Starting phenix.real_space_refine on Sat Feb 17 10:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/02_2024/6rwm_10042_updated.pdb" } resolution = 2.81 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= 0.001 sd= 0.172 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: 9 Type Number sf(0) Gaussians Zn 8 6.06 5 P 84 5.49 5 Mg 4 5.21 5 S 74 5.16 5 Cl 2 4.86 5 C 11354 2.51 5 N 3278 2.21 5 O 3640 1.98 5 F 6 1.80 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: 18450 Number of models: 1 Model: "" Number of chains: 36 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 36 Unusual residues: {' CL': 1, ' MG': 2, ' ZN': 1, 'KLQ': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "S" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 335 SG CYS A 40 79.792 61.576 30.481 1.00 17.41 S ATOM 357 SG CYS A 43 76.742 63.586 31.856 1.00 17.29 S ATOM 2468 SG CYS B 40 71.227 142.884 58.209 1.00 47.60 S ATOM 2490 SG CYS B 43 73.085 141.223 55.153 1.00 49.95 S ATOM 4455 SG CYS C 40 106.007 124.964 21.006 1.00 59.27 S ATOM 4477 SG CYS C 43 103.780 127.438 23.073 1.00 53.33 S ATOM 8211 SG CYS M 40 37.412 132.358 52.505 1.00 39.13 S ATOM 8233 SG CYS M 43 35.342 130.439 55.372 1.00 44.52 S ATOM 9467 SG CYS I 40 49.758 111.197 30.545 1.00 17.24 S ATOM 9489 SG CYS I 43 52.809 109.190 31.922 1.00 17.31 S ATOM 11600 SG CYS J 40 58.389 29.873 58.207 1.00 47.92 S ATOM 11622 SG CYS J 43 56.532 31.535 55.151 1.00 49.94 S ATOM 13587 SG CYS K 40 23.626 47.787 20.983 1.00 58.79 S ATOM 13609 SG CYS K 43 25.854 45.313 23.050 1.00 53.12 S ATOM 17343 SG CYS E 40 92.165 40.468 52.549 1.00 39.18 S ATOM 17365 SG CYS E 43 94.229 42.385 55.423 1.00 44.27 S Time building chain proxies: 10.53, per 1000 atoms: 0.57 Number of scatterers: 18450 At special positions: 0 Unit cell: (130.68, 173.88, 98.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 8 29.99 Cl 2 17.00 S 74 16.00 P 84 15.00 Mg 4 11.99 F 6 9.00 O 3640 8.00 N 3278 7.00 C 11354 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: 7.48 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 301 " pdb="ZN ZN A 301 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 301 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 40 " pdb="ZN ZN A 301 " - pdb=" SG CYS A 43 " pdb=" ZN B 500 " pdb="ZN ZN B 500 " - pdb=" NE2 HIS B 12 " pdb="ZN ZN B 500 " - pdb=" ND1 HIS B 16 " 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=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " 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 301 " pdb="ZN ZN I 301 " - pdb=" NE2 HIS I 12 " pdb="ZN ZN I 301 " - pdb=" ND1 HIS I 16 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 40 " pdb="ZN ZN I 301 " - pdb=" SG CYS I 43 " pdb=" ZN J 500 " pdb="ZN ZN J 500 " - pdb=" NE2 HIS J 12 " pdb="ZN ZN J 500 " - pdb=" ND1 HIS J 16 " 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=" NE2 HIS K 12 " pdb="ZN ZN K 500 " - pdb=" ND1 HIS K 16 " 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 : 10 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... running ksdssp... Secondary structure from input PDB file: 82 helices and 24 sheets defined 45.3% alpha, 18.3% beta 34 base pairs and 72 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 15 Processing helix chain 'A' and resid 19 through 25 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 94 through 107 Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 196 through 220 removed outlier: 4.331A pdb=" N ILE A 220 " --> pdb=" O GLN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 19 through 25 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 94 through 107 Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 151 through 164 Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 172 through 185 Processing helix chain 'B' and resid 196 through 222 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 19 through 26 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 151 through 164 Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 172 through 185 Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'D' and resid 94 through 107 Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 172 through 185 Processing helix chain 'D' and resid 196 through 222 removed outlier: 4.313A pdb=" N SER D 218 " --> pdb=" O GLN D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'F' and resid 204 through 220 Processing helix chain 'F' and resid 262 through 264 No H-bonds generated for 'chain 'F' and resid 262 through 264' Processing helix chain 'M' and resid 2 through 15 Processing helix chain 'M' and resid 19 through 26 Processing helix chain 'M' and resid 30 through 39 Processing helix chain 'I' and resid 2 through 15 Processing helix chain 'I' and resid 19 through 25 Processing helix chain 'I' and resid 30 through 38 Processing helix chain 'I' and resid 94 through 107 Processing helix chain 'I' and resid 124 through 133 Processing helix chain 'I' and resid 149 through 164 Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 172 through 185 Processing helix chain 'I' and resid 196 through 220 removed outlier: 4.331A pdb=" N ILE I 220 " --> pdb=" O GLN I 216 " (cutoff:3.500A) Processing helix chain 'I' and resid 262 through 264 No H-bonds generated for 'chain 'I' and resid 262 through 264' Processing helix chain 'J' and resid 2 through 15 Processing helix chain 'J' and resid 19 through 25 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 94 through 107 Processing helix chain 'J' and resid 124 through 133 Processing helix chain 'J' and resid 151 through 164 Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 172 through 185 Processing helix chain 'J' and resid 196 through 222 Processing helix chain 'J' and resid 262 through 264 No H-bonds generated for 'chain 'J' and resid 262 through 264' Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 19 through 26 Processing helix chain 'K' and resid 30 through 38 Processing helix chain 'K' and resid 95 through 107 Processing helix chain 'K' and resid 124 through 133 Processing helix chain 'K' and resid 