Starting phenix.real_space_refine on Sat Mar 16 15:57:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oh9_12897/03_2024/7oh9_12897.pdb" } resolution = 3.0 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= 0.003 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 25 5.16 5 C 8612 2.51 5 N 2782 2.21 5 O 3390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15099 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} 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: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1439 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Conformer: "B" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} bond proxies already assigned to first conformer: 1417 Chain: "L" Number of atoms: 823 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 96, 796 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'TRANS': 95} Chain breaks: 2 bond proxies already assigned to first conformer: 775 Chain: "M" Number of atoms: 815 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 104, 807 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 805 Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N ALEU K 134 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU K 134 " occ=0.50 residue: pdb=" N ALYS K 138 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS K 138 " occ=0.50 residue: pdb=" N ASER K 184 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER K 184 " occ=0.50 residue: pdb=" N AGLU L 11 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU L 11 " occ=0.50 residue: pdb=" N AGLN L 280 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN L 280 " occ=0.50 residue: pdb=" N AGLU L 282 " occ=0.60 ... (16 atoms not shown) pdb=" OE2BGLU L 282 " occ=0.40 residue: pdb=" N AILE M 79 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE M 79 " occ=0.50 Time building chain proxies: 9.83, per 1000 atoms: 0.65 Number of scatterers: 15099 At special positions: 0 Unit cell: (93.45, 129.15, 142.8, 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 25 16.00 P 290 15.00 O 3390 8.00 N 2782 7.00 C 8612 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: 7.78 Conformation dependent library (CDL) restraints added in 2.3 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 60.5% alpha, 13.3% beta 143 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 7.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.022A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.502A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.614A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.883A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.566A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.701A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.269A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing helix chain 'K' and resid 81 through 89 removed outlier: 4.191A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 128 through 147 Processing helix chain 'K' and resid 171 through 179 Processing helix chain 'K' and resid 219 through 236 removed outlier: 3.615A pdb=" N ILE K 223 " --> pdb=" O GLN K 219 " (cutoff:3.500A) Proline residue: K 232 - end of helix Processing helix chain 'L' and resid 4 through 19 Processing helix chain 'L' and resid 20 through 27 removed outlier: 4.665A pdb=" N ASP L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 47 Processing helix chain 'M' and resid 8 through 12 removed outlier: 4.298A pdb=" N ARG M 11 " --> pdb=" O GLU M 8 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 29 Processing helix chain 'M' and resid 33 through 55 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.092A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.463A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.072A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.235A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 93 through 95 removed outlier: 6.189A pdb=" N GLU K 93 " --> pdb=" O ALA K 101 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ALA K 101 " --> pdb=" O GLU K 93 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASN K 95 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR K 111 " --> pdb=" O ILE K 106 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL K 122 " --> pdb=" O LEU K 114 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE K 70 " --> pdb=" O GLY K 125 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL K 161 " --> pdb=" O GLN K 68 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE K 70 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN K 159 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA K 72 " --> pdb=" O ILE K 157 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 157 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL K 74 " --> pdb=" O PHE K 155 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE K 155 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 243 through 253 removed outlier: 7.512A pdb=" N LEU L 243 " --> pdb=" O VAL L 267 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL L 267 " --> pdb=" O LEU L 243 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU L 245 " --> pdb=" O GLY L 265 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLY L 265 " --> pdb=" O LEU L 245 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N SER L 261 " --> pdb=" O ASP L 249 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL L 251 " --> pdb=" O LYS L 259 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N LYS L 259 " --> pdb=" O VAL L 251 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP L 264 " --> pdb=" O GLN L 277 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLN L 277 " --> pdb=" O ASP L 264 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL L 266 " --> pdb=" O THR L 275 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR L 275 " --> pdb=" O VAL L 266 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU M 60 " --> pdb=" O PHE L 276 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS L 278 " --> pdb=" O LEU M 60 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL M 62 " --> pdb=" O LYS L 278 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N AGLN L 280 " --> pdb=" O VAL M 62 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY M 64 " --> pdb=" O AGLN L 280 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N AGLU L 282 " --> pdb=" O GLY M 64 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU M 66 " --> pdb=" O AGLU L 282 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LYS M 59 " --> pdb=" O VAL M 87 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL M 87 " --> pdb=" O LYS M 59 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N THR M 61 " --> pdb=" O VAL M 85 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N VAL M 85 " --> pdb=" O THR M 61 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LYS M 63 " --> pdb=" O CYS M 83 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N CYS M 83 " --> pdb=" O LYS M 63 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N AILE M 79 " --> pdb=" O ASP M 67 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N TYR M 69 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N THR M 77 " --> pdb=" O TYR M 69 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE M 71 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL M 75 " --> pdb=" O PHE M 71 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL M 75 " --> pdb=" O CYS M 116 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N CYS M 116 " --> pdb=" O VAL M 75 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR M 77 " --> pdb=" O VAL M 114 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL M 114 " --> pdb=" O THR M 77 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N AILE M 79 " --> pdb=" O ARG M 112 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ARG M 112 " --> pdb=" O AILE M 79 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS M 81 " --> pdb=" O LYS M 110 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LYS M 110 " --> pdb=" O LYS M 81 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS M 116 " --> pdb=" O CYS L 246 " (cutoff:3.500A) 566 hydrogen bonds defined for protein. 1669 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 8.