Starting phenix.real_space_refine on Mon Feb 19 12:40:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nj9_9384/02_2024/6nj9_9384_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5986 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 38 5.16 5 C 10962 2.51 5 N 3442 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B GLU 63": "OE1" <-> "OE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 11": "NH1" <-> "NH2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 30": "NH1" <-> "NH2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F GLU 63": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 30": "NH1" <-> "NH2" Residue "H ASP 51": "OD1" <-> "OD2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K ASP 28": "OD1" <-> "OD2" Residue "K ASP 32": "OD1" <-> "OD2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K ASP 83": "OD1" <-> "OD2" Residue "K TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 149": "OD1" <-> "OD2" Residue "K GLU 186": "OE1" <-> "OE2" Residue "K ASP 189": "OD1" <-> "OD2" Residue "K PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 255": "OE1" <-> "OE2" Residue "K ARG 278": "NH1" <-> "NH2" Residue "L GLU 34": "OE1" <-> "OE2" Residue "L ASP 39": "OD1" <-> "OD2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "L ASP 52": "OD1" <-> "OD2" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ARG 74": "NH1" <-> "NH2" Residue "M GLU 16": "OE1" <-> "OE2" Residue "M ASP 28": "OD1" <-> "OD2" Residue "M ASP 32": "OD1" <-> "OD2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 69": "OE1" <-> "OE2" Residue "M ASP 83": "OD1" <-> "OD2" Residue "M TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 149": "OD1" <-> "OD2" Residue "M GLU 186": "OE1" <-> "OE2" Residue "M ASP 189": "OD1" <-> "OD2" Residue "M PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 255": "OE1" <-> "OE2" Residue "M ARG 278": "NH1" <-> "NH2" Residue "N GLU 34": "OE1" <-> "OE2" Residue "N ASP 39": "OD1" <-> "OD2" Residue "N ARG 42": "NH1" <-> "NH2" Residue "N ASP 52": "OD1" <-> "OD2" Residue "N GLU 64": "OE1" <-> "OE2" Residue "N ARG 74": "NH1" <-> "NH2" 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: 18814 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 743 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Planarities with less than four sites: {'NLE:plan-1': 3} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 743 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2680 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain: "L" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "M" Number of atoms: 2680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2680 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain: "N" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N LEU N 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU N 73 " occ=0.45 Time building chain proxies: 9.72, per 1000 atoms: 0.52 Number of scatterers: 18814 At special positions: 0 Unit cell: (126.616, 175.56, 117.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 292 15.00 O 4080 8.00 N 3442 7.00 C 10962 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: 7.40 Conformation dependent library (CDL) restraints added in 2.4 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 4 sheets defined 48.6% alpha, 5.2% beta 136 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 9.09 Creating SS restraints... Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.661A pdb=" N ARG A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 77 removed outlier: 3.914A pdb=" N GLN A 76 " --> pdb=" O ARG A 72 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 113 removed outlier: 4.030A pdb=" N VAL A 101 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN A 108 " --> pdb=" O GLU A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.733A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.780A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.820A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 38 through 48 removed outlier: 3.600A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.946A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.661A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.914A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 113 removed outlier: 4.031A pdb=" N VAL E 101 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASN E 108 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 131 