Starting phenix.real_space_refine (version: dev) on Wed Apr 6 05:06:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_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_10042/04_2022/6rwm_10042_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rwm_10042/04_2022/6rwm_10042_updated.pdb" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Convert atoms to be neutral 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {' ZN': 1, ' MG': 2, 'KLQ': 1, ' CL': 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: {' ZN': 1, ' MG': 2, 'KLQ': 1, ' CL': 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: 10.82, per 1000 atoms: 0.59 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: 7.28 Conformation dependent library (CDL) restraints added in 3.1 seconds Dynamic metal coordination Zn2+ tetrahedral 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: 6.73 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: 6.40 Time building geometry restraints manager: 7.88 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 1.987 1.360 0.627 2.00e-02 2.50e+03 9.83e+02 bond pdb=" CAJ KLQ I 304 " pdb=" CAX KLQ I 304 " ideal model delta sigma weight residual 1.987 1.361 0.626 2.00e-02 2.50e+03 9.80e+02 bond pdb=" CAW KLQ A 304 " pdb=" CBA KLQ A 304 " ideal model delta sigma weight residual 0.988 1.447 -0.459 2.00e-02 2.50e+03 5.27e+02 bond pdb=" CAW KLQ I 304 " pdb=" CBA KLQ I 304 " ideal model delta sigma weight residual 0.988 1.442 -0.454 2.00e-02 2.50e+03 5.14e+02 bond pdb=" CBD KLQ I 304 " pdb=" OAQ KLQ I 304 " ideal model delta sigma weight residual 1.766 1.416 0.350 2.00e-02 2.50e+03 3.05e+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 144.65 118.09 26.56 3.00e+00 1.11e-01 7.84e+01 angle pdb=" CAY KLQ I 304 " pdb=" CAV KLQ I 304 " pdb=" FAG KLQ I 304 " ideal model delta sigma weight residual 144.65 118.19 26.46 3.00e+00 1.11e-01 7.78e+01 angle pdb=" CAI KLQ A 304 " pdb=" CAV KLQ A 304 " pdb=" FAG KLQ A 304 " ideal model delta sigma weight residual 94.22 115.14 -20.92 3.00e+00 1.11e-01 4.86e+01 angle pdb=" CAI KLQ I 304 " pdb=" CAV KLQ I 304 " pdb=" FAG KLQ I 304 " ideal model delta sigma weight residual 94.22 115.12 -20.90 3.00e+00 1.11e-01 4.86e+01 angle pdb=" CAX KLQ A 304 " pdb=" CAJ KLQ A 304 " pdb=" NBF KLQ A 304 " ideal model delta sigma weight residual 106.10 124.06 -17.96 3.00e+00 1.11e-01 3.58e+01 ... (remaining 25881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 9549 17.36 - 34.71: 842 34.71 - 52.07: 433 52.07 - 69.43: 94 69.43 - 86.79: 10 Dihedral angle restraints: 10928 sinusoidal: 4970 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 10925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2452 0.072 - 0.144: 364 0.144 - 0.216: 30 0.216 - 0.288: 4 0.288 - 0.360: 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 -2.56 -2.92 0.36 2.00e-01 2.50e+01 3.25e+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 -2.56 -2.91 0.36 2.00e-01 2.50e+01 3.17e+00 chirality pdb=" CBD KLQ I 304 " pdb=" CAO KLQ I 304 " pdb=" NBE KLQ I 304 " pdb=" OAQ KLQ I 304 " both_signs ideal model delta sigma weight residual False 2.56 2.30 0.26 2.00e-01 2.50e+01 1.72e+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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.430 Check model and map are aligned: 0.280 Convert atoms to be neutral: 0.160 Process input model: 60.140 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 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 : 0.012 0.627 18882 Z= 0.664 Angle : 0.853 26.559 25886 Z= 0.460 Chirality : 0.052 0.360 2852 Planarity : 0.006 0.055 3010 Dihedral : 16.838 86.786 7064 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 % 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 *********************** 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 : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 13 residues processed: 363 average time/residue: 1.4021 time to fit residues: 563.0770 Evaluate side-chains 203 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 190 time to evaluate : 2.149 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 1.7326 time to fit residues: 4.7043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 4.9990 chunk 159 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** B 9 GLN B 157 GLN C 17 ASN C 62 GLN 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** J 9 GLN J 157 GLN K 62 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: 0.8078 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 18882 Z= 0.193 Angle : 0.539 10.836 25886 Z= 0.294 Chirality : 0.041 0.145 2852 Planarity : 0.004 0.045 3010 Dihedral : 18.365 88.421 3034 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.97 % 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: -0.55 (0.17), residues: 2032 helix: 0.84 (0.16), residues: 950 sheet: 0.68 (0.23), residues: 438 loop : -3.05 (0.19), residues: 644 *********************** 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 261 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 209 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 25 residues processed: 245 average time/residue: 1.3407 time to fit residues: 367.5416 Evaluate side-chains 220 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 2.179 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 4 average time/residue: 0.9492 time to fit residues: 7.1774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 191 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 127 GLN ** I 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.046 18882 Z= 0.285 Angle : 0.586 11.446 25886 Z= 0.319 Chirality : 0.044 0.161 2852 Planarity : 0.004 0.042 3010 Dihedral : 18.492 86.692 3034 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 3.32 % 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: -0.01 (0.18), residues: 2032 helix: 1.46 (0.17), residues: 950 sheet: 0.76 (0.23), residues: 434 loop : -2.92 (0.20), residues: 648 *********************** 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 251 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 2.