Starting phenix.real_space_refine on Sun Apr 14 03:36:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y5d_10694/04_2024/6y5d_10694_updated.pdb" } resolution = 4.1 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= 0.006 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 612 5.49 5 S 54 5.16 5 C 17252 2.51 5 N 5588 2.21 5 O 6864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "K PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 478": "OE1" <-> "OE2" Residue "K GLU 487": "OE1" <-> "OE2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 325": "OE1" <-> "OE2" Residue "L PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 478": "OE1" <-> "OE2" Residue "L GLU 487": "OE1" <-> "OE2" Residue "L GLU 515": "OE1" <-> "OE2" Residue "L PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 91": "OD1" <-> "OD2" Residue "P TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 91": "OD1" <-> "OD2" Residue "T TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 30372 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 831 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "J" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "K" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "L" Number of atoms: 2980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2980 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain: "M" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 789 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "N" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "O" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 806 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "P" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 698 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "Q" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 772 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "R" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 618 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "S" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "T" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "U" Number of atoms: 3119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3119 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "V" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 3154 Classifications: {'DNA': 153} Link IDs: {'rna3p': 152} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 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: "L" 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PTD': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PTD:plan-2': 1, 'PTD:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PTD': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'PTD:plan-2': 2, 'PTD:plan-1': 2} Unresolved non-hydrogen planarities: 4 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14165 SG CYS K 396 76.480 20.279 43.285 0.00566.57 S ATOM 14171 SG CYS K 397 78.707 19.449 46.231 0.00570.62 S ATOM 14230 SG CYS K 404 80.023 21.567 43.400 0.00566.15 S ATOM 17145 SG CYS L 396 99.066 112.815 22.367 0.00600.00 S ATOM 17151 SG CYS L 397 96.012 114.889 23.197 0.00600.00 S ATOM 17210 SG CYS L 404 95.615 111.456 21.678 0.00600.00 S Time building chain proxies: 15.37, per 1000 atoms: 0.51 Number of scatterers: 30372 At special positions: 0 Unit cell: (163.4, 157.38, 141.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 54 16.00 P 612 15.00 O 6864 8.00 N 5588 7.00 C 17252 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.27 Conformation dependent library (CDL) restraints added in 3.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 601 " pdb="ZN ZN K 601 " - pdb=" NE2 HIS K 390 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 397 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 404 " pdb="ZN ZN K 601 " - pdb=" SG CYS K 396 " pdb=" ZN L 601 " pdb="ZN ZN L 601 " - pdb=" NE2 HIS L 390 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 397 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 404 " pdb="ZN ZN L 601 " - pdb=" SG CYS L 396 " Number of angles added : 6 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4176 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 99 helices and 5 sheets defined 57.9% alpha, 4.1% beta 306 base pairs and 562 stacking pairs defined. Time for finding SS restraints: 16.30 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 Processing helix chain 'A' and resid 65 through 78 removed outlier: 3.746A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 122 through 131 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 