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.733A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.781A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.819A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 38 through 48 removed outlier: 3.601A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.946A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS H 109 " --> pdb=" O GLU H 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 49 through 53 Processing helix chain 'K' and resid 68 through 88 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 190 through 209 removed outlier: 4.046A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 200 " --> pdb=" O GLU K 196 " (cutoff:3.500A) Processing helix chain 'K' and resid 229 through 233 Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 246 through 259 removed outlier: 3.549A pdb=" N GLN K 252 " --> pdb=" O GLU K 248 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA K 258 " --> pdb=" O LYS K 254 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ASN K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 290 Processing helix chain 'K' and resid 320 through 329 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 38 through 40 No H-bonds generated for 'chain 'L' and resid 38 through 40' Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing helix chain 'M' and resid 33 through 47 Processing helix chain 'M' and resid 49 through 53 Processing helix chain 'M' and resid 68 through 88 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 122 through 126 Processing helix chain 'M' and resid 141 through 150 Processing helix chain 'M' and resid 168 through 176 Processing helix chain 'M' and resid 190 through 209 removed outlier: 4.045A pdb=" N THR M 197 " --> pdb=" O LYS M 193 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG M 200 " --> pdb=" O GLU M 196 " (cutoff:3.500A) Processing helix chain 'M' and resid 229 through 233 Processing helix chain 'M' and resid 242 through 244 No H-bonds generated for 'chain 'M' and resid 242 through 244' Processing helix chain 'M' and resid 246 through 259 removed outlier: 3.549A pdb=" N GLN M 252 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN M 259 " --> pdb=" O GLU M 255 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 290 Processing helix chain 'M' and resid 320 through 329 Processing helix chain 'N' and resid 23 through 34 Processing helix chain 'N' and resid 38 through 40 No H-bonds generated for 'chain 'N' and resid 38 through 40' Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 291 through 294 removed outlier: 3.664A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU K 215 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N GLY K 184 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR K 217 " --> pdb=" O GLY K 184 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLU K 186 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU K 219 " --> pdb=" O GLU K 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.629A pdb=" N HIS L 68 " --> pdb=" O ILE L 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE L 44 " --> pdb=" O HIS L 68 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 291 through 294 removed outlier: 3.663A pdb=" N PHE M 159 " --> pdb=" O HIS M 181 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU M 215 " --> pdb=" O HIS M 182 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N GLY M 184 " --> pdb=" O GLU M 215 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N THR M 217 " --> pdb=" O GLY M 184 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N GLU M 186 " --> pdb=" O THR M 217 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N GLU M 219 " --> pdb=" O GLU M 186 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 12 through 16 removed outlier: 3.630A pdb=" N HIS N 68 " --> pdb=" O ILE N 44 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE N 44 " --> pdb=" O HIS N 68 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 353 hydrogen bonds 706 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 6.79 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 - 1.32: 3152 1.32 - 1.44: 6259 1.44 - 1.57: 9721 1.57 - 1.69: 580 1.69 - 1.81: 68 Bond restraints: 19780 Sorted by residual: bond pdb=" CG1 ILE A 51 " pdb=" CD1 ILE A 51 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.16e+00 bond pdb=" CG1 ILE E 51 " pdb=" CD1 ILE E 51 " ideal model delta sigma weight residual 1.513 1.402 0.111 3.90e-02 6.57e+02 8.09e+00 bond pdb=" CB ARG B 78 " pdb=" CG ARG B 78 