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2919 1.33 - 1.45: 4821 1.45 - 1.57: 7592 1.57 - 1.69: 579 1.69 - 1.81: 41 Bond restraints: 15952 Sorted by residual: bond pdb=" CB PRO A 38 " pdb=" CG PRO A 38 " ideal model delta sigma weight residual 1.492 1.600 -0.108 5.00e-02 4.00e+02 4.65e+00 bond pdb=" CD GLU L 20 " pdb=" OE1 GLU L 20 " ideal model delta sigma weight residual 1.249 1.211 0.038 1.90e-02 2.77e+03 3.92e+00 bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.482 -0.025 1.29e-02 6.01e+03 3.74e+00 bond pdb=" CB ASN M 55 " pdb=" CG ASN M 55 " ideal model delta sigma weight residual 1.516 1.564 -0.048 2.50e-02 1.60e+03 3.72e+00 bond pdb=" CG1 ILE D 58 " pdb=" CD1 ILE D 58 " ideal model delta sigma weight residual 1.513 1.447 0.066 3.90e-02 6.57e+02 2.89e+00 ... (remaining 15947 not shown) Histogram of bond angle deviations from ideal: 95.64 - 103.30: 728 103.30 - 110.96: 7139 110.96 - 118.62: 6043 118.62 - 126.28: 7960 126.28 - 133.94: 918 Bond angle restraints: 22788 Sorted by residual: angle pdb=" N GLU L 20 " pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " ideal model delta sigma weight residual 110.53 118.18 -7.65 1.47e+00 4.63e-01 2.71e+01 angle pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta sigma weight residual 121.92 113.28 8.64 1.73e+00 3.34e-01 2.50e+01 angle pdb=" CA GLU C 64 " pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 114.10 123.46 -9.36 2.00e+00 2.50e-01 2.19e+01 angle pdb=" CA GLU L 20 " pdb=" CB GLU L 20 " pdb=" CG GLU L 20 " ideal model delta sigma weight residual 114.10 123.04 -8.94 2.00e+00 2.50e-01 2.00e+01 angle pdb=" C CYS M 72 " pdb=" N ASP M 73 " pdb=" CA ASP M 73 " ideal model delta sigma weight residual 121.54 129.97 -8.43 1.91e+00 2.74e-01 1.95e+01 ... (remaining 22783 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.02: 6335 19.02 - 38.04: 1221 38.04 - 57.06: 1180 57.06 - 76.08: 152 76.08 - 95.10: 11 Dihedral angle restraints: 8899 sinusoidal: 5541 harmonic: 3358 Sorted by residual: dihedral pdb=" CA ASN L 19 " pdb=" C ASN L 19 " pdb=" N GLU L 20 " pdb=" CA GLU L 20 " ideal model delta harmonic sigma weight residual 180.00 145.51 34.49 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA GLU K 186 " pdb=" C GLU K 186 " pdb=" N PRO K 187 " pdb=" CA PRO K 187 " ideal model delta harmonic sigma weight residual -180.00 -146.31 -33.69 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -152.56 -27.44 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 8896 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2256 0.069 - 0.139: 314 0.139 - 0.208: 29 0.208 - 0.277: 3 0.277 - 0.347: 4 Chirality restraints: 2606 Sorted by residual: chirality pdb=" CG LEU L 262 " pdb=" CB LEU L 262 " pdb=" CD1 LEU L 262 " pdb=" CD2 LEU L 262 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CG LEU M 19 " pdb=" CB LEU M 19 " pdb=" CD1 LEU M 19 " pdb=" CD2 LEU M 19 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CG LEU A 61 " pdb=" CB LEU A 61 " pdb=" CD1 LEU A 61 " pdb=" CD2 LEU A 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 2603 not shown) Planarity restraints: 1879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN M 55 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ASN M 55 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN M 55 " 0.021 2.00e-02 2.50e+03 pdb=" N THR M 56 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 64 " 0.012 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" CD GLU C 64 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU C 64 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 64 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.02e+00 pdb=" N PRO C 80 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.034 5.00e-02 4.00e+02 ... (remaining 1876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2547 2.77 - 3.30: 13473 3.30 - 3.83: 30580 3.83 - 4.37: 35913 4.37 - 4.90: 51531 Nonbonded interactions: 134044 Sorted by model distance: nonbonded pdb=" O ASP M 21 " pdb=" OG1 THR M 25 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR M 7 " pdb=" OD1 ASN M 117 " model vdw 2.250 2.440 nonbonded pdb=" OE1 GLU L 32 " pdb=" NE2 GLN L 36 " model vdw 2.293 2.520 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.294 2.440 nonbonded pdb=" O ALA L 4 " pdb=" OG SER L 7 " model vdw 2.295 2.440 ... (remaining 134039 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' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 122) selection = chain 'H' } 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=0.99 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: 0.010 Normalize map: mean=0, sd=1: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.610 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 51.360 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.007 0.108 15952 Z= 0.391 Angle : 0.837 13.630 22788 Z= 0.468 Chirality : 0.050 0.347 2606 Planarity : 0.006 0.066 1879 Dihedral : 25.973 95.104 6729 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.09 % 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: -0.54 (0.23), residues: 1136 helix: 0.08 (0.18), residues: 678 sheet: 0.18 (0.49), residues: 120 loop : -1.25 (0.29), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP M 76 HIS 0.007 0.001 HIS B 75 PHE 0.031 0.002 PHE M 78 TYR 0.038 0.003 TYR G 57 ARG 0.009 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 54 LYS cc_start: 0.8631 (tptm) cc_final: 0.8424 (mmmt) REVERT: D 68 GLU cc_start: 0.7644 (tp30) cc_final: 0.7443 (tp30) REVERT: D 90 GLU cc_start: 0.8280 (mp0) cc_final: 0.8027 (mp0) REVERT: F 59 LYS cc_start: 0.8707 (tttm) cc_final: 0.8500 (ttpp) REVERT: H 53 SER cc_start: 0.9119 (p) cc_final: 0.8740 (p) REVERT: H 65 ASP cc_start: 0.8494 (t70) cc_final: 0.8242 (t0) REVERT: K 88 HIS cc_start: 0.9195 (m-70) cc_final: 0.8874 (m-70) REVERT: K 104 MET cc_start: 0.8851 (pmm) cc_final: 0.8533 (ppp) REVERT: K 139 TYR cc_start: 0.8699 (m-80) cc_final: 0.8089 (m-10) REVERT: K 212 ILE cc_start: 0.9074 (mm) cc_final: 0.8829 (pp) REVERT: K 221 GLU cc_start: 0.8992 (tp30) cc_final: 0.8325 (tp30) REVERT: K 222 GLU cc_start: 0.8486 (mt-10) cc_final: 0.8264 (mt-10) REVERT: K 224 TYR cc_start: 0.9266 (m-10) cc_final: 0.8985 (m-10) REVERT: K 225 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8705 (mm110) REVERT: L 248 TYR cc_start: 0.9024 (p90) cc_final: 0.8321 (p90) REVERT: M 78 PHE cc_start: 0.9298 (m-80) cc_final: 0.8918 (m-80) outliers start: 0 outliers final: 1 residues processed: 300 average time/residue: 1.5011 time to fit residues: 487.3970 Evaluate side-chains 260 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 259 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 124 optimal weight: 50.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 73 ASN C 104 GLN C 112 GLN D 92 GLN G 94 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS ** K 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15952 Z= 0.244 Angle : 0.641 11.280 22788 Z= 0.363 Chirality : 0.039 0.243 2606 Planarity : 0.004 0.054 1879 Dihedral : 29.491 106.294 4458 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.84 % Allowed : 16.09 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 0.62 (0.24), residues: 1136 helix: 1.17 (0.19), residues: 692 sheet: 0.36 (0.49), residues: 121 loop : -1.14 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.027 0.002 PHE M 44 TYR 0.050 0.002 TYR L 10 ARG 0.008 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 281 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 13 LYS cc_start: 0.8385 (tptp) cc_final: 0.8040 (tmtm) REVERT: D 68 GLU cc_start: 0.7662 (tp30) cc_final: 0.7207 (tp30) REVERT: D 90 GLU cc_start: 0.8339 (mp0) cc_final: 0.7998 (mp0) REVERT: E 120 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8325 (mtm) REVERT: H 65 ASP cc_start: 0.8483 (t70) cc_final: 0.8185 (t0) REVERT: H 76 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7912 (mtm110) REVERT: K 88 HIS cc_start: 0.9210 (m-70) cc_final: 0.8704 (m-70) REVERT: K 91 ASN cc_start: 0.9050 (m-40) cc_final: 0.8771 (m110) REVERT: K 121 MET cc_start: 0.8704 (ppp) cc_final: 0.8429 (ppp) REVERT: K 139 TYR cc_start: 0.8512 (m-80) cc_final: 0.7252 (m-80) REVERT: K 221 GLU cc_start: 0.9020 (tp30) cc_final: 0.8699 (tp30) REVERT: L 248 TYR cc_start: 0.9155 (p90) cc_final: 0.8492 (p90) REVERT: M 112 ARG cc_start: 0.8838 (tmm-80) cc_final: 0.8590 (tmm-80) outliers start: 18 outliers final: 10 residues processed: 287 average time/residue: 1.4175 time to fit residues: 441.6671 Evaluate side-chains 270 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 259 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 153 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 124 optimal weight: 20.0000 chunk 134 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 123 optimal weight: 8.9990 chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 73 ASN C 104 GLN G 38 ASN G 94 ASN H 44 GLN H 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15952 Z= 0.305 Angle : 0.647 12.600 22788 Z= 0.367 Chirality : 0.040 0.185 2606 Planarity : 0.004 0.047 1879 Dihedral : 29.511 108.992 4456 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.38 % Allowed : 18.65 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.06 (0.24), residues: 1136 helix: 1.56 (0.19), residues: 691 sheet: 0.43 (0.48), residues: 129 loop : -1.08 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 76 HIS 0.004 