151 through 164 Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 172 through 185 Processing helix chain 'K' and resid 196 through 216 Processing helix chain 'L' and resid 94 through 107 Processing helix chain 'L' and resid 124 through 133 Processing helix chain 'L' and resid 151 through 164 Processing helix chain 'L' and resid 166 through 168 No H-bonds generated for 'chain 'L' and resid 166 through 168' Processing helix chain 'L' and resid 172 through 185 Processing helix chain 'L' and resid 196 through 222 removed outlier: 4.313A pdb=" N SER L 218 " --> pdb=" O GLN L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 264 No H-bonds generated for 'chain 'L' and resid 262 through 264' Processing helix chain 'N' and resid 204 through 220 Processing helix chain 'N' and resid 262 through 264 No H-bonds generated for 'chain 'N' and resid 262 through 264' Processing helix chain 'E' and resid 2 through 15 Processing helix chain 'E' and resid 19 through 26 Processing helix chain 'E' and resid 30 through 39 Processing sheet with id= A, first strand: chain 'A' and resid 83 through 89 removed outlier: 4.373A pdb=" N VAL A 72 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N HIS A 112 " --> pdb=" O TRP A 61 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET A 63 " --> pdb=" O HIS A 112 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS A 114 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N CYS A 65 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A 136 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR A 115 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR A 138 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= C, first strand: chain 'A' and resid 256 through 261 removed outlier: 6.343A pdb=" N GLN A 252 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU A 241 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 83 through 89 removed outlier: 4.385A pdb=" N VAL B 72 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS B 112 " --> pdb=" O TRP B 61 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET B 63 " --> pdb=" O HIS B 112 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS B 114 " --> pdb=" O MET B 63 " (cutoff:3.500A) removed outlier: 8.944A pdb=" N CYS B 65 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU B 136 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N THR B 115 " --> pdb=" O GLU B 136 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR B 138 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 223 through 227 Processing sheet with id= F, first strand: chain 'B' and resid 256 through 261 removed outlier: 6.141A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL C 72 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS C 112 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET C 63 " --> pdb=" O HIS C 112 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS C 114 " --> pdb=" O MET C 63 " (cutoff:3.500A) removed outlier: 9.008A pdb=" N CYS C 65 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU C 136 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR C 115 " --> pdb=" O GLU C 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR C 138 " --> pdb=" O THR C 115 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL D 72 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS D 112 " --> pdb=" O TRP D 61 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N MET D 63 " --> pdb=" O HIS D 112 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS D 114 " --> pdb=" O MET D 63 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N CYS D 65 " --> pdb=" O HIS D 114 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N GLU D 136 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR D 115 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR D 138 " --> pdb=" O THR D 115 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 224 through 227 Processing sheet with id= J, first strand: chain 'D' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 265 through 268 removed outlier: 3.784A pdb=" N PHE F 227 " --> pdb=" O LYS F 236 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU F 229 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN F 234 " --> pdb=" O GLU F 229 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 257 through 261 removed outlier: 6.319A pdb=" N GLN F 252 " --> pdb=" O LEU F 241 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU F 241 " --> pdb=" O GLN F 252 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'I' and resid 83 through 89 removed outlier: 4.373A pdb=" N VAL I 72 " --> pdb=" O LEU I 89 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N HIS I 112 " --> pdb=" O TRP I 61 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N MET I 63 " --> pdb=" O HIS I 112 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N HIS I 114 " --> pdb=" O MET I 63 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N CYS I 65 " --> pdb=" O HIS I 114 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N GLU I 136 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N THR I 115 " --> pdb=" O GLU I 136 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N THR I 138 " --> pdb=" O THR I 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= O, first strand: chain 'I' and resid 256 through 261 removed outlier: 6.342A pdb=" N GLN I 252 " --> pdb=" O LEU I 241 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N LEU I 241 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'J' and resid 83 through 89 removed outlier: 4.384A pdb=" N VAL J 72 " --> pdb=" O LEU J 89 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS J 112 " --> pdb=" O TRP J 61 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET J 63 " --> pdb=" O HIS J 112 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N HIS J 114 " --> pdb=" O MET J 63 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N CYS J 65 " --> pdb=" O HIS J 114 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLU J 136 " --> pdb=" O LEU J 113 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N