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.04e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.435 0.085 3.00e-02 1.11e+03 8.01e+00 bond pdb=" CB ARG E 131 " pdb=" CG ARG E 131 " ideal model delta sigma weight residual 1.520 1.439 0.081 3.00e-02 1.11e+03 7.29e+00 ... (remaining 19775 not shown) Histogram of bond angle deviations from ideal: 94.55 - 102.45: 500 102.45 - 110.34: 7222 110.34 - 118.23: 8743 118.23 - 126.12: 10479 126.12 - 134.01: 1044 Bond angle restraints: 27988 Sorted by residual: angle pdb=" C LYS M 10 " pdb=" N SER M 11 " pdb=" CA SER M 11 " ideal model delta sigma weight residual 121.17 130.34 -9.17 1.62e+00 3.81e-01 3.21e+01 angle pdb=" C LYS K 10 " pdb=" N SER K 11 " pdb=" CA SER K 11 " ideal model delta sigma weight residual 121.17 130.31 -9.14 1.62e+00 3.81e-01 3.19e+01 angle pdb=" N TYR K 58 " pdb=" CA TYR K 58 " pdb=" CB TYR K 58 " ideal model delta sigma weight residual 114.17 107.91 6.26 1.14e+00 7.69e-01 3.01e+01 angle pdb=" N TYR M 58 " pdb=" CA TYR M 58 " pdb=" CB TYR M 58 " ideal model delta sigma weight residual 114.17 107.92 6.25 1.14e+00 7.69e-01 3.00e+01 angle pdb=" N TYR M 312 " pdb=" CA TYR M 312 " pdb=" C TYR M 312 " ideal model delta sigma weight residual 113.02 120.33 -7.31 1.49e+00 4.50e-01 2.40e+01 ... (remaining 27983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.83: 9569 34.83 - 69.66: 1636 69.66 - 104.50: 20 104.50 - 139.33: 0 139.33 - 174.16: 3 Dihedral angle restraints: 11228 sinusoidal: 6584 harmonic: 4644 Sorted by residual: dihedral pdb=" CA TYR K 312 " pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta harmonic sigma weight residual 180.00 151.05 28.95 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA TYR M 312 " pdb=" C TYR M 312 " pdb=" N TYR M 313 " pdb=" CA TYR M 313 " ideal model delta harmonic sigma weight residual 180.00 151.06 28.94 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA LYS E 37 " pdb=" C LYS E 37 " pdb=" N PRO E 38 " pdb=" CA PRO E 38 " ideal model delta harmonic sigma weight residual 180.00 155.25 24.75 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 11225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1862 0.052 - 0.104: 1005 0.104 - 0.156: 247 0.156 - 0.207: 25 0.207 - 0.259: 7 Chirality restraints: 3146 Sorted by residual: chirality pdb=" CA TYR M 312 " pdb=" N TYR M 312 " pdb=" C TYR M 312 " pdb=" CB TYR M 312 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA TYR K 312 " pdb=" N TYR K 312 " pdb=" C TYR K 312 " pdb=" CB TYR K 312 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ARG E 83 " pdb=" N ARG E 83 " pdb=" C ARG E 83 " pdb=" CB ARG E 83 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 3143 not shown) Planarity restraints: 2544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR K 312 " -0.021 2.00e-02 2.50e+03 2.43e-02 1.18e+01 pdb=" CG TYR K 312 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR K 312 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR K 312 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR K 312 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR K 312 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR K 312 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 312 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 312 " 0.021 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR M 312 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR M 312 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR M 312 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR M 312 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 312 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR M 312 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR M 312 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " -0.054 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO A 38 " 0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.045 5.00e-02 4.00e+02 ... (remaining 2541 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 5379 2.83 - 3.35: 15563 3.35 - 3.86: 32821 3.86 - 4.38: 41005 4.38 - 4.90: 60008 Nonbonded interactions: 154776 Sorted by model distance: nonbonded pdb=" OG1 THR M 40 " pdb=" OH TYR M 209 " model vdw 2.309 2.440 nonbonded pdb=" OG1 THR K 40 " pdb=" OH TYR K 209 " model vdw 2.309 2.440 nonbonded pdb=" O SER H 123 " pdb=" OG SER H 123 " model vdw 2.314 2.440 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.315 2.440 nonbonded pdb=" O2' SAM K 500 " pdb=" O3' SAM K 500 " model vdw 2.339 2.432 ... (remaining 154771 