0.001 HIS B 75 PHE 0.024 0.002 PHE M 44 TYR 0.046 0.002 TYR L 10 ARG 0.006 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 267 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8985 (t) REVERT: A 123 ASP cc_start: 0.8504 (m-30) cc_final: 0.8287 (m-30) REVERT: B 95 ARG cc_start: 0.8891 (mtt-85) cc_final: 0.8675 (mtt90) REVERT: C 13 LYS cc_start: 0.8367 (tptp) cc_final: 0.8064 (tmtm) REVERT: D 68 GLU cc_start: 0.7663 (tp30) cc_final: 0.7180 (tp30) REVERT: D 90 GLU cc_start: 0.8394 (mp0) cc_final: 0.7935 (mp0) REVERT: E 120 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8460 (mtp) REVERT: H 65 ASP cc_start: 0.8551 (t70) cc_final: 0.8257 (t0) REVERT: K 88 HIS cc_start: 0.9222 (m-70) cc_final: 0.8697 (m-70) REVERT: K 111 THR cc_start: 0.9390 (t) cc_final: 0.9140 (t) REVERT: K 121 MET cc_start: 0.8783 (ppp) cc_final: 0.8434 (ppp) REVERT: K 214 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8924 (pt) REVERT: K 221 GLU cc_start: 0.9017 (tp30) cc_final: 0.8046 (tp30) REVERT: K 225 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8717 (mm110) REVERT: L 20 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: L 248 TYR cc_start: 0.9162 (p90) cc_final: 0.8477 (p90) REVERT: M 112 ARG cc_start: 0.8812 (tmm-80) cc_final: 0.8562 (tmm-80) outliers start: 33 outliers final: 15 residues processed: 277 average time/residue: 1.4803 time to fit residues: 444.5342 Evaluate side-chains 275 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 256 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 20 GLU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 75 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 123 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 59 optimal weight: 0.2980 chunk 83 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 132 optimal weight: 50.0000 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN B 93 GLN C 104 GLN E 125 GLN G 94 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 46 HIS K 158 GLN K 159 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15952 Z= 0.300 Angle : 0.638 13.257 22788 Z= 0.362 Chirality : 0.039 0.180 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.483 111.626 4456 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.18 % Allowed : 19.98 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.30 (0.25), residues: 1136 helix: 1.74 (0.19), residues: 692 sheet: 0.60 (0.49), residues: 129 loop : -0.98 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.024 0.002 PHE M 44 TYR 0.041 0.002 TYR L 10 ARG 0.006 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 270 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8779 (t) REVERT: A 59 GLU cc_start: 0.8380 (pm20) cc_final: 0.7658 (pm20) REVERT: B 95 ARG cc_start: 0.8909 (mtt-85) cc_final: 0.8707 (mtt90) REVERT: C 13 LYS cc_start: 0.8370 (tptp) cc_final: 0.8071 (tmtm) REVERT: D 68 GLU cc_start: 0.7662 (tp30) cc_final: 0.7202 (tp30) REVERT: D 90 GLU cc_start: 0.8443 (mp0) cc_final: 0.7894 (mp0) REVERT: E 120 MET cc_start: 0.8719 (OUTLIER) cc_final: 0.8511 (mtp) REVERT: H 65 ASP cc_start: 0.8561 (t70) cc_final: 0.8262 (t0) REVERT: K 88 HIS cc_start: 0.9242 (m-70) cc_final: 0.8714 (m-70) REVERT: K 121 MET cc_start: 0.8753 (ppp) cc_final: 0.8392 (ppp) REVERT: K 144 GLN cc_start: 0.8456 (mm110) cc_final: 0.8185 (mm-40) REVERT: K 221 GLU cc_start: 0.9034 (tp30) cc_final: 0.8076 (tp30) REVERT: K 225 GLN cc_start: 0.9181 (mm-40) cc_final: 0.8717 (mm110) outliers start: 31 outliers final: 17 residues processed: 280 average time/residue: 1.4368 time to fit residues: 436.3602 Evaluate side-chains 278 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 259 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 110 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN E 125 GLN G 94 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 15952 Z= 0.281 Angle : 0.637 14.088 22788 Z= 0.359 Chirality : 0.038 0.188 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.437 113.123 4456 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.28 % Allowed : 20.90 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.45 (0.25), residues: 1136 helix: 1.86 (0.19), residues: 692 sheet: 0.47 (0.49), residues: 134 loop : -0.84 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP L 258 HIS 0.004 0.001 HIS B 75 PHE 0.023 0.002 PHE M 44 TYR 0.037 0.002 TYR L 10 ARG 0.006 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 266 time to evaluate : 1.