THR J 115 " --> pdb=" O GLU J 136 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N THR J 138 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'J' and resid 223 through 227 Processing sheet with id= R, first strand: chain 'J' and resid 256 through 261 removed outlier: 6.141A pdb=" N GLN J 252 " --> pdb=" O LEU J 241 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU J 241 " --> pdb=" O GLN J 252 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'K' and resid 83 through 89 removed outlier: 4.338A pdb=" N VAL K 72 " --> pdb=" O LEU K 89 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N HIS K 112 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N MET K 63 " --> pdb=" O HIS K 112 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N HIS K 114 " --> pdb=" O MET K 63 " (cutoff:3.500A) removed outlier: 9.009A pdb=" N CYS K 65 " --> pdb=" O HIS K 114 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N GLU K 136 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N THR K 115 " --> pdb=" O GLU K 136 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N THR K 138 " --> pdb=" O THR K 115 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'L' and resid 83 through 89 removed outlier: 4.226A pdb=" N VAL L 72 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS L 112 " --> pdb=" O TRP L 61 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N MET L 63 " --> pdb=" O HIS L 112 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N HIS L 114 " --> pdb=" O MET L 63 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N CYS L 65 " --> pdb=" O HIS L 114 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLU L 136 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR L 115 " --> pdb=" O GLU L 136 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N THR L 138 " --> pdb=" O THR L 115 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= V, first strand: chain 'L' and resid 257 through 261 removed outlier: 5.986A pdb=" N GLN L 252 " --> pdb=" O LEU L 241 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N LEU L 241 " --> pdb=" O GLN L 252 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'N' and resid 265 through 268 removed outlier: 3.784A pdb=" N PHE N 227 " --> pdb=" O LYS N 236 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU N 229 " --> pdb=" O GLN N 234 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN N 234 " --> pdb=" O GLU N 229 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 257 through 261 removed outlier: 6.319A pdb=" N GLN N 252 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU N 241 " --> pdb=" O GLN N 252 " (cutoff:3.500A) 834 hydrogen bonds defined for protein. 2424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 72 stacking parallelities Total time for adding SS restraints: 6.20 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4466 1.33 - 1.46: 4963 1.46 - 1.58: 9183 1.58 - 1.71: 162 1.71 - 1.84: 108 Bond restraints: 18882 Sorted by residual: bond pdb=" CAJ KLQ A 304 " pdb=" CAX KLQ A 304 " ideal model delta sigma weight residual 2.011 1.360 0.651 2.00e-02 2.50e+03 1.06e+03 bond pdb=" CAJ KLQ I 304 " pdb=" CAX KLQ I 304 " ideal model delta sigma weight residual 2.011 1.361 0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" CAW KLQ A 304 " pdb=" CBA KLQ A 304 " ideal model delta sigma weight residual 0.990 1.447 -0.457 2.00e-02 2.50e+03 5.22e+02 bond pdb=" CAW KLQ I 304 " pdb=" CBA KLQ I 304 " ideal model delta sigma weight residual 0.990 1.442 -0.452 2.00e-02 2.50e+03 5.10e+02 bond pdb=" CAW KLQ I 304 " pdb=" CAZ KLQ I 304 " ideal model delta sigma weight residual 1.723 1.365 0.358 2.00e-02 2.50e+03 3.20e+02 ... (remaining 18877 not shown) Histogram of bond angle deviations from ideal: 97.50 - 104.82: 530 104.82 - 112.14: 9530 112.14 - 119.47: 6598 119.47 - 126.79: 8635 126.79 - 134.11: 593 Bond angle restraints: 25886 Sorted by residual: angle pdb=" CAY KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 142.84 118.09 24.75 3.00e+00 1.11e-01 6.81e+01 angle pdb=" CAY KLQ I 304 " pdb=" CAV KLQ I 304 " pdb=" FAG KLQ I 304 " ideal model delta sigma weight residual 142.84 118.19 24.65 3.00e+00 1.11e-01 6.75e+01 angle pdb=" CAI KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 97.12 115.14 -18.02 3.00e+00 1.11e-01 3.61e+01 angle pdb=" CAI KLQ I 304 " pdb=" CAV KLQ I 304 " pdb=" FAG KLQ I 304 " ideal model delta sigma weight residual 97.12 115.12 -18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" CAX KLQ A 304 " pdb=" CAJ KLQ A 304 " pdb=" NBF KLQ A 304 " ideal model delta sigma weight residual 106.14 124.06 -17.92 3.00e+00 1.11e-01 3.57e+01 ... (remaining 25881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9613 17.36 - 34.71: 904 34.71 - 52.07: 441 52.07 - 69.43: 92 69.43 - 86.79: 10 Dihedral angle restraints: 11060 sinusoidal: 5102 harmonic: 5958 Sorted by residual: dihedral pdb=" CA TYR A 194 " pdb=" C TYR A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA TYR I 194 " pdb=" C TYR I 194 " pdb=" N SER I 195 " pdb=" CA SER I 195 " ideal model delta harmonic sigma weight residual 180.00 158.15 21.85 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA LYS M 14 " pdb=" C LYS M 14 " pdb=" N TYR M 15 " pdb=" CA TYR M 15 " ideal model delta harmonic sigma weight residual 180.00 -159.60 -20.40 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 11057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2511 0.079 - 0.158: 318 0.158 - 0.237: 19 0.237 - 0.316: 2 0.316 - 0.395: 2 Chirality restraints: 2852 Sorted by residual: chirality pdb=" CBC KLQ I 304 " pdb=" CAM KLQ I 304 " pdb=" CAN KLQ I 304 " pdb=" NBE KLQ I 304 " both_signs ideal model delta sigma weight residual False -2.52 -2.92 0.39 2.00e-01 2.50e+01 3.89e+00 chirality pdb=" CBC KLQ A 304 " pdb=" CAM KLQ A 304 " pdb=" CAN KLQ A 304 " pdb=" NBE KLQ A 304 " both_signs ideal model delta sigma weight residual False -2.52 -2.91 0.39 2.00e-01 2.50e+01 3.81e+00 chirality pdb=" CBB KLQ A 304 " pdb=" CAL KLQ A 304 " pdb=" CAN KLQ A 304 " pdb=" OAQ KLQ A 304 