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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=0.45 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.020 Extract box with map and model: 4.400 Check model and map are aligned: 0.270 Set scattering table: 0.180 Process input model: 54.840 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 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 : 0.015 0.111 19780 Z= 0.888 Angle : 0.997 9.623 27988 Z= 0.570 Chirality : 0.061 0.259 3146 Planarity : 0.006 0.081 2544 Dihedral : 24.776 174.160 8224 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.29 % Allowed : 5.55 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.18), residues: 1548 helix: -1.56 (0.15), residues: 824 sheet: -0.89 (0.39), residues: 162 loop : -2.28 (0.22), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 43 HIS 0.010 0.002 HIS N 68 PHE 0.031 0.004 PHE K 68 TYR 0.060 0.003 TYR K 312 ARG 0.026 0.001 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.588 Fit side-chains REVERT: C 61 GLU cc_start: 0.7988 (tp30) cc_final: 0.7744 (tp30) REVERT: D 76 GLU cc_start: 0.8110 (tp30) cc_final: 0.7823 (tp30) REVERT: G 61 GLU cc_start: 0.7995 (tp30) cc_final: 0.7758 (tp30) REVERT: G 74 LYS cc_start: 0.8522 (mttp) cc_final: 0.8319 (mttm) REVERT: H 76 GLU cc_start: 0.8035 (tp30) cc_final: 0.7768 (tp30) REVERT: K 55 MET cc_start: 0.2536 (mmm) cc_final: 0.1835 (mmt) REVERT: K 153 MET cc_start: 0.6662 (mtp) cc_final: 0.6261 (ttm) REVERT: K 201 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7963 (mm-30) REVERT: M 55 MET cc_start: 0.2473 (mmm) cc_final: 0.1752 (mmt) REVERT: M 201 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7983 (mm-30) outliers start: 4 outliers final: 3 residues processed: 191 average time/residue: 2.0619 time to fit residues: 425.3844 Evaluate side-chains 134 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 0.0980 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 139 optimal weight: 0.0970 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 40 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19780 Z= 0.164 Angle : 0.563 7.723 27988 Z= 0.327 Chirality : 0.037 0.136 3146 Planarity : 0.005 0.059 2544 Dihedral : 27.283 178.288 5030 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.31 % Allowed : 11.68 % Favored : 87.01 % 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: -0.83 (0.21), residues: 1548 helix: 0.13 (0.18), residues: 822 sheet: 0.34 (0.46), residues: 128 loop : -1.66 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 205 HIS 0.003 0.001 HIS M 251 PHE 0.031 0.002 PHE M 68 TYR 0.008 0.001 TYR K 312 ARG 0.007 0.000 ARG A 129 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 160 time to evaluate : 1.677 Fit side-chains REVERT: D 33 ARG cc_start: 0.7585 (mmm160) cc_final: 0.7306 (mtp-110) REVERT: D 76 GLU cc_start: 0.8114 (tp30) cc_final: 0.7823 (tp30) REVERT: G 99 ARG cc_start: 0.8193 (mtp180) cc_final: 0.7979 (mmm160) REVERT: H 33 ARG cc_start: 0.7420 (mmm160) cc_final: 0.7155 (mtp-110) REVERT: H 76 GLU cc_start: 0.8114 (tp30) cc_final: 0.7815 (tp30) REVERT: K 55 MET cc_start: 0.2320 (mmm) cc_final: 0.1666 (mmt) REVERT: K 153 MET cc_start: 0.6657 (mtp) cc_final: 0.6425 (ttm) REVERT: K 201 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8062 (mm-30) REVERT: M 55 MET cc_start: 0.2366 (mmm) cc_final: 0.1710 (mmt) REVERT: M 96 MET cc_start: 0.2356 (ptt) cc_final: 0.1413 (tpp) REVERT: M 153 MET cc_start: 0.6708 (mtp) cc_final: 0.6175 (ttm) REVERT: M 201 GLU cc_start: 0.8378 (mm-30) cc_final: 0.8065 (mm-30) outliers start: 18 outliers final: 4 residues processed: 166 average time/residue: 1.6975 time to fit residues: 307.9240 Evaluate side-chains 137 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 133 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 113 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 174 optimal weight: 0.1980 chunk 144 optimal weight: 0.4980 chunk 160 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 9.