimal weight: 0.3980 chunk 191 optimal weight: 5.9990 chunk 202 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 222 ASN L 222 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18810 Z= 0.159 Angle : 0.455 8.411 25776 Z= 0.261 Chirality : 0.040 0.158 2846 Planarity : 0.003 0.035 3002 Dihedral : 18.218 76.950 3022 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2032 helix: 2.21 (0.17), residues: 958 sheet: 0.37 (0.24), residues: 446 loop : -2.64 (0.21), residues: 628 *********************** 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 278 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 260 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 outliers start: 18 outliers final: 8 residues processed: 270 average time/residue: 0.3441 time to fit residues: 135.8030 Evaluate side-chains 247 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 239 time to evaluate : 2.078 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1556 time to fit residues: 5.1351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 83 optimal weight: 0.0470 chunk 173 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.0084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 120 ASN C 155 ASN D 222 ASN J 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.3187 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= 0.242 Angle : 0.499 7.853 25776 Z= 0.284 Chirality : 0.041 0.167 2846 Planarity : 0.003 0.042 3002 Dihedral : 18.347 75.564 3022 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 2032 helix: 2.28 (0.17), residues: 960 sheet: 0.42 (0.24), residues: 456 loop : -2.60 (0.22), residues: 616 *********************** 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 281 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 263 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 9 residues processed: 273 average time/residue: 0.3457 time to fit residues: 137.1998 Evaluate side-chains 265 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 1.891 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1473 time to fit residues: 5.1439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 0.0040 chunk 50 optimal weight: 0.8980 chunk 203 optimal weight: 0.9980 chunk 168 optimal weight: 0.0060 chunk 94 optimal weight: 7.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.9810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN I 252 GLN J 17 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3324 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= 0.159 Angle : 0.464 7.321 25776 Z= 0.263 Chirality : 0.040 0.146 2846 Planarity : 0.003 0.047 3002 Dihedral : 18.127 74.110 3022 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.69 % 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: 0.98 (0.19), residues: 2032 helix: 2.53 (0.17), residues: 958 sheet: 0.52 (0.24), residues: 456 loop : -2.47 (0.23), residues: 618 *********************** 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 278 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 266 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 7 residues processed: 269 average time/residue: 0.3396 time to fit residues: 133.7897 Evaluate side-chains 247 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 1.893 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1650 time to fit residues: 5.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 4.9990 chunk 22 optimal weight: 0.0030 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 chunk 113 optimal weight: 0.0040 chunk 202 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 overall best weight: 0.6806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 18810 Z= 0.138 Angle : 0.454 8.716 25776 Z= 0.257 Chirality : 0.039 0.131 2846 Planarity : 0.003 0.034 3002 Dihedral : 18.007 73.082 3022 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.46 % 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: 1.12 (0.20), residues: 2032 helix: 2.65 (0.17), residues: 964 sheet: 0.51 (0.24), residues: 476 loop : -2.49 (0.24), residues: 592 *********************** 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 270 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 262 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 268 average time/residue: 0.3360 time to fit residues: 133.4217 Evaluate side-chains 249 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 245 time to evaluate : 2.041 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1739 time to fit residues: 4.0646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN B 134 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN M 39 GLN I 214 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 18810 Z= 0.231 Angle : 0.497 7.913 25776 Z= 0.282 Chirality : 0.041 0.128 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.260 71.926 3022 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 0.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 2032 helix: 2.59 (0.17), residues: 960 sheet: 0.57 (0.24), residues: 450 loop : -2.44 (0.23), residues: 622 *********************** 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 270 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 255 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 259 average time/residue: 0.3507 time to fit residues: 132.0079 Evaluate side-chains 249 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 243 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1750 time to fit residues: 4.8119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 113 optimal weight: 0.0050 chunk 82 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 187 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN J 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 18810 Z= 0.174 Angle : 0.478 9.178 25776 Z= 0.271 Chirality : 0.040 0.147 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.120 71.170 3022 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 2032 helix: 2.71 (0.17), residues: 962 sheet: 0.61 (0.25), residues: 450 loop : -2.44 (0.23), residues: 620 *********************** 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 261 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 252 time to evaluate : 2.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 255 average time/residue: 0.3484 time to fit residues: 129.8952 Evaluate side-chains 252 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 247 time to evaluate : 2.232 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1719 time to fit residues: 4.6006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 128 optimal weight: 0.0270 chunk 102 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN J 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18810 Z= 0.209 Angle : 0.497 9.401 25776 Z= 0.280 Chirality : 0.041 0.135 2846 Planarity : 0.003 0.036 3002 Dihedral : 18.203 70.565 3022 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer Outliers : 0.34 % 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: 1.11 (0.20), residues: 2032 helix: 2.66 (0.17), residues: 960 sheet: 0.59 (0.24), residues: 448 loop : -2.44 (0.23), residues: 624 ********************** 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 255 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 249 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 251 average time/residue: 0.3505 time to fit residues: 129.5758 Evaluate side-chains 247 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 242 time to evaluate : 2.122 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1625 time to fit residues: 4.4190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 HIS ** D 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 ASN J 134 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.152393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.114979 restraints weight = 26162.773| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.34 r_work: 0.3341 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18810 Z= 0.145 Angle : 0.465 7.923 25776 Z= 0.262 Chirality : 0.040 0.132 2846 Planarity : 0.003 0.036 3002 Dihedral : 17.994 70.229 3022 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 0.23 % 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: 1.23 (0.20), residues: 2032 helix: 2.80 (0.17), residues: 960 sheet: 0.58 (0.25), residues: 428 loop : -2.28 (0.23), residues: 644 =============================================================================== Job complete usr+sys time: 3968.03 seconds wall clock time: 72 minutes 26.11 seconds (4346.11 seconds total)