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 33 residues processed: 237 average time/residue: 1.3380 time to fit residues: 354.1229 Evaluate side-chains 224 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 191 time to evaluate : 2.090 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 31 residues processed: 5 average time/residue: 0.2336 time to fit residues: 4.6897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 5.9990 chunk 143 optimal weight: 0.0370 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 191 optimal weight: 0.9980 chunk 202 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 181 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 HIS A 148 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 HIS I 127 GLN I 148 GLN J 112 HIS K 214 GLN N 252 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 18882 Z= 0.133 Angle : 0.482 11.599 25886 Z= 0.260 Chirality : 0.039 0.137 2852 Planarity : 0.003 0.038 3010 Dihedral : 18.298 88.169 3034 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer Outliers : 2.69 % 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: 0.66 (0.19), residues: 2032 helix: 2.04 (0.17), residues: 958 sheet: 0.90 (0.23), residues: 440 loop : -2.59 (0.21), residues: 634 *********************** 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 252 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 205 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 29 residues processed: 241 average time/residue: 1.2920 time to fit residues: 350.1258 Evaluate side-chains 211 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 182 time to evaluate : 2.138 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 27 residues processed: 3 average time/residue: 1.1710 time to fit residues: 6.7017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 20.0000 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 0.0370 chunk 151 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 140 optimal weight: 0.9980 chunk 0 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 overall best weight: 1.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN C 214 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 18882 Z= 0.175 Angle : 0.510 11.577 25886 Z= 0.274 Chirality : 0.040 0.141 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.359 87.274 3034 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 2032 helix: 2.20 (0.17), residues: 960 sheet: 0.91 (0.23), residues: 440 loop : -2.46 (0.22), residues: 632 *********************** 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 259 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 194 time to evaluate : 2.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 38 residues processed: 244 average time/residue: 1.3741 time to fit residues: 376.3325 Evaluate side-chains 224 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 186 time to evaluate : 2.020 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 35 residues processed: 5 average time/residue: 0.5531 time to fit residues: 6.2819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 168 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN B 221 GLN C 214 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 27 GLN J 221 GLN K 99 HIS K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2375 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= 0.181 Angle : 0.513 11.581 25886 Z= 0.275 Chirality : 0.041 0.142 2852 Planarity : 0.003 0.036 3010 Dihedral : 18.366 86.843 3034 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer Outliers : 3.32 % 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: 0.93 (0.19), residues: 2032 helix: 2.24 (0.17), residues: 962 sheet: 1.07 (0.23), residues: 434 loop : -2.44 (0.22), residues: 636 *********************** 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 251 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 193 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 37 residues processed: 235 average time/residue: 1.3697 time to fit residues: 359.9733 Evaluate side-chains 226 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 189 time to evaluate : 2.237 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 34 residues processed: 4 average time/residue: 0.7101 time to fit residues: 6.5088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 0.9980 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 113 optimal weight: 50.0000 chunk 202 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN C 214 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 221 GLN K 214 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2369 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= 0.213 Angle : 0.535 11.565 25886 Z= 0.288 Chirality : 0.042 0.146 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.418 86.502 3034 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 3.