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 2849 not shown) Planarity restraints: 3010 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL I 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.83e+00 pdb=" C VAL I 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL I 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS I 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 45 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C VAL A 45 " 0.045 2.00e-02 2.50e+03 pdb=" O VAL A 45 " -0.017 2.00e-02 2.50e+03 pdb=" N LYS A 46 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE E 28 " 0.037 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO E 29 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.031 5.00e-02 4.00e+02 ... (remaining 3007 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 131 2.58 - 3.16: 13078 3.16 - 3.74: 26601 3.74 - 4.32: 39732 4.32 - 4.90: 63956 Nonbonded interactions: 143498 Sorted by model distance: nonbonded pdb="MG MG A 303 " pdb=" OAC KLQ A 304 " model vdw 2.005 2.170 nonbonded pdb="MG MG I 303 " pdb=" OAC KLQ I 304 " model vdw 2.010 2.170 nonbonded pdb="MG MG I 302 " pdb=" O HOH I 404 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 302 " pdb=" O HOH A 403 " model vdw 2.011 2.170 nonbonded pdb="MG MG A 303 " pdb=" O HOH T 103 " model vdw 2.021 2.170 ... (remaining 143493 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)) selection = (chain 'B' and resid 1 through 269) selection = (chain 'I' and (resid 1 through 44 or resid 57 through 141 or resid 151 through \ 269)) selection = (chain 'J' and resid 1 through 269) } 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: 4.690 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: 17.950 Check model and map are aligned: 0.290 Set scattering table: 0.200 Process input model: 59.190 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.140 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:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.013 0.651 18882 Z= 0.679 Angle : 0.852 24.749 25886 Z= 0.460 Chirality : 0.052 0.395 2852 Planarity : 0.006 0.055 3010 Dihedral : 16.934 86.786 7196 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.20 % Allowed : 5.26 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.15), residues: 2032 helix: -1.77 (0.12), residues: 954 sheet: 0.11 (0.23), residues: 446 loop : -3.28 (0.19), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 19 HIS 0.005 0.001 HIS I 51 PHE 0.016 0.002 PHE A 1 TYR 0.011 0.002 TYR K 83 ARG 0.003 0.000 ARG L 228 *********************** 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 373 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 317 time to evaluate : 2.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 MET cc_start: 0.8813 (mtm) cc_final: 0.8449 (mtp) REVERT: B 154 MET cc_start: 0.7468 (mmt) cc_final: 0.7051 (mmt) REVERT: C 62 GLN cc_start: 0.7430 (mt0) cc_final: 0.7126 (mt0) REVERT: C 194 TYR cc_start: 0.6580 (OUTLIER) cc_final: 0.5792 (t80) REVERT: D 234 GLN cc_start: 0.7653 (mt0) cc_final: 0.7409 (mp10) REVERT: M 7 LYS cc_start: 0.8180 (mttt) cc_final: 0.7801 (mtmt) REVERT: M 35 GLU cc_start: 0.7884 (tp30) cc_final: 0.7575 (tp30) REVERT: I 10 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7259 (mt-10) REVERT: I 22 MET cc_start: 0.8936 (mtm) cc_final: 0.8666 (mtp) REVERT: I 50 MET cc_start: 0.8776 (ppp) cc_final: 0.8549 (ppp) REVERT: I 154 MET cc_start: 0.8689 (mmt) cc_final: 0.8283 (mmt) REVERT: J 39 GLN cc_start: 0.7365 (mt0) cc_final: 0.7131 (mm110) REVERT: J 154 MET cc_start: 0.7558 (mmt) cc_final: 0.7302 (mmt) REVERT: J 224 ARG cc_start: 0.7610 (tpp80) cc_final: 0.7076 (mmt-90) REVERT: K 62 GLN cc_start: 0.7511 (mt0) cc_final: 0.7179 (mt0) REVERT: K 194 TYR cc_start: 0.6545 (OUTLIER) cc_final: 0.5549 (t80) REVERT: L 194 TYR cc_start: 0.5764 (m-80) cc_final: 0.5334 (m-80) REVERT: L 234 GLN cc_start: 0.7643 (mt0) cc_final: 0.7407 (mp10) REVERT: E 7 LYS cc_start: 0.8135 (mttt) cc_final: 0.7758 (mtmt) REVERT: E 32 VAL cc_start: 0.8342 (OUTLIER) cc_final: 0.8041 (t) REVERT: E 35 GLU cc_start: 0.7882 (tp30) cc_final: 0.7578 (tp30) outliers start: 56 outliers final: 13 residues processed: 363 average time/residue: 1.5202 time to fit residues: 607.4236 Evaluate side-chains 210 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 194 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain E residue 32 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: 4.9990 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 164 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 9 GLN B 157 GLN C 17 ASN C 112 HIS C 114 HIS C 168 GLN C 214 GLN C 216 GLN D 67 HIS D 134 GLN D 214 GLN M 17 ASN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 9 GLN J 157 GLN K 112 HIS K 114 HIS K 168 GLN K 214 GLN K 216 GLN L 67 HIS L 134 GLN L 157 GLN L 214 GLN E 17 ASN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18882 Z= 0.219 Angle : 0.560 12.292 25886 Z= 0.305 Chirality : 0.042 0.149 2852 Planarity : 0.004 0.045 3010 Dihedral : 18.605 87.441 3187 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.26 % Allowed : 12.70 % Favored : 84.04 % 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 (0.17), residues: 2032 helix: 0.83 (0.16), residues: 950 sheet: 0.64 (0.23), residues: 438 loop : -3.09 (0.19), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 19 HIS 0.006 0.001 HIS E 12 PHE 0.017 0.001 PHE E 1 TYR 0.011 0.001 TYR J 83 ARG 0.004 0.000 ARG N 263 *********************** 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 263 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 206 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7137 (mm-30) REVERT: C 194 TYR cc_start: 0.6655 (OUTLIER) cc_final: 0.5461 (t80) REVERT: D 68 LEU cc_start: 0.7770 (tp) cc_final: 0.7554 (tt) REVERT: D 152 GLU cc_start: 0.6054 (pm20) cc_final: 0.5801 (pm20) REVERT: D 234 GLN cc_start: 0.7733 (mt0) cc_final: 0.7500 (mp10) REVERT: M 7 LYS cc_start: 0.8034 (mttt) cc_final: 0.7627 (mtmt) REVERT: M 35 GLU cc_start: 0.7911 (tp30) cc_final: 