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 126 ASN L 41 GLN M 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19780 Z= 0.195 Angle : 0.547 5.849 27988 Z= 0.316 Chirality : 0.037 0.160 3146 Planarity : 0.005 0.046 2544 Dihedral : 27.348 178.812 5026 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.92 % Allowed : 12.34 % Favored : 84.74 % 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: -0.07 (0.22), residues: 1548 helix: 0.75 (0.18), residues: 822 sheet: 0.14 (0.46), residues: 142 loop : -1.19 (0.26), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 205 HIS 0.003 0.001 HIS K 315 PHE 0.023 0.002 PHE M 68 TYR 0.010 0.001 TYR E 54 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 140 time to evaluate : 1.532 Fit side-chains REVERT: A 131 ARG cc_start: 0.8570 (OUTLIER) cc_final: 0.8316 (mtp85) REVERT: B 77 LYS cc_start: 0.8593 (mttt) cc_final: 0.8363 (mttt) REVERT: D 33 ARG cc_start: 0.7720 (mmm160) cc_final: 0.7427 (mtp-110) REVERT: D 76 GLU cc_start: 0.8149 (tp30) cc_final: 0.7845 (tp30) REVERT: E 131 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.8319 (mtp85) REVERT: G 75 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8528 (mttp) REVERT: G 99 ARG cc_start: 0.8184 (mtp180) cc_final: 0.7958 (mmm160) REVERT: H 33 ARG cc_start: 0.7562 (mmm160) cc_final: 0.7213 (mtp-110) REVERT: H 76 GLU cc_start: 0.8124 (tp30) cc_final: 0.7817 (tp30) REVERT: K 55 MET cc_start: 0.2389 (mmm) cc_final: 0.1826 (mmt) REVERT: K 71 MET cc_start: 0.5655 (mtt) cc_final: 0.5335 (mtp) REVERT: K 96 MET cc_start: 0.2172 (ptt) cc_final: 0.1758 (tpp) REVERT: K 153 MET cc_start: 0.6739 (mtp) cc_final: 0.6409 (ttm) REVERT: M 55 MET cc_start: 0.2332 (mmm) cc_final: 0.1750 (mmt) REVERT: M 71 MET cc_start: 0.5535 (mtt) cc_final: 0.5224 (mtp) REVERT: M 96 MET cc_start: 0.2195 (OUTLIER) cc_final: 0.1320 (tpp) REVERT: M 153 MET cc_start: 0.6718 (mtp) cc_final: 0.6429 (ttm) outliers start: 40 outliers final: 16 residues processed: 158 average time/residue: 1.7229 time to fit residues: 297.7175 Evaluate side-chains 155 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 10.0000 chunk 121 optimal weight: 0.0170 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 162 optimal weight: 7.9990 chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 overall best weight: 2.7224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 ASN G 38 ASN K 181 HIS K 251 HIS L 41 GLN M 181 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 19780 Z= 0.374 Angle : 0.629 6.405 27988 Z= 0.356 Chirality : 0.042 0.176 3146 Planarity : 0.006 0.048 2544 Dihedral : 27.688 177.608 5026 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.80 % Allowed : 12.99 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.22), residues: 1548 helix: 0.63 (0.18), residues: 826 sheet: 0.25 (0.46), residues: 142 loop : -1.15 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 22 HIS 0.005 0.001 HIS K 315 PHE 0.020 0.002 PHE M 68 TYR 0.011 0.002 TYR H 37 ARG 0.005 0.001 ARG K 282 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 130 time to evaluate : 1.613 Fit side-chains REVERT: A 131 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8503 (mtp85) REVERT: B 77 LYS cc_start: 0.8638 (mttt) cc_final: 0.8426 (mttt) REVERT: D 76 GLU cc_start: 0.8147 (tp30) cc_final: 0.7832 (tp30) REVERT: E 131 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8481 (mtp85) REVERT: F 23 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7064 (ptp90) REVERT: G 75 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8435 (mttp) REVERT: K 55 MET cc_start: 0.2829 (mmm) cc_final: 0.2204 (mmt) REVERT: K 96 MET cc_start: 0.2049 (ptt) cc_final: 0.1470 (tpp) REVERT: K 153 MET cc_start: 0.6797 (mtp) cc_final: 0.6294 (ttm) REVERT: K 155 ASP cc_start: 0.7763 (m-30) cc_final: 0.7523 (m-30) REVERT: M 55 MET cc_start: 0.2777 (mmm) cc_final: 0.2159 (mmt) REVERT: M 71 MET cc_start: 0.5630 (mtt) cc_final: 0.5251 (mtp) REVERT: M 96 MET cc_start: 0.2285 (OUTLIER) cc_final: 0.0515 (ttp) REVERT: M 153 MET cc_start: 0.6804 (mtp) cc_final: 0.6541 (ttp) REVERT: M 180 LYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7601 (mtpm) outliers start: 52 outliers final: 21 residues processed: 160 average time/residue: 1.8114 time to fit residues: 316.4959 Evaluate side-chains 154 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 127 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 23 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 206 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 128 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19780 Z= 0.169 Angle : 0.559 7.780 27988 Z= 0.325 Chirality : 0.038 0.140 3146 Planarity : 0.004 0.044 2544 Dihedral : 27.570 177.986 5026 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.92 % Allowed : 14.60 % Favored : 82.48 % 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: 0.17 (0.22), residues: 1548 helix: 0.90 (0.18), residues: 826 sheet: 0.32 (0.47), residues: 142 loop : -1.03 