32 through 41 Processing helix chain 'B' and resid 51 through 76 removed outlier: 4.043A pdb=" N VAL B 61 " --> pdb=" O GLY B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 4.177A pdb=" N GLN B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.423A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 114 through 116 No H-bonds generated for 'chain 'C' and resid 114 through 116' Processing helix chain 'D' and resid 39 through 49 removed outlier: 3.501A pdb=" N LYS D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 84 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 106 through 124 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 65 through 79 removed outlier: 3.934A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 114 Processing helix chain 'E' and resid 122 through 132 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 32 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.686A pdb=" N TYR F 52 " --> pdb=" O GLY F 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU F 53 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N LYS F 60 " --> pdb=" O GLY F 57 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ILE F 67 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG F 68 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 84 through 94 Processing helix chain 'G' and resid 18 through 22 Processing helix chain 'G' and resid 29 through 36 removed outlier: 3.987A pdb=" N ARG G 36 " --> pdb=" O HIS G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 73 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 114 through 116 No H-bonds generated for 'chain 'G' and resid 114 through 116' Processing helix chain 'H' and resid 39 through 49 Processing helix chain 'H' and resid 57 through 84 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'H' and resid 107 through 124 removed outlier: 3.612A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 176 removed outlier: 4.020A pdb=" N ARG K 176 " --> pdb=" O LEU K 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 179 through 199 removed outlier: 3.611A pdb=" N ALA K 183 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP K 191 " --> pdb=" O GLY K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 261 through 265 removed outlier: 3.990A pdb=" N GLN K 264 " --> pdb=" O PRO K 261 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 290 removed outlier: 3.895A pdb=" N ASP K 290 " --> pdb=" O GLU K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 332 through 334 No H-bonds generated for 'chain 'K' and resid 332 through 334' Processing helix chain 'K' and resid 346 through 354 Processing helix chain 'K' and resid 380 through 389 Processing helix chain 'K' and resid 400 through 402 No H-bonds generated for 'chain 'K' and resid 400 through 402' Processing helix chain 'K' and resid 406 through 423 Processing helix chain 'K' and resid 435 through 448 Processing helix chain 'K' and resid 452 through 455 Processing helix chain 'K' and resid 457 through 477 removed outlier: 5.037A pdb=" N GLY K 461 " --> pdb=" O LYS K 458 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE K 464 " --> pdb=" O GLY K 461 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR K 477 " --> pdb=" O CYS K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 498 through 514 Processing helix chain 'K' and resid 517 through 519 No H-bonds generated for 'chain 'K' and resid 517 through 519' Processing helix chain 'L' and resid 162 through 176 removed outlier: 3.881A pdb=" N ARG L 176 " --> pdb=" O LEU L 172 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 199 removed outlier: 3.660A pdb=" N ALA L 183 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP L 191 " --> pdb=" O GLY L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 265 removed outlier: 4.036A pdb=" N GLN L 264 " --> pdb=" O PRO L 261 " (cutoff:3.500A) Processing helix chain 'L' and resid 273 through 290 removed outlier: 3.680A pdb=" N GLU L 286 " --> pdb=" O LYS L 282 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN L 289 " --> pdb=" O LYS L 285 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASP L 290 " --> pdb=" O GLU L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 332 through 334 No H-bonds generated for 'chain 'L' and resid 332 through 334' Processing helix chain 'L' and resid 346 through 354 Processing helix chain 'L' and resid 380 through 388 Processing helix chain 'L' and resid 400 through 402 No H-bonds generated for 'chain 'L' and resid 400 through 402' Processing helix chain 'L' and resid 406 