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 2032 helix: 2.21 (0.17), residues: 962 sheet: 1.09 (0.23), residues: 434 loop : -2.44 (0.22), residues: 636 *********************** 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 245 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 192 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 38 residues processed: 234 average time/residue: 1.3758 time to fit residues: 359.4740 Evaluate side-chains 227 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 2.173 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 33 residues processed: 6 average time/residue: 0.6098 time to fit residues: 7.4904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 120 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 128 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN C 214 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 18882 Z= 0.146 Angle : 0.488 11.576 25886 Z= 0.261 Chirality : 0.040 0.139 2852 Planarity : 0.003 0.036 3010 Dihedral : 18.307 87.311 3034 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.19), residues: 2032 helix: 2.43 (0.17), residues: 962 sheet: 1.24 (0.23), residues: 434 loop : -2.32 (0.23), residues: 636 *********************** 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 241 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 34 residues processed: 233 average time/residue: 1.3217 time to fit residues: 345.6436 Evaluate side-chains 220 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 2.177 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 33 residues processed: 1 average time/residue: 1.8382 time to fit residues: 4.8472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 188 optimal weight: 0.6980 chunk 113 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 170 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN L 134 GLN N 252 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 18882 Z= 0.241 Angle : 0.554 11.555 25886 Z= 0.299 Chirality : 0.043 0.176 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.447 86.152 3034 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 2032 helix: 2.29 (0.16), residues: 954 sheet: 1.17 (0.23), residues: 434 loop : -2.40 (0.22), residues: 644 *********************** 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 244 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 195 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 39 residues processed: 235 average time/residue: 1.3353 time to fit residues: 351.5248 Evaluate side-chains 227 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 1.954 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 34 residues processed: 5 average time/residue: 1.2499 time to fit residues: 9.5427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 166 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 214 GLN D 134 GLN F 252 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN L 134 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2500 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= 0.202 Angle : 0.531 11.558 25886 Z= 0.285 Chirality : 0.041 0.153 2852 Planarity : 0.003 0.037 3010 Dihedral : 18.415 86.131 3034 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 2032 helix: 2.35 (0.17), residues: 954 sheet: 1.21 (0.23), residues: 434 loop : -2.38 (0.22), residues: 644 ********************** 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 243 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 198 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 35 residues processed: 240 average time/residue: 1.3299 time to fit residues: 357.5431 Evaluate side-chains 234 residues out of total 1750 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 199 time to evaluate : 2.255 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 35 residues processed: 0 time to fit residues: 3.0882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 153 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.0470 chunk 146 optimal weight: 9.9990 overall best weight: 1.0682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 252 GLN C 214 GLN D 134 GLN ** M 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN L 134 GLN ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.201442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.160740 restraints weight = 17609.017| |-----------------------------------------------------------------------------| r_work (start): 0.3849 rms_B_bonded: 2.52 r_work: 0.3756 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work: 0.3603 rms_B_bonded: 3.69 restraints_weight: 0.1250 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 18882 Z= 0.147 Angle : 0.495 11.588 25886 Z= 0.264 Chirality : 0.040 0.141 2852 Planarity : 0.003 0.036 3010 Dihedral : 18.320 87.051 3034 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 2.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 2032 helix: 2.49 (0.17), residues: 962 sheet: 1.14 (0.23), residues: 446 loop : -2.22 (0.23), residues: 624 =============================================================================== Job complete usr+sys time: 5689.04 seconds wall clock time: 102 minutes 23.23 seconds (6143.23 seconds total)