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 205 HIS 0.004 0.001 HIS M 315 PHE 0.017 0.001 PHE M 68 TYR 0.010 0.001 TYR M 312 ARG 0.005 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 1.776 Fit side-chains REVERT: A 131 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8416 (mtp85) REVERT: D 33 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.7079 (mtp-110) REVERT: D 76 GLU cc_start: 0.8133 (tp30) cc_final: 0.7833 (tp30) REVERT: E 131 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8378 (mtp85) REVERT: G 75 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8402 (mttp) REVERT: H 33 ARG cc_start: 0.7529 (OUTLIER) cc_final: 0.7131 (mtp-110) REVERT: H 76 GLU cc_start: 0.8116 (tp30) cc_final: 0.7824 (tp30) REVERT: K 55 MET cc_start: 0.2832 (mmm) cc_final: 0.2199 (mmt) REVERT: K 75 CYS cc_start: 0.5206 (OUTLIER) cc_final: 0.5004 (p) REVERT: K 96 MET cc_start: 0.2006 (ptt) cc_final: 0.1479 (tpp) REVERT: K 153 MET cc_start: 0.6739 (mtp) cc_final: 0.6248 (ttm) REVERT: K 155 ASP cc_start: 0.7833 (m-30) cc_final: 0.7586 (m-30) REVERT: M 55 MET cc_start: 0.2784 (mmm) cc_final: 0.2237 (mmt) REVERT: M 71 MET cc_start: 0.5624 (mtt) cc_final: 0.5338 (mtt) REVERT: M 96 MET cc_start: 0.2228 (OUTLIER) cc_final: 0.0523 (ttp) REVERT: M 180 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.7577 (mtpm) outliers start: 40 outliers final: 23 residues processed: 163 average time/residue: 1.7825 time to fit residues: 316.7367 Evaluate side-chains 166 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 1.9990 chunk 34 optimal weight: 0.0000 chunk 101 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN M 251 HIS N 40 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19780 Z= 0.313 Angle : 0.589 6.246 27988 Z= 0.337 Chirality : 0.040 0.161 3146 Planarity : 0.005 0.046 2544 Dihedral : 27.533 177.622 5026 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.21 % Allowed : 15.04 % Favored : 81.75 % 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: 0.23 (0.22), residues: 1548 helix: 0.90 (0.18), residues: 828 sheet: 0.42 (0.48), residues: 140 loop : -0.94 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.019 0.002 PHE M 68 TYR 0.012 0.002 TYR A 54 ARG 0.006 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 128 time to evaluate : 1.600 Fit side-chains REVERT: A 131 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (mtp85) REVERT: D 76 GLU cc_start: 0.8144 (tp30) cc_final: 0.7833 (tp30) REVERT: G 75 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8425 (mttp) REVERT: H 33 ARG cc_start: 0.7761 (OUTLIER) cc_final: 0.7251 (mtp-110) REVERT: H 76 GLU cc_start: 0.8129 (tp30) cc_final: 0.7823 (tp30) REVERT: K 55 MET cc_start: 0.2950 (mmm) cc_final: 0.2216 (mmt) REVERT: K 71 MET cc_start: 0.5729 (mtt) cc_final: 0.5510 (mtt) REVERT: K 75 CYS cc_start: 0.5346 (OUTLIER) cc_final: 0.5121 (p) REVERT: K 96 MET cc_start: 0.2279 (ptt) cc_final: 0.0650 (ttp) REVERT: K 153 MET cc_start: 0.6823 (mtp) cc_final: 0.6275 (ttm) REVERT: K 155 ASP cc_start: 0.7883 (m-30) cc_final: 0.7643 (m-30) REVERT: L 1 MET cc_start: 0.3255 (mmm) cc_final: 0.2940 (tpt) REVERT: M 55 MET cc_start: 0.2824 (mmm) cc_final: 0.2274 (mmt) REVERT: M 71 MET cc_start: 0.5487 (mtt) cc_final: 0.5150 (mtp) REVERT: M 96 MET cc_start: 0.2260 (OUTLIER) cc_final: 0.0517 (ttp) REVERT: M 153 MET cc_start: 0.7215 (ttm) cc_final: 0.6921 (ttp) REVERT: M 180 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7692 (ptpp) outliers start: 44 outliers final: 24 residues processed: 154 average time/residue: 1.7469 time to fit residues: 293.8239 Evaluate side-chains 158 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 75 CYS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 0.5980 chunk 97 optimal weight: 4.9990 chunk 144 optimal weight: 0.0000 chunk 96 optimal weight: 4.9990 chunk 171 optimal weight: 30.0000 chunk 107 optimal weight: 20.0000 chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 4.9990 chunk 106 optimal weight: 0.0570 overall best weight: 1.7306 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19780 Z= 0.260 Angle : 0.573 6.338 27988 Z= 0.330 Chirality : 0.039 0.152 3146 Planarity : 0.005 0.045 2544 Dihedral : 27.514 177.693 5026 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.63 % Allowed : 15.62 % Favored : 81.75 % 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: 0.26 (0.22), residues: 1548 helix: 0.92 (0.18), residues: 828 sheet: 0.41 (0.48), residues: 140 loop : -0.91 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 205 HIS 0.005 0.001 HIS K 315 PHE 0.016 0.002 PHE M 223 TYR 0.012 0.001 TYR A 54 ARG 0.004 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 127 time to evaluate : 1.763 Fit side-chains REVERT: A 131 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8455 (mtp85) REVERT: D 33 ARG cc_start: 0.7478 (OUTLIER) cc_final: 0.7111 (mtp-110) REVERT: D 76 GLU cc_start: 0.8139 (tp30) cc_final: 0.7832 (tp30) REVERT: G 75 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8415 (mttp) REVERT: H 33 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7248 (mtp-110) REVERT: H 76 GLU cc_start: 0.8127 (tp30) cc_final: 0.7825 (tp30) REVERT: K 55 MET cc_start: 0.2951 (mmm) cc_final: 0.2211 (mmt) REVERT: K 71 MET cc_start: 0.5852 (mtt) cc_final: 0.5610 (mtt) REVERT: K 96 MET cc_start: 0.2274 (ptt) cc_final: 0.0654 (ttp) REVERT: K 153 MET cc_start: 0.6784 (mtp) cc_final: 0.6291 (ttm) REVERT: K 155 ASP cc_start: 0.7878 (m-30) cc_final: 0.7632 (m-30) REVERT: L 1 MET cc_start: 0.3254 (mmm) cc_final: 0.2943 (tpt) REVERT: M 55 MET cc_start: 0.2823 (mmm) cc_final: 0.2263 (mmt) REVERT: M 71 MET cc_start: 0.5505 (mtt) cc_final: 0.5157 (mtp) REVERT: M 96 MET cc_start: 0.2257 (OUTLIER) cc_final: 0.0522 (ttp) REVERT: M 153 MET cc_start: 0.7268 (ttm) cc_final: 0.7064 (ttp) REVERT: M 180 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7735 (ptpp) outliers start: 36 outliers final: 27 residues processed: 148 average time/residue: 1.7953 time to fit residues: 290.2103 Evaluate side-chains 157 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 156 optimal weight: 0.0980 chunk 164 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19780 Z= 0.192 Angle : 0.553 6.132 27988 Z= 0.322 Chirality : 0.037 0.141 3146 Planarity : 0.004 0.044 2544 Dihedral : 27.490 177.830 5026 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.77 % Allowed : 15.62 % Favored : 81.61 % 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: 0.35 (0.22), residues: 1548 helix: 1.00 (0.18), residues: 828 sheet: 0.41 (0.48), residues: 140 loop : -0.86 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 205 HIS 0.004 0.001 HIS M 315 PHE 0.015 0.001 PHE M 223 TYR 0.013 0.001 TYR A 54 ARG 0.004 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 126 time to evaluate : 1.528 Fit side-chains REVERT: A 131 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.8424 (mtp85) REVERT: D 33 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7137 (mtp-110) REVERT: D 76 GLU cc_start: 0.8129 (tp30) cc_final: 0.7819 (tp30) REVERT: G 75 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8359 (mttp) REVERT: H 33 ARG cc_start: 0.7749 (OUTLIER) cc_final: 0.7247 (mtp-110) REVERT: H 76 GLU cc_start: 0.8121 (tp30) cc_final: 0.7818 (tp30) REVERT: K 55 MET cc_start: 0.3008 (mmm) cc_final: 0.2265 (mmt) REVERT: K 96 MET cc_start: 0.2202 (ptt) cc_final: 0.0555 (ttp) REVERT: K 153 MET cc_start: 0.6818 (mtp) cc_final: 0.6287 (ttm) REVERT: K 155 ASP cc_start: 0.7874 (m-30) cc_final: 0.7630 (m-30) REVERT: L 1 MET cc_start: 0.3252 (mmm) cc_final: 0.2943 (tpt) REVERT: M 55 MET cc_start: 0.2842 (mmm) cc_final: 0.2338 (mmt) REVERT: M 71 MET cc_start: 0.5505 (mtt) cc_final: 0.5158 (mtp) REVERT: M 96 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.0438 (ttp) REVERT: M 180 LYS cc_start: 0.8135 (OUTLIER) cc_final: 0.7714 (ptpp) outliers start: 38 outliers final: 27 residues processed: 147 average time/residue: 1.7991 time to fit residues: 289.2369 Evaluate side-chains 159 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 144 optimal weight: 20.0000 chunk 151 optimal weight: 0.1980 chunk 104 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 19780 Z= 0.161 Angle : 0.545 8.255 27988 Z= 0.317 Chirality : 0.037 0.145 3146 Planarity : 0.004 0.043 2544 Dihedral : 27.444 178.167 5026 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.55 % Allowed : 15.91 % Favored : 81.53 % 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: 0.44 (0.22), residues: 1548 helix: 1.09 (0.18), residues: 826 sheet: 0.39 (0.48), residues: 140 loop : -0.83 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 205 HIS 0.003 0.001 HIS M 315 PHE 0.014 0.001 PHE M 223 TYR 0.010 0.001 TYR A 54 ARG 0.004 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.711 Fit side-chains REVERT: A 131 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: D 33 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7138 (mtp-110) REVERT: D 76 GLU cc_start: 0.8137 (tp30) cc_final: 0.7828 (tp30) REVERT: G 75 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8350 (mttp) REVERT: H 33 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7247 (mtp-110) REVERT: H 76 GLU cc_start: 0.8100 (tp30) cc_final: 0.7801 (tp30) REVERT: K 55 MET cc_start: 0.2985 (mmm) cc_final: 0.2233 (mmt) REVERT: K 96 MET cc_start: 0.2181 (ptt) cc_final: 0.0553 (ttp) REVERT: K 153 MET cc_start: 0.6803 (mtp) cc_final: 0.6288 (ttm) REVERT: K 155 ASP cc_start: 0.7868 (m-30) cc_final: 0.7624 (m-30) REVERT: L 1 MET cc_start: 0.3250 (mmm) cc_final: 0.2939 (tpt) REVERT: M 55 MET cc_start: 0.2844 (mmm) cc_final: 0.2339 (mmt) REVERT: M 71 MET cc_start: 0.5445 (mtt) cc_final: 0.5098 (mtp) REVERT: M 96 MET cc_start: 0.2175 (OUTLIER) cc_final: 0.0426 (ttp) REVERT: M 180 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7676 (ptpp) outliers start: 35 outliers final: 24 residues processed: 147 average time/residue: 1.7871 time to fit residues: 287.2373 Evaluate side-chains 158 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 50 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Chi-restraints excluded: chain N residue 50 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 177 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 141 optimal weight: 30.0000 chunk 14 optimal weight: 2.9990 chunk 109 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19780 Z= 0.298 Angle : 0.582 6.237 27988 Z= 0.333 Chirality : 0.040 0.158 3146 Planarity : 0.005 0.045 2544 Dihedral : 27.502 177.833 5026 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.48 % Allowed : 15.84 % Favored : 81.68 % 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: 0.35 (0.22), residues: 1548 helix: 1.00 (0.18), residues: 826 sheet: 0.37 (0.48), residues: 140 loop : -0.86 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 205 HIS 0.005 0.001 HIS M 315 PHE 0.016 0.002 PHE M 223 TYR 0.011 0.002 TYR M 216 ARG 0.004 0.000 ARG E 129 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 132 time to evaluate : 1.541 Fit side-chains REVERT: A 131 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.8479 (mtp85) REVERT: D 33 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7224 (mtp-110) REVERT: D 76 GLU cc_start: 0.8146 (tp30) cc_final: 0.7835 (tp30) REVERT: G 75 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8413 (mttp) REVERT: H 33 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7429 (mtp-110) REVERT: H 76 GLU cc_start: 0.8111 (tp30) cc_final: 0.7811 (tp30) REVERT: K 55 MET cc_start: 0.3171 (mmm) cc_final: 0.2423 (mmt) REVERT: K 96 MET cc_start: 0.2104 (ptt) cc_final: 0.0489 (ttp) REVERT: K 153 MET cc_start: 0.6789 (mtp) cc_final: 0.6328 (ttm) REVERT: K 155 ASP cc_start: 0.7927 (m-30) cc_final: 0.7694 (m-30) REVERT: M 55 MET cc_start: 0.3047 (mmm) cc_final: 0.2387 (mmt) REVERT: M 71 MET cc_start: 0.5439 (mtt) cc_final: 0.5093 (mtp) REVERT: M 96 MET cc_start: 0.2294 (OUTLIER) cc_final: 0.0513 (ttp) REVERT: M 180 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7693 (ptpp) outliers start: 34 outliers final: 24 residues processed: 152 average time/residue: 1.7730 time to fit residues: 293.6664 Evaluate side-chains 158 residues out of total 1370 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 128 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 279 ILE Chi-restraints excluded: chain K residue 286 ASP Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain M residue 96 MET Chi-restraints excluded: chain M residue 160 VAL Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 279 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 40 GLN L 41 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.137580 restraints weight = 20777.007| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 1.93 r_work: 0.3004 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19780 Z= 0.173 Angle : 0.545 6.103 27988 Z= 0.317 Chirality : 0.037 0.144 3146 Planarity : 0.004 0.043 2544 Dihedral : 27.438 178.203 5026 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.19 % Allowed : 16.35 % Favored : 81.46 % 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: 0.51 (0.22), residues: 1548 helix: 1.15 (0.18), residues: 826 sheet: 0.38 (0.48), residues: 140 loop : -0.79 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 205 HIS 0.003 0.001 HIS M 315 PHE 0.015 0.001 PHE M 223 TYR 0.011 0.001 TYR E 54 ARG 0.004 0.000 ARG E 129 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5465.19 seconds wall clock time: 98 minutes 3.75 seconds (5883.75 seconds total)