0.7660 (tp30) REVERT: I 22 MET cc_start: 0.8969 (mtm) cc_final: 0.8756 (mtp) REVERT: I 25 ASP cc_start: 0.7641 (m-30) cc_final: 0.7414 (m-30) REVERT: J 136 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: J 154 MET cc_start: 0.7438 (mmt) cc_final: 0.7173 (mmt) REVERT: L 68 LEU cc_start: 0.7720 (tp) cc_final: 0.7477 (tt) REVERT: L 234 GLN cc_start: 0.7695 (mt0) cc_final: 0.7468 (mp10) REVERT: N 224 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7046 (mtp-110) REVERT: N 252 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: E 7 LYS cc_start: 0.7996 (mttt) cc_final: 0.7589 (mtmt) REVERT: E 35 GLU cc_start: 0.7908 (tp30) cc_final: 0.7703 (tp30) outliers start: 57 outliers final: 24 residues processed: 243 average time/residue: 1.4023 time to fit residues: 379.1518 Evaluate side-chains 221 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 221 GLN Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 18 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 221 GLN Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 224 ARG Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 18 ASN 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: 0.0980 chunk 59 optimal weight: 9.9990 chunk 158 optimal weight: 10.0000 chunk 129 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 153 optimal weight: 0.0370 overall best weight: 1.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 127 GLN ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 216 GLN C 62 GLN C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS I 127 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN K 62 GLN K 214 GLN L 134 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18882 Z= 0.177 Angle : 0.513 11.661 25886 Z= 0.277 Chirality : 0.041 0.142 2852 Planarity : 0.004 0.041 3010 Dihedral : 18.505 87.186 3180 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.09 % Allowed : 13.73 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.18), residues: 2032 helix: 1.73 (0.17), residues: 950 sheet: 0.85 (0.23), residues: 438 loop : -2.78 (0.20), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 19 HIS 0.005 0.001 HIS M 12 PHE 0.013 0.001 PHE E 1 TYR 0.012 0.001 TYR J 83 ARG 0.003 0.000 ARG F 263 *********************** 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 252 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 198 time to evaluate : 2.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 273 ARG cc_start: 0.7737 (mpt180) cc_final: 0.7479 (mmt180) REVERT: C 62 GLN cc_start: 0.7286 (mt0) cc_final: 0.6890 (mt0) REVERT: C 115 THR cc_start: 0.7657 (OUTLIER) cc_final: 0.7338 (p) REVERT: D 234 GLN cc_start: 0.7742 (mt0) cc_final: 0.7520 (mp10) REVERT: F 252 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: M 7 LYS cc_start: 0.7991 (mttt) cc_final: 0.7598 (mtmt) REVERT: M 17 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7286 (m110) REVERT: I 22 MET cc_start: 0.8931 (mtm) cc_final: 0.8704 (mtp) REVERT: J 154 MET cc_start: 0.7452 (mmt) cc_final: 0.7236 (mmt) REVERT: J 273 ARG cc_start: 0.7682 (mpt180) cc_final: 0.7416 (mmt180) REVERT: K 115 THR cc_start: 0.7556 (OUTLIER) cc_final: 0.7170 (p) REVERT: K 154 MET cc_start: 0.8091 (mmt) cc_final: 0.7323 (mmt) REVERT: L 234 GLN cc_start: 0.7736 (mt0) cc_final: 0.7512 (mp10) REVERT: N 252 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.7669 (tt0) REVERT: E 7 LYS cc_start: 0.7924 (mttt) cc_final: 0.7536 (mtmt) outliers start: 54 outliers final: 22 residues processed: 235 average time/residue: 1.5511 time to fit residues: 406.3251 Evaluate side-chains 217 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 93 THR Chi-restraints excluded: chain K residue 115 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain N residue 236 LYS 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 42 LYS 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: 7.9990 chunk 143 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 0.0070 chunk 128 optimal weight: 0.0020 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 112 HIS C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 112 HIS K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18882 Z= 0.122 Angle : 0.464 11.486 25886 Z= 0.247 Chirality : 0.039 0.138 2852 Planarity : 0.003 0.038 3010 Dihedral : 18.308 87.425 3180 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.63 % Allowed : 15.22 % Favored : 82.15 % 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: 0.91 (0.19), residues: 2032 helix: 2.27 (0.17), residues: 956 sheet: 1.01 (0.23), residues: 440 loop : -2.49 (0.22), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 132 HIS 0.002 0.000 HIS E 12 PHE 0.006 0.001 PHE E 1 TYR 0.009 0.001 TYR J 83 ARG 0.003 0.000 ARG F 224 *********************** 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 245 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 2.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 136 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: B 258 LYS cc_start: 0.7991 (ptmm) cc_final: 0.7299 (ptpt) REVERT: B 273 ARG cc_start: 0.7699 (mpt180) cc_final: 0.7467 (mmt180) REVERT: C 62 GLN cc_start: 0.7365 (mt0) cc_final: 0.6998 (mt0) REVERT: C 159 LYS cc_start: 0.7999 (OUTLIER) cc_final: 0.7665 (mtpt) REVERT: D 234 GLN cc_start: 0.7678 (mt0) cc_final: 0.7463 (mp10) REVERT: M 7 LYS cc_start: 0.7774 (mttt) cc_final: 0.7394 (mtmt) REVERT: J 136 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7030 (mm-30) REVERT: J 154 MET cc_start: 0.7381 (mmt) cc_final: 0.7093 (mmt) REVERT: J 273 ARG cc_start: 0.7679 (mpt180) cc_final: 0.7432 (mmt180) REVERT: K 132 TRP cc_start: 0.8678 (t60) cc_final: 0.8451 (t60) REVERT: L 234 GLN cc_start: 0.7667 (mt0) cc_final: 0.7453 (mp10) REVERT: E 7 LYS cc_start: 0.7690 (mttt) cc_final: 0.7381 (mtmt) outliers start: 46 outliers final: 20 residues processed: 236 average time/residue: 1.4187 time to fit residues: 372.2476 Evaluate side-chains 215 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 192 time to evaluate : 2.