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9294 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 59 GLU cc_start: 0.8419 (pm20) cc_final: 0.7677 (pm20) REVERT: A 123 ASP cc_start: 0.8499 (m-30) cc_final: 0.8280 (m-30) REVERT: B 95 ARG cc_start: 0.8915 (mtt-85) cc_final: 0.8694 (mtt90) REVERT: C 13 LYS cc_start: 0.8352 (tptp) cc_final: 0.8039 (tmtm) REVERT: D 68 GLU cc_start: 0.7650 (tp30) cc_final: 0.7176 (tp30) REVERT: D 90 GLU cc_start: 0.8389 (mp0) cc_final: 0.7847 (mp0) REVERT: E 120 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8509 (mtp) REVERT: E 125 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.7554 (mp-120) REVERT: H 65 ASP cc_start: 0.8540 (t70) cc_final: 0.8181 (t0) REVERT: K 69 ASN cc_start: 0.8942 (t0) cc_final: 0.8111 (m110) REVERT: K 88 HIS cc_start: 0.9250 (m-70) cc_final: 0.8914 (m90) REVERT: K 121 MET cc_start: 0.8809 (ppp) cc_final: 0.8444 (ppp) REVERT: K 144 GLN cc_start: 0.8503 (mm110) cc_final: 0.8209 (mm-40) REVERT: K 154 ASP cc_start: 0.8164 (t0) cc_final: 0.7944 (t0) REVERT: K 221 GLU cc_start: 0.9055 (tp30) cc_final: 0.8180 (tp30) REVERT: K 225 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8684 (mm110) REVERT: K 240 MET cc_start: 0.7051 (ttt) cc_final: 0.6589 (tpp) REVERT: M 81 LYS cc_start: 0.9108 (ptpp) cc_final: 0.8848 (pmtt) outliers start: 32 outliers final: 19 residues processed: 276 average time/residue: 1.4663 time to fit residues: 438.5955 Evaluate side-chains 280 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 258 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 164 CYS Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 105 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 44 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 132 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 44 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15952 Z= 0.195 Angle : 0.627 13.904 22788 Z= 0.353 Chirality : 0.037 0.195 2606 Planarity : 0.004 0.045 1879 Dihedral : 29.168 113.550 4456 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.66 % Allowed : 22.64 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.63 (0.25), residues: 1136 helix: 2.02 (0.19), residues: 691 sheet: 0.37 (0.48), residues: 134 loop : -0.72 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP M 76 HIS 0.003 0.001 HIS B 75 PHE 0.025 0.001 PHE M 44 TYR 0.032 0.002 TYR L 10 ARG 0.007 0.000 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 269 time to evaluate : 1.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9356 (OUTLIER) cc_final: 0.8657 (t) REVERT: A 59 GLU cc_start: 0.8383 (pm20) cc_final: 0.7732 (pm20) REVERT: C 110 ASN cc_start: 0.8877 (OUTLIER) cc_final: 0.8300 (p0) REVERT: D 68 GLU cc_start: 0.7643 (tp30) cc_final: 0.7240 (tp30) REVERT: D 76 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7878 (mtp180) REVERT: D 90 GLU cc_start: 0.8349 (mp0) cc_final: 0.7815 (mp0) REVERT: E 120 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: H 31 LYS cc_start: 0.7889 (mppt) cc_final: 0.7685 (mptt) REVERT: H 65 ASP cc_start: 0.8560 (t70) cc_final: 0.8286 (t0) REVERT: K 69 ASN cc_start: 0.8842 (t0) cc_final: 0.8203 (m-40) REVERT: K 88 HIS cc_start: 0.9229 (m-70) cc_final: 0.8952 (m90) REVERT: K 121 MET cc_start: 0.8791 (ppp) cc_final: 0.8394 (ppp) REVERT: K 221 GLU cc_start: 0.8999 (tp30) cc_final: 0.8129 (tp30) REVERT: K 225 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8679 (mm110) REVERT: K 240 MET cc_start: 0.7010 (ttt) cc_final: 0.6556 (tpp) outliers start: 26 outliers final: 12 residues processed: 276 average time/residue: 1.4366 time to fit residues: 434.8016 Evaluate side-chains 270 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 76 ARG Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 85 VAL Chi-restraints excluded: chain M residue 113 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 127 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 82 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 38 ASN C 104 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 73 ASN G 94 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 15952 Z= 0.476 Angle : 0.717 20.096 22788 Z= 0.398 Chirality : 0.043 0.194 2606 Planarity : 0.004 0.042 1879 Dihedral : 29.921 113.140 4456 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.38 % Allowed : 23.57 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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 (0.25), residues: 1136 helix: 1.73 (0.19), residues: 692 sheet: 0.47 (0.49), residues: 130 loop : -0.87 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.004 TRP M 76 HIS 0.008 0.001 HIS K 179 PHE 0.023 0.002 PHE M 44 TYR 0.036 0.002 TYR L 10 ARG 0.008 0.001 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 244 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8643 (m-30) cc_final: 0.8381 (m-30) REVERT: C 13 LYS cc_start: 0.8354 (tptp) cc_final: 0.8112 (tmtm) REVERT: D 68 GLU cc_start: 0.7754 (tp30) cc_final: 0.7263 (tp30) REVERT: D 90 GLU cc_start: 0.8460 (mp0) cc_final: 0.7912 (mp0) REVERT: E 125 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: H 65 ASP cc_start: 0.8591 (t70) cc_final: 0.8176 (t0) REVERT: K 69 ASN cc_start: 0.8857 (t0) cc_final: 0.8045 (m110) REVERT: K 88 HIS cc_start: 0.9188 (m90) cc_final: 0.8922 (m90) REVERT: K 121 MET cc_start: 0.8850 (ppp) cc_final: 0.8437 (ppp) REVERT: K 195 TYR cc_start: 0.8411 (t80) cc_final: 0.8198 (t80) REVERT: K 221 GLU cc_start: 0.9055 (tp30) cc_final: 0.8173 (tp30) REVERT: K 225 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8619 (mm110) REVERT: K 240 MET cc_start: 0.7080 (ttt) cc_final: 0.6681 (tpp) outliers start: 33 outliers final: 19 residues processed: 258 average time/residue: 1.4129 time to fit residues: 396.0356 Evaluate side-chains 261 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 241 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 52 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15952 Z= 0.272 Angle : 0.680 18.717 22788 Z= 0.375 Chirality : 0.039 0.368 2606 Planarity : 0.004 0.044 1879 Dihedral : 29.487 117.577 4456 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.46 % Allowed : 24.69 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.43 (0.25), residues: 1136 helix: 1.87 (0.20), residues: 691 sheet: 0.40 (0.49), residues: 130 loop : -0.87 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.004 TRP M 76 HIS 0.004 0.001 HIS K 179 PHE 0.033 0.002 PHE M 44 TYR 0.032 0.002 TYR L 10 ARG 0.007 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 254 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8495 (m-30) cc_final: 0.8289 (m-30) REVERT: C 64 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7463 (tp30) REVERT: D 68 GLU cc_start: 0.7706 (tp30) cc_final: 0.7230 (tp30) REVERT: D 90 GLU cc_start: 0.8393 (mp0) cc_final: 0.7818 (mp0) REVERT: E 81 ASP cc_start: 0.8214 (p0) cc_final: 0.7821 (p0) REVERT: E 125 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7743 (mp10) REVERT: H 65 ASP cc_start: 0.8555 (t70) cc_final: 0.8167 (t0) REVERT: H 105 LYS cc_start: 0.8734 (ttmm) cc_final: 0.8522 (mtpp) REVERT: K 69 ASN cc_start: 0.8916 (t0) cc_final: 0.8632 (m-40) REVERT: K 88 HIS cc_start: 0.9124 (m90) cc_final: 0.8859 (m90) REVERT: K 121 MET cc_start: 0.8824 (ppp) cc_final: 0.8374 (ppp) REVERT: K 221 GLU cc_start: 0.9099 (tp30) cc_final: 0.8228 (tp30) REVERT: K 225 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8603 (mm110) REVERT: K 240 MET cc_start: 0.7049 (ttt) cc_final: 0.6628 (tpp) outliers start: 24 outliers final: 18 residues processed: 266 average time/residue: 1.4231 time to fit residues: 411.4777 Evaluate side-chains 268 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 248 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 9.9990 chunk 123 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN C 104 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 94 ASN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 15952 Z= 0.460 Angle : 0.723 16.552 22788 Z= 0.402 Chirality : 0.043 0.295 2606 Planarity : 0.004 0.041 1879 Dihedral : 29.945 118.389 4456 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.38 % Allowed : 24.08 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.25), residues: 1136 helix: 1.68 (0.19), residues: 691 sheet: 0.32 (0.47), residues: 136 loop : -0.98 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP M 76 HIS 0.005 0.001 HIS K 179 PHE 0.034 0.002 PHE M 44 TYR 0.035 0.002 TYR L 10 ARG 0.007 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 68 GLU cc_start: 0.7754 (tp30) cc_final: 0.7293 (tp30) REVERT: D 90 GLU cc_start: 0.8479 (mp0) cc_final: 0.7935 (mp0) REVERT: E 125 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7845 (mp10) REVERT: H 65 ASP cc_start: 0.8591 (t70) cc_final: 0.8189 (t0) REVERT: K 69 ASN cc_start: 0.8966 (t0) cc_final: 0.8654 (m-40) REVERT: K 88 HIS cc_start: 0.9056 (m90) cc_final: 0.8479 (m-70) REVERT: K 104 MET cc_start: 0.8083 (pmm) cc_final: 0.7882 (pmm) REVERT: K 121 MET cc_start: 0.8798 (ppp) cc_final: 0.8338 (ppp) REVERT: K 195 TYR cc_start: 0.8657 (t80) cc_final: 0.8107 (t80) REVERT: K 221 GLU cc_start: 0.9082 (tp30) cc_final: 0.8226 (tp30) REVERT: K 225 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8613 (mm110) REVERT: K 240 MET cc_start: 0.7303 (ttt) cc_final: 0.6903 (tpp) REVERT: M 26 LEU cc_start: 0.9471 (pp) cc_final: 0.9241 (pp) REVERT: M 85 VAL cc_start: 0.9667 (OUTLIER) cc_final: 0.9419 (p) outliers start: 33 outliers final: 22 residues processed: 257 average time/residue: 1.4447 time to fit residues: 402.4328 Evaluate side-chains 259 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 130 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN E 76 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15952 Z= 0.315 Angle : 0.712 17.550 22788 Z= 0.391 Chirality : 0.040 0.288 2606 Planarity : 0.004 0.042 1879 Dihedral : 29.771 120.609 4456 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.66 % Allowed : 24.49 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1136 helix: 1.78 (0.20), residues: 690 sheet: 0.25 (0.47), residues: 136 loop : -0.97 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP M 76 HIS 0.005 0.001 HIS K 179 PHE 0.039 0.002 PHE M 44 TYR 0.033 0.002 TYR L 10 ARG 0.011 0.001 ARG G 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 245 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 GLU cc_start: 0.7717 (tp30) cc_final: 0.7251 (tp30) REVERT: D 90 GLU cc_start: 0.8451 (mp0) cc_final: 0.7881 (mp0) REVERT: E 125 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: H 65 ASP cc_start: 0.8554 (t70) cc_final: 0.8161 (t0) REVERT: K 69 ASN cc_start: 0.8995 (t0) cc_final: 0.8538 (m-40) REVERT: K 88 HIS cc_start: 0.9041 (m90) cc_final: 0.8459 (m-70) REVERT: K 104 MET cc_start: 0.8132 (pmm) cc_final: 0.7926 (pmm) REVERT: K 121 MET cc_start: 0.8787 (ppp) cc_final: 0.8330 (ppp) REVERT: K 195 TYR cc_start: 0.8585 (t80) cc_final: 0.8022 (t80) REVERT: K 221 GLU cc_start: 0.9096 (tp30) cc_final: 0.8271 (tp30) REVERT: K 225 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8637 (mm110) REVERT: K 240 MET cc_start: 0.7292 (ttt) cc_final: 0.6907 (tpp) REVERT: M 26 LEU cc_start: 0.9450 (pp) cc_final: 0.9221 (pp) REVERT: M 85 VAL cc_start: 0.9657 (OUTLIER) cc_final: 0.9406 (p) outliers start: 26 outliers final: 21 residues processed: 255 average time/residue: 1.4520 time to fit residues: 402.7332 Evaluate side-chains 265 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 242 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 124 THR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 83 CYS Chi-restraints excluded: chain M residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 115 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 111 optimal weight: 20.0000 chunk 13 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 125 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN E 76 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.097253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.058087 restraints weight = 137286.772| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.54 r_work: 0.2584 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2580 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2580 r_free = 0.2580 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 71 | |-----------------------------------------------------------------------------| r_final: 0.2580 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15952 Z= 0.211 Angle : 0.697 18.324 22788 Z= 0.381 Chirality : 0.039 0.369 2606 Planarity : 0.004 0.043 1879 Dihedral : 29.419 122.249 4456 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.15 % Allowed : 25.31 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % 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: 1.47 (0.25), residues: 1136 helix: 1.99 (0.20), residues: 684 sheet: 0.38 (0.49), residues: 126 loop : -0.99 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP M 76 HIS 0.004 0.001 HIS B 75 PHE 0.040 0.002 PHE M 44 TYR 0.031 0.002 TYR L 10 ARG 0.010 0.000 ARG G 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6399.29 seconds wall clock time: 113 minutes 2.90 seconds (6782.90 seconds total)