through 423 Processing helix chain 'L' and resid 435 through 448 Processing helix chain 'L' and resid 452 through 455 Processing helix chain 'L' and resid 457 through 476 removed outlier: 4.981A pdb=" N GLY L 461 " --> pdb=" O LYS L 458 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE L 464 " --> pdb=" O GLY L 461 " (cutoff:3.500A) Processing helix chain 'L' and resid 498 through 514 Processing helix chain 'L' and resid 517 through 519 No H-bonds generated for 'chain 'L' and resid 517 through 519' Processing helix chain 'M' and resid 46 through 57 Processing helix chain 'M' and resid 65 through 78 removed outlier: 3.731A pdb=" N ASP M 78 " --> pdb=" O GLU M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 114 Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'N' and resid 26 through 29 No H-bonds generated for 'chain 'N' and resid 26 through 29' Processing helix chain 'N' and resid 32 through 41 Processing helix chain 'N' and resid 51 through 76 removed outlier: 4.118A pdb=" N VAL N 61 " --> pdb=" O GLY N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 84 through 94 removed outlier: 4.014A pdb=" N GLN N 94 " --> pdb=" O ALA N 90 " (cutoff:3.500A) Processing helix chain 'O' and resid 18 through 21 No H-bonds generated for 'chain 'O' and resid 18 through 21' Processing helix chain 'O' and resid 29 through 36 Processing helix chain 'O' and resid 48 through 73 Processing helix chain 'O' and resid 81 through 89 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 114 through 116 No H-bonds generated for 'chain 'O' and resid 114 through 116' Processing helix chain 'P' and resid 39 through 49 Processing helix chain 'P' and resid 57 through 84 Processing helix chain 'P' and resid 92 through 102 Processing helix chain 'P' and resid 106 through 124 Processing helix chain 'Q' and resid 46 through 57 Processing helix chain 'Q' and resid 65 through 78 removed outlier: 3.866A pdb=" N ASP Q 78 " --> pdb=" O GLU Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 114 Processing helix chain 'Q' and resid 122 through 131 Processing helix chain 'R' and resid 26 through 29 Processing helix chain 'R' and resid 32 through 41 Processing helix chain 'R' and resid 51 through 76 removed outlier: 4.133A pdb=" N VAL R 61 " --> pdb=" O GLY R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 94 removed outlier: 3.994A pdb=" N GLN R 94 " --> pdb=" O ALA R 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 18 through 22 Processing helix chain 'S' and resid 29 through 36 Processing helix chain 'S' and resid 48 through 73 Processing helix chain 'S' and resid 81 through 89 Processing helix chain 'S' and resid 92 through 97 Processing helix chain 'T' and resid 39 through 49 Processing helix chain 'T' and resid 57 through 84 Processing helix chain 'T' and resid 92 through 102 Processing helix chain 'T' and resid 106 through 124 Processing sheet with id= A, first strand: chain 'K' and resid 225 through 233 removed outlier: 6.523A pdb=" N SER K 317 " --> pdb=" O PHE K 226 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N VAL K 228 " --> pdb=" O SER K 317 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ASP K 319 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N PHE K 230 " --> pdb=" O ASP K 319 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N THR K 321 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU K 232 " --> pdb=" O THR K 321 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA K 323 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 237 through 241 Processing sheet with id= C, first strand: chain 'K' and resid 364 through 366 removed outlier: 3.619A pdb=" N GLY K 369 " --> pdb=" O GLU K 366 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'L' and resid 206 through 208 removed outlier: 6.403A pdb=" N SER L 317 " --> pdb=" O PHE L 226 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL L 228 " --> pdb=" O SER L 317 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N ASP L 319 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N PHE L 230 " --> pdb=" O ASP L 319 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR L 321 " --> pdb=" O PHE L 230 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N LEU L 232 " --> pdb=" O THR L 321 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA L 323 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'L' and resid 237 through 241 921 hydrogen bonds defined for protein. 