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASN Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 159 LYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain F residue 236 LYS Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 236 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 173 optimal weight: 0.0970 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 0.0060 chunk 51 optimal weight: 4.9990 overall best weight: 2.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 155 ASN A 216 GLN B 112 HIS B 221 GLN C 214 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 216 GLN J 112 HIS J 221 GLN K 214 GLN N 252 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18882 Z= 0.211 Angle : 0.528 11.411 25886 Z= 0.284 Chirality : 0.041 0.145 2852 Planarity : 0.003 0.036 3010 Dihedral : 18.477 86.662 3172 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.97 % Allowed : 15.90 % Favored : 81.12 % 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: 0.90 (0.19), residues: 2032 helix: 2.26 (0.17), residues: 952 sheet: 1.03 (0.23), residues: 434 loop : -2.47 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 19 HIS 0.005 0.001 HIS E 12 PHE 0.015 0.001 PHE M 1 TYR 0.010 0.001 TYR B 83 ARG 0.004 0.000 ARG N 263 *********************** 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 249 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 197 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7351 (tt0) cc_final: 0.7068 (tt0) REVERT: B 136 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.7061 (mm-30) REVERT: B 258 LYS cc_start: 0.7987 (ptmm) cc_final: 0.7291 (ptpt) REVERT: D 68 LEU cc_start: 0.7692 (tp) cc_final: 0.7412 (tt) REVERT: D 159 LYS cc_start: 0.7136 (OUTLIER) cc_final: 0.6357 (ttmt) REVERT: D 234 GLN cc_start: 0.7769 (mt0) cc_final: 0.7530 (mp10) REVERT: M 7 LYS cc_start: 0.8041 (mttt) cc_final: 0.7658 (mtmt) REVERT: M 17 ASN cc_start: 0.8396 (OUTLIER) cc_final: 0.7319 (m110) REVERT: J 136 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7059 (mm-30) REVERT: J 154 MET cc_start: 0.7493 (mmt) cc_final: 0.7236 (mmt) REVERT: J 258 LYS cc_start: 0.8008 (ptmm) cc_final: 0.7269 (ptpt) REVERT: L 68 LEU cc_start: 0.7679 (tp) cc_final: 0.7437 (tt) REVERT: L 234 GLN cc_start: 0.7758 (mt0) cc_final: 0.7518 (mp10) REVERT: N 229 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.6665 (pp20) REVERT: N 252 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8185 (tp-100) REVERT: E 7 LYS cc_start: 0.8017 (mttt) cc_final: 0.7637 (mtmt) REVERT: E 17 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7382 (m110) outliers start: 52 outliers final: 21 residues processed: 232 average time/residue: 1.4910 time to fit residues: 383.5659 Evaluate side-chains 216 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 188 time to evaluate : 2.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU 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: 10.0000 chunk 182 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 94 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 ASN A 216 GLN B 221 GLN C 62 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 155 ASN I 216 GLN J 221 GLN K 62 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18882 Z= 0.210 Angle : 0.530 11.451 25886 Z= 0.285 Chirality : 0.041 0.145 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.486 86.427 3172 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.97 % Allowed : 16.59 % Favored : 80.43 % 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: 0.92 (0.19), residues: 2032 helix: 2.25 (0.17), residues: 952 sheet: 1.10 (0.23), residues: 434 loop : -2.46 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 19 HIS 0.004 0.001 HIS E 12 PHE 0.015 0.001 PHE E 1 TYR 0.010 0.001 TYR B 83 ARG 0.004 0.000 ARG F 263 *********************** 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 244 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 192 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7367 (tt0) cc_final: 0.7092 (tt0) REVERT: B 136 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: B 258 LYS cc_start: 0.7979 (ptmm) cc_final: 0.7275 (ptpt) REVERT: C 62 GLN cc_start: 0.7357 (mt0) cc_final: 0.7017 (mt0) REVERT: D 68 LEU cc_start: 0.7754 (tp) cc_final: 0.7498 (tt) REVERT: D 159 LYS cc_start: 0.7148 (OUTLIER) cc_final: 0.6366 (ttmt) REVERT: D 234 GLN cc_start: 0.7771 (mt0) cc_final: 0.7530 (mp10) REVERT: M 7 LYS cc_start: 0.8066 (mttt) cc_final: 0.7693 (mtmt) REVERT: M 17 ASN cc_start: 0.8460 (OUTLIER) cc_final: 0.7404 (m110) REVERT: J 136 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: J 154 MET cc_start: 0.7488 (mmt) cc_final: 0.7248 (mmt) REVERT: J 258 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7290 (ptpt) REVERT: K 62 GLN cc_start: 0.7314 (mt0) cc_final: 0.6993 (mt0) REVERT: L 68 LEU cc_start: 0.7645 (tp) cc_final: 0.7398 (tt) REVERT: L 234 GLN cc_start: 0.7767 (mt0) cc_final: 0.7523 (mp10) REVERT: N 229 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6639 (pp20) REVERT: E 7 LYS cc_start: 0.8052 (mttt) cc_final: 0.7669 (mtmt) REVERT: E 17 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.7419 (m110) outliers start: 52 outliers final: 24 residues processed: 227 average time/residue: 1.4524 time to fit residues: 365.5853 Evaluate side-chains 218 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 188 time to evaluate : 2.