2478 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 782 hydrogen bonds 1564 hydrogen bond angles 0 basepair planarities 306 basepair parallelities 562 stacking parallelities Total time for adding SS restraints: 15.34 Time building geometry restraints manager: 15.20 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: 5979 1.33 - 1.46: 12378 1.46 - 1.59: 12863 1.59 - 1.72: 857 1.72 - 1.86: 87 Bond restraints: 32164 Sorted by residual: bond pdb=" NE ARG L 423 " pdb=" CZ ARG L 423 " ideal model delta sigma weight residual 1.326 1.388 -0.062 1.10e-02 8.26e+03 3.22e+01 bond pdb=" CG ARG G 30 " pdb=" CD ARG G 30 " ideal model delta sigma weight residual 1.520 1.384 0.136 3.00e-02 1.11e+03 2.06e+01 bond pdb=" CG ARG G 33 " pdb=" CD ARG G 33 " ideal model delta sigma weight residual 1.520 1.387 0.133 3.00e-02 1.11e+03 1.98e+01 bond pdb=" NE ARG K 423 " pdb=" CZ ARG K 423 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.10e-02 8.26e+03 1.97e+01 bond pdb=" CD ARG B 96 " pdb=" NE ARG B 96 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.94e+01 ... (remaining 32159 not shown) Histogram of bond angle deviations from ideal: 97.87 - 105.10: 2869 105.10 - 112.34: 17250 112.34 - 119.58: 10248 119.58 - 126.81: 14085 126.81 - 134.05: 1534 Bond angle restraints: 45986 Sorted by residual: angle pdb=" N THR L 395 " pdb=" CA THR L 395 " pdb=" C THR L 395 " ideal model delta sigma weight residual 113.61 101.66 11.95 1.50e+00 4.44e-01 6.35e+01 angle pdb=" N GLY C 38 " pdb=" CA GLY C 38 " pdb=" C GLY C 38 " ideal model delta sigma weight residual 115.30 104.35 10.95 1.39e+00 5.18e-01 6.20e+01 angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.47 128.45 -8.98 1.16e+00 7.43e-01 5.99e+01 angle pdb=" C LYS L 355 " pdb=" N PRO L 356 " pdb=" CA PRO L 356 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" C HIS T 50 " pdb=" N PRO T 51 " pdb=" CA PRO T 51 " ideal model delta sigma weight residual 119.47 128.29 -8.82 1.16e+00 7.43e-01 5.78e+01 ... (remaining 45981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 15087 35.76 - 71.53: 2699 71.53 - 107.29: 47 107.29 - 143.05: 0 143.05 - 178.82: 6 Dihedral angle restraints: 17839 sinusoidal: 11381 harmonic: 6458 Sorted by residual: dihedral pdb=" C4' DC I 81 " pdb=" C3' DC I 81 " pdb=" O3' DC I 81 " pdb=" P DC I 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.18 178.82 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC U 81 " pdb=" C3' DC U 81 " pdb=" O3' DC U 81 " pdb=" P DC U 82 " ideal model delta sinusoidal sigma weight residual 220.00 41.36 178.64 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT V 60 " pdb=" C3' DT V 60 " pdb=" O3' DT V 60 " pdb=" P DT V 61 " ideal model delta sinusoidal sigma weight residual 220.00 44.45 175.55 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 17836 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 4271 0.093 - 0.187: 807 0.187 - 0.280: 73 0.280 - 0.374: 20 0.374 - 0.467: 3 Chirality restraints: 5174 Sorted by residual: chirality pdb=" C3' DA J 4 " pdb=" C4' DA J 4 " pdb=" O3' DA J 4 " pdb=" C2' DA J 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.46e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C3' DA V 4 " pdb=" C4' DA V 4 " pdb=" O3' DA V 4 " pdb=" C2' DA V 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 5171 not shown) Planarity restraints: 3704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 265 " 0.073 2.00e-02 2.50e+03 4.45e-02 3.46e+01 pdb=" CG PHE K 265 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE K 265 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 PHE K 265 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE K 265 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE K 265 " 0.015 2.00e-02 2.50e+03 pdb=" CZ PHE K 265 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 71 " 0.069 2.00e-02 2.50e+03 4.40e-02 3.39e+01 pdb=" CG PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE P 71 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 PHE P 71 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE P 71 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE P 71 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE P 71 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.028 2.00e-02 2.50e+03 5.59e-02 3.12e+01 pdb=" C GLY B 103 " 0.097 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.035 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.034 2.00e-02 2.50e+03 ... (remaining 3701 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6207 2.78 - 3.31: 26558 3.31 - 3.84: 58752 3.84 - 4.37: 74815 4.37 - 4.90: 101329 Nonbonded interactions: 267661 Sorted by model distance: nonbonded pdb=" O TYR C 40 " pdb=" OG SER D 79 " model vdw 2.251 2.440 nonbonded pdb=" O GLY B 102 " pdb=" OG SER H 65 " model vdw 2.287 2.440 nonbonded pdb=" O ASN K 260 " pdb=" OG SER K 263 " model vdw 2.303 2.440 nonbonded pdb=" NH2 ARG Q 43 " pdb=" OP1 DG V 72 " model vdw 2.390 2.520 nonbonded pdb=" O PHE L 491 " pdb=" NZ LYS L 501 " model vdw 2.394 2.520 ... (remaining 267656 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 41 through 134) selection = (chain 'E' and resid 41 through 134) selection = (chain 'M' and resid 41 through 134) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 25 through 101) selection = (chain 'F' and resid 25 through 101) selection = (chain 'N' and resid 25 through 101) selection = chain 'R' } ncs_group { reference = (chain 'C' and (resid 14 through 113 or resid 201)) selection = (chain 'G' and (resid 14 through 113 or resid 701)) selection = (chain 'O' and (resid 14 through 113 or resid 201)) selection = (chain 'S' and (resid 14 through 113 or resid 702)) } ncs_group { reference = (chain 'D' and resid 36 through 125) selection = (chain 'H' and resid 36 through 125) selection = chain 'P' selection = (chain 'T' and resid 36 through 125) } ncs_group { reference = chain 'I' selection = chain 'U' } ncs_group { reference = chain 'J' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=0.84 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.500 Check model and map are aligned: 0.460 Set scattering table: 0.320 Process input model: 99.960 Find NCS groups from input model: 1.650 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.136 32164 Z= 0.795 Angle : 1.229 11.949 45986 Z= 0.833 Chirality : 0.074 0.467 5174 Planarity : 0.011 0.068 3704 Dihedral : 25.763 178.819 13663 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.97 % Favored : 97.94 % Rotamer: Outliers : 0.11 % Allowed : 0.95 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.16), residues: 2182 helix: 0.70 (0.13), residues: 1384 sheet: -0.06 (0.44), residues: 92 loop : 0.10 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.016 TRP K 455 HIS 0.018 0.004 HIS L 390 PHE 0.073 0.010 PHE K 265 TYR 0.064 0.010 TYR L 436 ARG 0.023 0.003 ARG F 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 445 time to evaluate : 2.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8004 (mtt) cc_final: 0.7672 (mpp) REVERT: C 19 SER cc_start: 0.8358 (m) cc_final: 0.8123 (t) REVERT: C 39 ASN cc_start: 0.7804 (m-40) cc_final: 0.7233 (m110) REVERT: C 84 LEU cc_start: 0.9563 (mt) cc_final: 0.9194 (mp) REVERT: C 91 ASP cc_start: 0.8232 (t70) cc_final: 0.7882 (t0) REVERT: C 94 LEU cc_start: 0.9606 (mt) cc_final: 0.9398 (mm) REVERT: E 75 ILE cc_start: 0.9428 (mt) cc_final: 0.9113 (mm) REVERT: F 67 ILE cc_start: 0.9079 (mt) cc_final: 0.8867 (pt) REVERT: F 69 ASP cc_start: 0.8240 (m-30) cc_final: 0.7886 (m-30) REVERT: F 99 TYR cc_start: 0.8825 (m-10) cc_final: 0.8275 (m-80) REVERT: G 26 PHE cc_start: 0.8461 (m-80) cc_final: 0.8134 (m-10) REVERT: G 31 VAL cc_start: 0.8422 (t) cc_final: 0.8160 (t) REVERT: G 56 LEU cc_start: 0.9700 (mt) cc_final: 0.9471 (mt) REVERT: G 57 GLU cc_start: 0.8649 (tt0) cc_final: 0.7694 (tt0) REVERT: H 88 SER cc_start: 0.8448 (m) cc_final: 0.8049 (p) REVERT: N 66 VAL cc_start: 0.9021 (t) cc_final: 0.8807 (m) REVERT: P 55 ILE cc_start: 0.4843 (tt) cc_final: 0.4640 (tt) outliers start: 2 outliers final: 1 residues processed: 447 average time/residue: 0.4127 time to fit residues: 294.6550 Evaluate side-chains 223 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 222 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 231 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 115 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 chunk 140 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 HIS M 114 HIS O 39 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 32164 Z= 0.326 Angle : 0.691 16.655 45986 Z= 0.399 Chirality : 0.039 0.176 5174 Planarity : 0.005 0.063 3704 Dihedral : 29.470 178.811 9158 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.28 % Favored : 98.63 % Rotamer: Outliers : 0.11 % Allowed : 1.84 % Favored : 98.05 % 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: 1.37 (0.17), residues: 2182 helix: 1.49 (0.13), residues: 1388 sheet: -0.60 (0.45), residues: 96 loop : 0.11 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP K 330 HIS 0.009 0.002 HIS F 76 PHE 0.039 0.003 PHE P 71 TYR 0.026 0.002 TYR O 51 ARG 0.015 0.001 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 292 time to evaluate : 2.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LEU cc_start: 0.9612 (mt) cc_final: 0.9406 (mm) REVERT: B 85 MET cc_start: 0.8520 (tpt) cc_final: 0.8263 (mmm) REVERT: C 39 ASN cc_start: 0.7984 (m-40) cc_final: 0.7736 (m110) REVERT: C 91 ASP cc_start: 0.8072 (t70) cc_final: 0.7850 (t0) REVERT: C 94 LEU cc_start: 0.9585 (mt) cc_final: 0.9340 (mm) REVERT: E 98 GLU cc_start: 0.8918 (mp0) cc_final: 0.8420 (mp0) REVERT: F 38 LEU cc_start: 0.9555 (mt) cc_final: 0.9241 (tt) REVERT: F 99 TYR cc_start: 0.8792 (m-10) cc_final: 0.8200 (m-80) REVERT: G 97 LEU cc_start: 0.9478 (tp) cc_final: 0.9252 (tt) REVERT: G 105 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8183 (tm-30) REVERT: N 66 VAL cc_start: 0.9243 (t) cc_final: 0.9017 (m) outliers start: 2 outliers final: 1 residues processed: 292 average time/residue: 0.4040 time to fit residues: 191.0324 Evaluate side-chains 183 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 182 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 138 optimal weight: 50.0000 chunk 77 optimal weight: 10.0000 chunk 207 optimal weight: 8.9990 chunk 169 optimal weight: 30.0000 chunk 68 optimal weight: 10.0000 chunk 249 optimal weight: 20.0000 chunk 269 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 247 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 199 optimal weight: 0.5980 overall best weight: 7.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 32164 Z= 0.324 Angle : 0.665 15.209 45986 Z= 0.386 Chirality : 0.038 0.179 5174 Planarity : 0.005 0.056 3704 Dihedral : 29.604 178.434 9158 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.88 % Favored : 98.03 % Rotamer: Outliers : 0.32 % Allowed : 2.37 % Favored : 97.32 % 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: 1.22 (0.17), residues: 2182 helix: 1.37 (0.13), residues: 1381 sheet: -0.52 (0.45), residues: 90 loop : 0.03 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 375 HIS 0.008 0.002 HIS B 76 PHE 0.040 0.002 PHE E 68 TYR 0.023 0.002 TYR O 51 ARG 0.020 0.001 ARG N 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 250 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8830 (mt-10) REVERT: A 107 ASP cc_start: 0.8722 (m-30) cc_final: 0.8416 (m-30) REVERT: C 39 ASN cc_start: 0.8362 (m-40) cc_final: 0.8086 (m110) REVERT: E 98 GLU cc_start: 0.8983 (mp0) cc_final: 0.8438 (mp0) REVERT: E 106 GLU cc_start: 0.8393 (tm-30) cc_final: 0.8160 (tm-30) REVERT: E 107 ASP cc_start: 0.9177 (m-30) cc_final: 0.8914 (m-30) REVERT: G 31 VAL cc_start: 0.9091 (t) cc_final: 0.8758 (p) outliers start: 6 outliers final: 1 residues processed: 255 average time/residue: 0.3858 time to fit residues: 161.9434 Evaluate side-chains 162 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 246 optimal weight: 30.0000 chunk 187 optimal weight: 8.9990 chunk 129 optimal weight: 30.0000 chunk 27 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 250 optimal weight: 20.0000 chunk 264 optimal weight: 20.0000 chunk 130 optimal weight: 5.9990 chunk 237 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 HIS ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 32164 Z= 0.233 Angle : 0.590 10.604 45986 Z= 0.346 Chirality : 0.036 0.172 5174 Planarity : 0.004 0.047 3704 Dihedral : 29.471 177.506 9158 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.51 % Favored : 98.40 % Rotamer: Outliers : 0.16 % Allowed : 1.47 % Favored : 98.37 % 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: 1.37 (0.18), residues: 2182 helix: 1.56 (0.14), residues: 1363 sheet: -0.42 (0.46), residues: 90 loop : -0.05 (0.23), residues: 729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 375 HIS 0.005 0.001 HIS B 76 PHE 0.022 0.002 PHE L 280 TYR 0.025 0.002 TYR S 51 ARG 0.005 0.000 ARG R 93 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 235 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8431 (mm-30) REVERT: A 98 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8871 (mp0) REVERT: A 107 ASP cc_start: 0.8613 (m-30) cc_final: 0.8318 (m-30) REVERT: A 121 MET cc_start: 0.8116 (mpp) cc_final: 0.7684 (mpp) REVERT: D 60 MET cc_start: 0.9148 (tpp) cc_final: 0.8830 (tpp) REVERT: E 98 GLU cc_start: 0.9032 (mp0) cc_final: 0.8532 (mp0) REVERT: E 106 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8144 (tm-30) REVERT: E 107 ASP cc_start: 0.9187 (m-30) cc_final: 0.8883 (m-30) REVERT: F 99 TYR cc_start: 0.9095 (m-10) cc_final: 0.8482 (m-80) REVERT: G 88 ILE cc_start: 0.9670 (tp) cc_final: 0.9167 (tp) outliers start: 3 outliers final: 0 residues processed: 236 average time/residue: 0.3860 time to fit residues: 151.5358 Evaluate side-chains 162 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 220 optimal weight: 40.0000 chunk 150 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 197 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 226 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 50.0000 chunk 237 optimal weight: 50.0000 chunk 66 optimal weight: 1.