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 202 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 221 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN I 216 GLN J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18882 Z= 0.244 Angle : 0.555 11.466 25886 Z= 0.300 Chirality : 0.043 0.146 2852 Planarity : 0.004 0.037 3010 Dihedral : 18.556 85.807 3172 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.03 % Allowed : 16.59 % Favored : 80.38 % 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: 0.82 (0.19), residues: 2032 helix: 2.16 (0.16), residues: 954 sheet: 1.13 (0.24), residues: 430 loop : -2.52 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 19 HIS 0.005 0.001 HIS M 12 PHE 0.016 0.001 PHE M 1 TYR 0.009 0.002 TYR C 194 ARG 0.005 0.000 ARG F 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 249 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 196 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7376 (tt0) cc_final: 0.7164 (tt0) REVERT: B 136 GLU cc_start: 0.7421 (OUTLIER) cc_final: 0.7090 (mm-30) REVERT: B 258 LYS cc_start: 0.7989 (ptmm) cc_final: 0.7272 (ptpt) REVERT: B 273 ARG cc_start: 0.7742 (mpt180) cc_final: 0.7461 (mmt180) REVERT: C 62 GLN cc_start: 0.7346 (mt0) cc_final: 0.6965 (mt0) REVERT: D 159 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6456 (ttmt) REVERT: D 234 GLN cc_start: 0.7801 (mt0) cc_final: 0.7561 (mp10) REVERT: M 7 LYS cc_start: 0.8103 (mttt) cc_final: 0.7719 (mtmt) REVERT: M 17 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.7501 (m110) REVERT: J 136 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7023 (mm-30) REVERT: J 258 LYS cc_start: 0.8023 (ptmm) cc_final: 0.7314 (ptpt) REVERT: J 273 ARG cc_start: 0.7678 (mpt180) cc_final: 0.7391 (mmt180) REVERT: K 62 GLN cc_start: 0.7405 (mt0) cc_final: 0.7033 (mt0) REVERT: L 68 LEU cc_start: 0.7829 (tp) cc_final: 0.7604 (tt) REVERT: L 150 VAL cc_start: 0.6857 (t) cc_final: 0.6593 (t) REVERT: L 152 GLU cc_start: 0.6010 (pm20) cc_final: 0.5771 (pm20) REVERT: L 234 GLN cc_start: 0.7783 (mt0) cc_final: 0.7540 (mp10) REVERT: N 229 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.6642 (pp20) REVERT: N 252 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: E 7 LYS cc_start: 0.8101 (mttt) cc_final: 0.7714 (mtmt) REVERT: E 17 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7522 (m110) outliers start: 53 outliers final: 26 residues processed: 231 average time/residue: 1.3778 time to fit residues: 354.4399 Evaluate side-chains 225 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 192 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 100 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 184 optimal weight: 30.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 221 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18882 Z= 0.228 Angle : 0.545 11.429 25886 Z= 0.294 Chirality : 0.042 0.145 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.533 85.538 3172 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.03 % Allowed : 17.28 % Favored : 79.69 % 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: 0.88 (0.19), residues: 2032 helix: 2.20 (0.16), residues: 954 sheet: 1.13 (0.23), residues: 430 loop : -2.48 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 19 HIS 0.004 0.001 HIS M 12 PHE 0.016 0.001 PHE E 1 TYR 0.009 0.001 TYR K 194 ARG 0.004 0.000 ARG F 263 *********************** 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 247 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 2.195 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7428 (tt0) cc_final: 0.7192 (tt0) REVERT: B 136 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7081 (mm-30) REVERT: B 258 LYS cc_start: 0.7965 (ptmm) cc_final: 0.7258 (ptpt) REVERT: B 273 ARG cc_start: 0.7754 (mpt180) cc_final: 0.7445 (mmt180) REVERT: C 62 GLN cc_start: 0.7384 (mt0) cc_final: 0.7003 (mt0) REVERT: D 68 LEU cc_start: 0.7750 (tp) cc_final: 0.7345 (tt) REVERT: D 159 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6444 (ttmt) REVERT: D 234 GLN cc_start: 0.7799 (mt0) cc_final: 0.7571 (mp10) REVERT: F 252 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: M 7 LYS cc_start: 0.8091 (mttt) cc_final: 0.7708 (mtmt) REVERT: M 17 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.7548 (m110) REVERT: J 136 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6995 (mm-30) REVERT: J 258 LYS cc_start: 0.8042 (ptmm) cc_final: 0.7307 (ptpt) REVERT: J 273 ARG cc_start: 0.7723 (mpt180) cc_final: 0.7404 (mmt180) REVERT: K 62 GLN cc_start: 0.7403 (mt0) cc_final: 0.7033 (mt0) REVERT: L 68 LEU cc_start: 0.7825 (tp) cc_final: 0.7603 (tt) REVERT: L 152 GLU cc_start: 0.5990 (pm20) cc_final: 0.5789 (pm20) REVERT: L 234 GLN cc_start: 0.7779 (mt0) cc_final: 0.7537 (mp10) REVERT: N 229 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6567 (pp20) REVERT: N 252 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7635 (tt0) REVERT: E 7 LYS cc_start: 0.8088 (mttt) cc_final: 0.7702 (mtmt) REVERT: E 17 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.7571 (m110) outliers start: 53 outliers final: 32 residues processed: 226 average time/residue: 1.4808 time to fit residues: 374.0900 Evaluate side-chains 235 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 236 LYS Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 188 optimal weight: 0.0670 chunk 113 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 0.0470 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 123 optimal weight: 0.8980 overall best weight: 2.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 221 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 221 GLN K 214 GLN L 134 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18882 Z= 0.259 Angle : 0.566 11.454 25886 Z= 0.307 Chirality : 0.043 0.148 2852 Planarity : 0.004 0.037 3010 Dihedral : 18.592 85.471 3172 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.86 % Allowed : 17.68 % 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: 0.79 (0.19), residues: 2032 helix: 2.12 (0.16), residues: 954 sheet: 1.06 (0.24), residues: 432 loop : -2.48 (0.22), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 19 HIS 0.005 0.001 HIS E 12 PHE 0.017 0.002 PHE M 1 TYR 0.010 0.002 TYR K 194 ARG 0.005 0.000 ARG F 263 *********************** 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 245 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7402 (tt0) cc_final: 0.7174 (tt0) REVERT: B 136 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7067 (mm-30) REVERT: B 258 LYS cc_start: 0.7895 (ptmm) cc_final: 0.7221 (ptpt) REVERT: B 273 ARG cc_start: 0.7752 (mpt180) cc_final: 0.7398 (mmt180) REVERT: C 62 GLN cc_start: 0.7328 (mt0) cc_final: 0.6958 (mt0) REVERT: D 68 LEU cc_start: 0.7749 (tp) cc_final: 0.7326 (tt) REVERT: D 159 LYS cc_start: 0.7226 (OUTLIER) cc_final: 0.6481 (ttmt) REVERT: F 229 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: F 252 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7737 (tt0) REVERT: M 7 LYS cc_start: 0.8144 (mttt) cc_final: 0.7748 (mtmt) REVERT: M 17 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.7567 (m110) REVERT: J 136 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7027 (mm-30) REVERT: J 258 LYS cc_start: 0.8029 (ptmm) cc_final: 0.7305 (ptpt) REVERT: J 273 ARG cc_start: 0.7720 (mpt180) cc_final: 0.7364 (mmt180) REVERT: K 62 GLN cc_start: 0.7378 (mt0) cc_final: 0.7006 (mt0) REVERT: L 150 VAL cc_start: 0.6814 (t) cc_final: 0.6550 (t) REVERT: L 152 GLU cc_start: 0.5947 (pm20) cc_final: 0.5742 (pm20) REVERT: N 229 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: N 252 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: E 7 LYS cc_start: 0.8144 (mttt) cc_final: 0.7747 (mtmt) REVERT: E 17 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.7527 (m110) outliers start: 50 outliers final: 33 residues processed: 225 average time/residue: 1.4164 time to fit residues: 354.5147 Evaluate side-chains 236 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 229 GLU Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL 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: 3.9990 chunk 94 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 216 GLN B 221 GLN C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18882 Z= 0.302 Angle : 0.596 11.447 25886 Z= 0.324 Chirality : 0.044 0.160 2852 Planarity : 0.004 0.039 3010 Dihedral : 18.670 84.984 3172 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.80 % Allowed : 18.08 % Favored : 79.12 % 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: 0.66 (0.19), residues: 2032 helix: 1.97 (0.16), residues: 956 sheet: 1.03 (0.24), residues: 432 loop : -2.52 (0.22), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 19 HIS 0.005 0.001 HIS E 12 PHE 0.020 0.002 PHE E 1 TYR 0.011 0.002 TYR K 194 ARG 0.006 0.001 ARG F 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 242 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 193 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 87 GLU cc_start: 0.7447 (tt0) cc_final: 0.7225 (tt0) REVERT: B 136 GLU cc_start: 0.7442 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: C 62 GLN cc_start: 0.7352 (mt0) cc_final: 0.6984 (mt0) REVERT: D 159 LYS cc_start: 0.7142 (OUTLIER) cc_final: 0.6405 (ttmt) REVERT: F 252 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.7763 (tt0) REVERT: M 7 LYS cc_start: 0.8183 (mttt) cc_final: 0.7796 (mtmt) REVERT: M 17 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7610 (m110) REVERT: J 136 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7063 (mm-30) REVERT: J 258 LYS cc_start: 0.8082 (ptmm) cc_final: 0.7339 (ptpt) REVERT: K 62 GLN cc_start: 0.7361 (mt0) cc_final: 0.7004 (mt0) REVERT: L 150 VAL cc_start: 0.6863 (t) cc_final: 0.6585 (t) REVERT: L 152 GLU cc_start: 0.6021 (pm20) cc_final: 0.5732 (pm20) REVERT: N 229 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.6610 (pp20) REVERT: N 252 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7675 (tt0) REVERT: E 7 LYS cc_start: 0.8181 (mttt) cc_final: 0.7788 (mtmt) REVERT: E 17 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.7588 (m110) outliers start: 49 outliers final: 33 residues processed: 224 average time/residue: 1.4285 time to fit residues: 355.7227 Evaluate side-chains 231 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 190 time to evaluate : 2.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 63 MET Chi-restraints excluded: chain B residue 136 GLU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 188 LYS Chi-restraints excluded: chain C residue 194 TYR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 159 LYS Chi-restraints excluded: chain D residue 222 ASN Chi-restraints excluded: chain D residue 240 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain M residue 17 ASN Chi-restraints excluded: chain M residue 42 LYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain I residue 31 VAL Chi-restraints excluded: chain I residue 48 GLU Chi-restraints excluded: chain I residue 225 VAL Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 270 ASP Chi-restraints excluded: chain K residue 84 ILE Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 188 LYS Chi-restraints excluded: chain K residue 194 TYR Chi-restraints excluded: chain L residue 57 SER Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain L residue 222 ASN Chi-restraints excluded: chain L residue 240 THR Chi-restraints excluded: chain N residue 229 GLU Chi-restraints excluded: chain N residue 252 GLN Chi-restraints excluded: chain E residue 17 ASN Chi-restraints excluded: chain E residue 42 LYS Chi-restraints excluded: chain E residue 45 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 153 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 146 optimal weight: 5.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN B 221 GLN C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 216 GLN J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.156932 restraints weight = 17550.052| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.55 r_work: 0.3324 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18882 Z= 0.188 Angle : 0.527 11.414 25886 Z= 0.284 Chirality : 0.041 0.141 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.487 84.967 3172 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.75 % Allowed : 18.19 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.19), residues: 2032 helix: 2.26 (0.17), residues: 954 sheet: 1.15 (0.24), residues: 430 loop : -2.41 (0.22), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 19 HIS 0.003 0.001 HIS E 12 PHE 0.014 0.001 PHE E 1 TYR 0.010 0.001 TYR J 83 ARG 0.004 0.000 ARG F 224 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6464.37 seconds wall clock time: 116 minutes 23.87 seconds (6983.87 seconds total)