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** E 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32164 Z= 0.199 Angle : 0.563 12.881 45986 Z= 0.332 Chirality : 0.035 0.140 5174 Planarity : 0.004 0.046 3704 Dihedral : 29.294 177.348 9158 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.65 % Favored : 98.26 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.46 (0.18), residues: 2182 helix: 1.68 (0.14), residues: 1358 sheet: -0.23 (0.49), residues: 90 loop : -0.13 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 375 HIS 0.005 0.001 HIS T 83 PHE 0.035 0.002 PHE E 68 TYR 0.018 0.001 TYR O 51 ARG 0.015 0.000 ARG O 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 95 GLU cc_start: 0.8725 (tt0) cc_final: 0.8459 (tt0) REVERT: A 98 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8864 (mp0) REVERT: A 107 ASP cc_start: 0.8601 (m-30) cc_final: 0.8275 (m-30) REVERT: A 121 MET cc_start: 0.8279 (mpp) cc_final: 0.8057 (mpp) REVERT: E 98 GLU cc_start: 0.9020 (mp0) cc_final: 0.8330 (mp0) REVERT: E 106 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8104 (tm-30) REVERT: E 107 ASP cc_start: 0.9219 (m-30) cc_final: 0.8895 (m-30) REVERT: F 99 TYR cc_start: 0.8857 (m-10) cc_final: 0.8478 (m-80) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.3912 time to fit residues: 146.6984 Evaluate side-chains 156 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 2.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 89 optimal weight: 10.0000 chunk 238 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 155 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 265 optimal weight: 20.0000 chunk 220 optimal weight: 7.9990 chunk 122 optimal weight: 50.0000 chunk 22 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 32164 Z= 0.265 Angle : 0.597 11.995 45986 Z= 0.351 Chirality : 0.035 0.277 5174 Planarity : 0.004 0.046 3704 Dihedral : 29.357 177.459 9158 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 1.31 (0.18), residues: 2182 helix: 1.53 (0.14), residues: 1359 sheet: -0.55 (0.49), residues: 100 loop : -0.08 (0.23), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 343 HIS 0.007 0.001 HIS A 114 PHE 0.020 0.002 PHE L 280 TYR 0.020 0.002 TYR O 51 ARG 0.010 0.001 ARG S 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 2.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8375 (tp30) REVERT: A 52 ILE cc_start: 0.9499 (mt) cc_final: 0.9296 (mm) REVERT: A 95 GLU cc_start: 0.8824 (tt0) cc_final: 0.8457 (tt0) REVERT: A 98 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8940 (mp0) REVERT: A 107 ASP cc_start: 0.8583 (m-30) cc_final: 0.8315 (m-30) REVERT: A 121 MET cc_start: 0.8321 (mpp) cc_final: 0.8092 (mpp) REVERT: D 101 LEU cc_start: 0.9517 (mm) cc_final: 0.9157 (tp) REVERT: E 98 GLU cc_start: 0.9187 (mp0) cc_final: 0.8486 (mp0) REVERT: E 106 GLU cc_start: 0.8502 (tm-30) cc_final: 0.8161 (tm-30) REVERT: E 107 ASP cc_start: 0.9145 (m-30) cc_final: 0.8820 (m-30) REVERT: F 99 TYR cc_start: 0.9101 (m-10) cc_final: 0.8501 (m-80) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.4207 time to fit residues: 140.3103 Evaluate side-chains 150 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 255 optimal weight: 20.0000 chunk 29 optimal weight: 8.9990 chunk 151 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 149 optimal weight: 0.9990 chunk 223 optimal weight: 20.0000 chunk 148 optimal weight: 0.6980 chunk 264 optimal weight: 20.0000 chunk 165 optimal weight: 0.6980 chunk 161 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32164 Z= 0.201 Angle : 0.561 11.384 45986 Z= 0.330 Chirality : 0.034 0.153 5174 Planarity : 0.004 0.066 3704 Dihedral : 29.328 178.076 9158 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.88 % Favored : 98.08 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.26 % 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: 1.38 (0.18), residues: 2182 helix: 1.59 (0.14), residues: 1349 sheet: -0.43 (0.50), residues: 100 loop : -0.02 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 343 HIS 0.007 0.001 HIS G 83 PHE 0.019 0.001 PHE L 280 TYR 0.019 0.001 TYR G 40 ARG 0.012 0.000 ARG P 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 2.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8446 (tp30) REVERT: A 52 ILE cc_start: 0.9498 (mt) cc_final: 0.9288 (mm) REVERT: A 95 GLU cc_start: 0.8813 (tt0) cc_final: 0.8406 (tt0) REVERT: A 107 ASP cc_start: 0.8561 (m-30) cc_final: 0.8252 (m-30) REVERT: D 60 MET cc_start: 0.9165 (tpp) cc_final: 0.8878 (tpp) REVERT: E 98 GLU cc_start: 0.9078 (mp0) cc_final: 0.8322 (mp0) REVERT: E 106 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8205 (tm-30) REVERT: E 107 ASP cc_start: 0.9173 (m-30) cc_final: 0.8968 (m-30) REVERT: E 121 MET cc_start: 0.9160 (tpp) cc_final: 0.8773 (mmm) REVERT: F 99 TYR cc_start: 0.8768 (m-10) cc_final: 0.8386 (m-80) outliers start: 1 outliers final: 0 residues processed: 207 average time/residue: 0.4221 time to fit residues: 144.1363 Evaluate side-chains 142 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 163 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 157 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 167 optimal weight: 7.9990 chunk 179 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 207 optimal weight: 20.0000 chunk 240 optimal weight: 30.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32164 Z= 0.252 Angle : 0.586 9.887 45986 Z= 0.345 Chirality : 0.035 0.165 5174 Planarity : 0.004 0.047 3704 Dihedral : 29.313 177.837 9158 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.31 (0.18), residues: 2182 helix: 1.51 (0.14), residues: 1344 sheet: -0.50 (0.48), residues: 102 loop : -0.00 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 343 HIS 0.009 0.001 HIS H 110 PHE 0.020 0.001 PHE L 280 TYR 0.019 0.001 TYR G 40 ARG 0.017 0.000 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 2.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9004 (mm-30) cc_final: 0.8612 (mm-30) REVERT: A 52 ILE cc_start: 0.9512 (mt) cc_final: 0.9306 (mm) REVERT: A 107 ASP cc_start: 0.8587 (m-30) cc_final: 0.8292 (m-30) REVERT: E 106 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8216 (tm-30) REVERT: E 107 ASP cc_start: 0.9164 (m-30) cc_final: 0.8961 (m-30) REVERT: F 99 TYR cc_start: 0.9142 (m-10) cc_final: 0.8460 (m-80) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.3960 time to fit residues: 120.3828 Evaluate side-chains 133 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 253 optimal weight: 20.0000 chunk 230 optimal weight: 30.0000 chunk 246 optimal weight: 30.0000 chunk 252 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 193 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 222 optimal weight: 20.0000 chunk 232 optimal weight: 9.9990 chunk 245 optimal weight: 40.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 109 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 HIS ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.6774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 32164 Z= 0.439 Angle : 0.752 12.631 45986 Z= 0.432 Chirality : 0.042 0.242 5174 Planarity : 0.006 0.093 3704 Dihedral : 30.114 178.873 9158 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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 (0.17), residues: 2182 helix: 0.61 (0.13), residues: 1343 sheet: -0.96 (0.47), residues: 102 loop : -0.34 (0.23), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP K 330 HIS 0.013 0.002 HIS H 83 PHE 0.018 0.002 PHE L 280 TYR 0.036 0.002 TYR G 40 ARG 0.022 0.001 ARG R 93 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4364 Ramachandran restraints generated. 2182 Oldfield, 0 Emsley, 2182 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.8510 (tt0) cc_final: 0.8132 (tt0) REVERT: A 107 ASP cc_start: 0.8801 (m-30) cc_final: 0.8572 (m-30) REVERT: D 60 MET cc_start: 0.9206 (tpp) cc_final: 0.8856 (tpp) REVERT: E 98 GLU cc_start: 0.9052 (mp0) cc_final: 0.8572 (mp0) REVERT: E 106 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8248 (tm-30) REVERT: G 57 GLU cc_start: 0.8903 (tt0) cc_final: 0.8421 (tt0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.4109 time to fit residues: 118.8248 Evaluate side-chains 121 residues out of total 1902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 274 random chunks: chunk 161 optimal weight: 30.0000 chunk 260 optimal weight: 30.0000 chunk 158 optimal weight: 40.0000 chunk 123 optimal weight: 5.9990 chunk 180 optimal weight: 9.9990 chunk 272 optimal weight: 30.0000 chunk 251 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 167 optimal weight: 40.0000 chunk 133 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 GLN ** N 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.6934 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: