Starting phenix.real_space_refine on Thu Mar 5 12:36:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ud5_26454/03_2026/7ud5_26454.map" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 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 1 6.06 5 P 292 5.49 5 S 60 5.16 5 C 13457 2.51 5 N 4083 2.21 5 O 4820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22713 Number of models: 1 Model: "" Number of chains: 18 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} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 820 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'NLE:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 1398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1398 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "L" Number of atoms: 2382 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 303, 2350 Classifications: {'peptide': 303} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 293} bond proxies already assigned to first conformer: 2366 Chain: "M" Number of atoms: 2625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2625 Classifications: {'peptide': 328} Link IDs: {'PTRANS': 24, 'TRANS': 303} Chain: "N" Number of atoms: 2879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2879 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain breaks: 2 Chain: "O" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 597 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "P" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 413 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 5, 'TRANS': 46} Chain: "Q" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 404 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 5, 'TRANS': 45} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13306 SG CYS K3959 58.276 81.672 16.227 1.00 68.53 S ATOM 13339 SG CYS K3964 57.281 80.118 14.907 1.00 51.13 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASN L 225 " occ=0.91 ... (6 atoms not shown) pdb=" ND2 ASN L 225 " occ=0.91 residue: pdb=" N LEU O 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU O 73 " occ=0.45 residue: pdb=" N ARG O 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG O 74 " occ=0.45 residue: pdb=" N GLY O 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY O 75 " occ=0.25 Time building chain proxies: 5.37, per 1000 atoms: 0.24 Number of scatterers: 22713 At special positions: 0 Unit cell: (148.12, 155.526, 119.554, 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 1 29.99 S 60 16.00 P 292 15.00 O 4820 8.00 N 4083 7.00 C 13457 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 - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3964 " 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 31 sheets defined 33.7% alpha, 12.9% beta 142 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.014A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.647A pdb=" N ILE A 124 " --> pdb=" O NLE A 120 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.165A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.686A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.024A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.503A pdb=" N ALA C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.541A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.693A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.807A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.157A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.004A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.779A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.572A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.670A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.043A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.595A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.893A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.758A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.535A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.646A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.645A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 3816 through 3818 No H-bonds generated for 'chain 'K' and resid 3816 through 3818' Processing helix chain 'K' and resid 3819 through 3825 removed outlier: 4.064A pdb=" N LEU K3823 " --> pdb=" O ARG K3819 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3879 Processing helix chain 'K' and resid 3901 through 3905 removed outlier: 3.698A pdb=" N PHE K3904 " --> pdb=" O ALA K3901 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE K3905 " --> pdb=" O ALA K3902 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3901 through 3905' Processing helix chain 'M' and resid 202 through 211 removed outlier: 4.190A pdb=" N ARG M 206 " --> pdb=" O ARG M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 504 through 526 removed outlier: 3.691A pdb=" N VAL M 508 " --> pdb=" O GLY M 504 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY M 526 " --> pdb=" O THR M 522 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 234 Processing helix chain 'N' and resid 328 through 332 removed outlier: 3.922A pdb=" N PHE N 332 " --> pdb=" O TRP N 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.619A pdb=" N TYR O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 60 Processing helix chain 'P' and resid 61 through 75 removed outlier: 4.768A pdb=" N GLN P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 Processing helix chain 'Q' and resid 52 through 60 Processing helix chain 'Q' and resid 64 through 74 Processing helix chain 'Q' and resid 79 through 91 removed outlier: 4.286A pdb=" N PHE Q 83 " --> pdb=" O ASN Q 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN Q 91 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.652A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.376A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.697A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.045A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 3831 through 3835 Processing sheet with id=AA6, first strand: chain 'K' and resid 3854 through 3857 removed outlier: 6.730A pdb=" N ILE K3928 " --> pdb=" O VAL K3855 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU K3857 " --> pdb=" O ILE K3926 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K3926 " --> pdb=" O GLU K3857 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE K3929 " --> pdb=" O TYR K3914 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR K3914 " --> pdb=" O PHE K3929 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3854 through 3857 removed outlier: 6.730A pdb=" N ILE K3928 " --> pdb=" O VAL K3855 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU K3857 " --> pdb=" O ILE K3926 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K3926 " --> pdb=" O GLU K3857 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 3860 through 3864 Processing sheet with id=AA9, first strand: chain 'L' and resid 36 through 37 removed outlier: 4.541A pdb=" N LYS L 328 " --> pdb=" O SER L 318 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER L 318 " --> pdb=" O LYS L 328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 48 through 50 removed outlier: 3.682A pdb=" N SER L 50 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 90 through 95 removed outlier: 4.687A pdb=" N ASP L 92 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.482A pdb=" N ILE L 113 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 132 through 137 removed outlier: 4.409A pdb=" N ILE L 144 " --> pdb=" O TRP L 156 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP L 156 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE L 155 " --> pdb=" O LYS L 165 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS L 165 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 174 through 179 removed outlier: 7.295A pdb=" N SER L 189 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL L 177 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL L 187 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE L 179 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 185 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG L 196 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS L 195 " --> pdb=" O THR L 208 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 197 " --> pdb=" O LEU L 206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 228 through 231 removed outlier: 3.871A pdb=" N ALA L 231 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS L 239 " --> pdb=" O ALA L 231 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP L 242 " --> pdb=" O LYS L 247 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS L 247 " --> pdb=" O ASP L 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 264 through 267 removed outlier: 3.788A pdb=" N GLN L 295 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 247 through 250 removed outlier: 3.531A pdb=" N ILE M 250 " --> pdb=" O PHE M 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 299 through 300 Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 Processing sheet with id=AC2, first strand: chain 'M' and resid 391 through 394 Processing sheet with id=AC3, first strand: chain 'M' and resid 373 through 375 Processing sheet with id=AC4, first strand: chain 'M' and resid 450 through 451 removed outlier: 4.032A pdb=" N VAL M 454 " --> pdb=" O LYS M 451 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 16 through 18 removed outlier: 3.941A pdb=" N ILE N 320 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA N 311 " --> pdb=" O VAL N 301 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL N 301 " --> pdb=" O ALA N 311 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE N 313 " --> pdb=" O LEU N 299 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 38 through 42 removed outlier: 6.493A pdb=" N ILE N 48 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE N 61 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE N 50 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.937A pdb=" N TRP N 93 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP N 94 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS N 100 " --> pdb=" O ASP N 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 114 through 116 removed outlier: 3.672A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS N 116 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 133 through 136 removed outlier: 3.591A pdb=" N LYS N 141 " --> pdb=" O THR N 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.690A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 201 through 206 Processing sheet with id=AD3, first strand: chain 'N' and resid 265 through 268 Processing sheet with id=AD4, first strand: chain 'O' and resid 12 through 15 612 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5974 1.34 - 1.46: 5644 1.46 - 1.57: 11488 1.57 - 1.69: 582 1.69 - 1.81: 83 Bond restraints: 23771 Sorted by residual: bond pdb=" C ILE M 250 " pdb=" N LEU M 251 " ideal model delta sigma weight residual 1.334 1.389 -0.054 1.52e-02 4.33e+03 1.28e+01 bond pdb=" CA ASN M 243 " pdb=" CB ASN M 243 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.56e-02 4.11e+03 1.04e+01 bond pdb=" C TYR M 249 " pdb=" N ILE M 250 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.37e-02 5.33e+03 9.49e+00 bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.73e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.352 -0.053 2.00e-02 2.50e+03 7.01e+00 ... (remaining 23766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 33121 2.35 - 4.71: 252 4.71 - 7.06: 21 7.06 - 9.42: 6 9.42 - 11.77: 2 Bond angle restraints: 33402 Sorted by residual: angle pdb=" CA PRO M 241 " pdb=" C PRO M 241 " pdb=" N PHE M 242 " ideal model delta sigma weight residual 115.50 121.22 -5.72 1.27e+00 6.20e-01 2.03e+01 angle pdb=" C ASN M 243 " pdb=" CA ASN M 243 " pdb=" CB ASN M 243 " ideal model delta sigma weight residual 110.79 118.18 -7.39 1.66e+00 3.63e-01 1.98e+01 angle pdb=" CA PRO M 241 " pdb=" C PRO M 241 " pdb=" O PRO M 241 " ideal model delta sigma weight residual 121.31 116.36 4.95 1.20e+00 6.94e-01 1.70e+01 angle pdb=" C GLY M 246 " pdb=" N TYR M 247 " pdb=" CA TYR M 247 " ideal model delta sigma weight residual 123.05 117.45 5.60 1.40e+00 5.10e-01 1.60e+01 angle pdb=" N PRO M 241 " pdb=" CA PRO M 241 " pdb=" C PRO M 241 " ideal model delta sigma weight residual 111.19 104.98 6.21 1.57e+00 4.06e-01 1.57e+01 ... (remaining 33397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.49: 11830 29.49 - 58.98: 1590 58.98 - 88.48: 122 88.48 - 117.97: 1 117.97 - 147.46: 3 Dihedral angle restraints: 13546 sinusoidal: 7411 harmonic: 6135 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -160.43 -19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" C4' DG J 244 " pdb=" C3' DG J 244 " pdb=" O3' DG J 244 " pdb=" P DG J 245 " ideal model delta sinusoidal sigma weight residual 220.00 72.54 147.46 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA MET K3816 " pdb=" C MET K3816 " pdb=" N PRO K3817 " pdb=" CA PRO K3817 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 13543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3499 0.077 - 0.154: 246 0.154 - 0.231: 3 0.231 - 0.307: 0 0.307 - 0.384: 1 Chirality restraints: 3749 Sorted by residual: chirality pdb=" CA ASN M 243 " pdb=" N ASN M 243 " pdb=" C ASN M 243 " pdb=" CB ASN M 243 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.69e+00 chirality pdb=" CA ARG P 76 " pdb=" N ARG P 76 " pdb=" C ARG P 76 " pdb=" CB ARG P 76 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.30e-01 chirality pdb=" CA ASP M 223 " pdb=" N ASP M 223 " pdb=" C ASP M 223 " pdb=" CB ASP M 223 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.64e-01 ... (remaining 3746 not shown) Planarity restraints: 3230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR M 442 " -0.060 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO M 443 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO M 443 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO M 443 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS M 240 " 0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C HIS M 240 " -0.061 2.00e-02 2.50e+03 pdb=" O HIS M 240 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO M 241 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 40 " 0.251 9.50e-02 1.11e+02 1.13e-01 8.24e+00 pdb=" NE ARG F 40 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG F 40 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG F 40 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG F 40 " 0.013 2.00e-02 2.50e+03 ... (remaining 3227 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 813 2.70 - 3.25: 21693 3.25 - 3.80: 39831 3.80 - 4.35: 50377 4.35 - 4.90: 75242 Nonbonded interactions: 187956 Sorted by model distance: nonbonded pdb=" OD1 ASN M 397 " pdb=" OH TYR M 450 " model vdw 2.144 3.040 nonbonded pdb=" N ASP M 410 " pdb=" OD1 ASP M 410 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR K3875 " pdb=" OD1 ASP K3894 " model vdw 2.182 3.040 nonbonded pdb=" OE2 GLU M 330 " pdb=" ND2 ASN M 483 " model vdw 2.195 3.120 nonbonded pdb=" OD1 ASN L 34 " pdb=" OG SER L 332 " model vdw 2.199 3.040 ... (remaining 187951 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = (chain 'G' and resid 15 through 117) } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } ncs_group { reference = (chain 'P' and resid 46 through 96) selection = chain 'Q' } 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=1.00 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: 1.780 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5995 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 : 0.003 0.059 23774 Z= 0.157 Angle : 0.586 11.770 33402 Z= 0.344 Chirality : 0.039 0.384 3749 Planarity : 0.005 0.113 3230 Dihedral : 22.038 147.460 9592 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 1.50 % Allowed : 6.37 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.18), residues: 2061 helix: 0.54 (0.21), residues: 631 sheet: -1.87 (0.28), residues: 320 loop : -2.42 (0.18), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG F 40 TYR 0.009 0.001 TYR L 243 PHE 0.012 0.001 PHE M 464 TRP 0.006 0.001 TRP N 35 HIS 0.006 0.000 HIS M 240 Details of bonding type rmsd covalent geometry : bond 0.00282 (23771) covalent geometry : angle 0.58560 (33402) hydrogen bonds : bond 0.15621 ( 975) hydrogen bonds : angle 6.34440 ( 2459) metal coordination : bond 0.00168 ( 2) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.696 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: A 45 THR cc_start: 0.7817 (p) cc_final: 0.7541 (p) REVERT: A 60 LEU cc_start: 0.6596 (tp) cc_final: 0.6272 (pt) REVERT: D 76 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.7605 (ttp80) REVERT: F 63 GLU cc_start: 0.8019 (pp20) cc_final: 0.7706 (pp20) REVERT: M 410 ASP cc_start: 0.1510 (OUTLIER) cc_final: 0.0899 (t0) REVERT: N 13 TYR cc_start: 0.6773 (p90) cc_final: 0.6474 (p90) REVERT: N 310 ILE cc_start: 0.7184 (pt) cc_final: 0.6259 (tt) outliers start: 26 outliers final: 0 residues processed: 295 average time/residue: 0.2060 time to fit residues: 86.0378 Evaluate side-chains 138 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 9.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 38 ASN C 112 GLN F 25 ASN G 112 GLN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS K3906 ASN ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 375 HIS M 397 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 250 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.114807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098001 restraints weight = 222488.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.096114 restraints weight = 239798.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.095152 restraints weight = 179089.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.094965 restraints weight = 178678.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.094621 restraints weight = 160268.729| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3797 r_free = 0.3797 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3794 r_free = 0.3794 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| r_final: 0.3794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 23774 Z= 0.376 Angle : 0.847 10.097 33402 Z= 0.462 Chirality : 0.049 0.285 3749 Planarity : 0.008 0.180 3230 Dihedral : 27.150 153.619 5509 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 21.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.33 % Allowed : 5.54 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.17), residues: 2061 helix: -0.32 (0.19), residues: 645 sheet: -1.99 (0.28), residues: 308 loop : -2.72 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.054 0.003 TYR P 87 PHE 0.030 0.003 PHE P 83 TRP 0.021 0.002 TRP N 35 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00861 (23771) covalent geometry : angle 0.84704 (33402) hydrogen bonds : bond 0.08286 ( 975) hydrogen bonds : angle 5.58007 ( 2459) metal coordination : bond 0.00261 ( 2) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 155 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7877 (p) cc_final: 0.7578 (p) REVERT: B 44 LYS cc_start: 0.7695 (mtmt) cc_final: 0.7056 (mttt) REVERT: C 87 VAL cc_start: 0.9455 (t) cc_final: 0.9206 (t) REVERT: C 89 ASN cc_start: 0.8549 (p0) cc_final: 0.8113 (t0) REVERT: D 76 ARG cc_start: 0.8710 (ptm-80) cc_final: 0.8411 (ttm170) REVERT: E 97 GLU cc_start: 0.8603 (mp0) cc_final: 0.8194 (mp0) REVERT: E 105 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7782 (tm-30) REVERT: F 25 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.6970 (t0) REVERT: F 63 GLU cc_start: 0.8709 (pp20) cc_final: 0.8354 (pp20) REVERT: H 68 GLU cc_start: 0.7704 (mp0) cc_final: 0.7388 (mp0) REVERT: K 3854 MET cc_start: 0.7185 (tmm) cc_final: 0.6837 (tmm) REVERT: M 284 TYR cc_start: 0.3812 (m-10) cc_final: 0.2618 (m-80) REVERT: M 382 TYR cc_start: 0.3671 (t80) cc_final: 0.3310 (t80) REVERT: N 26 MET cc_start: 0.7673 (pmm) cc_final: 0.7095 (pmm) REVERT: N 128 MET cc_start: 0.0849 (mmt) cc_final: 0.0626 (mmt) REVERT: N 310 ILE cc_start: 0.8026 (pt) cc_final: 0.7465 (tt) outliers start: 5 outliers final: 2 residues processed: 159 average time/residue: 0.1795 time to fit residues: 42.8843 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 114 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 225 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 223 optimal weight: 3.9990 chunk 170 optimal weight: 0.0170 chunk 192 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 143 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 227 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 25 ASN F 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K3822 HIS K3906 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 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 = 0.4257 r_free = 0.4257 target = 0.119393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.105088 restraints weight = 233412.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.103723 restraints weight = 252974.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.102277 restraints weight = 189241.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.102127 restraints weight = 185717.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.101758 restraints weight = 149559.129| |-----------------------------------------------------------------------------| r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3937 r_free = 0.3937 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| r_final: 0.3937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23774 Z= 0.141 Angle : 0.605 10.276 33402 Z= 0.338 Chirality : 0.040 0.222 3749 Planarity : 0.005 0.138 3230 Dihedral : 26.850 152.964 5509 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.06 % Allowed : 4.27 % Favored : 95.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 2061 helix: 0.74 (0.20), residues: 649 sheet: -1.95 (0.28), residues: 320 loop : -2.55 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 40 TYR 0.012 0.001 TYR P 87 PHE 0.014 0.001 PHE G 25 TRP 0.026 0.001 TRP N 35 HIS 0.006 0.001 HIS N 304 Details of bonding type rmsd covalent geometry : bond 0.00296 (23771) covalent geometry : angle 0.60471 (33402) hydrogen bonds : bond 0.05002 ( 975) hydrogen bonds : angle 4.56029 ( 2459) metal coordination : bond 0.00045 ( 2) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.719 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: A 45 THR cc_start: 0.7697 (p) cc_final: 0.7390 (p) REVERT: A 60 LEU cc_start: 0.6974 (tp) cc_final: 0.6351 (mt) REVERT: A 123 ASP cc_start: 0.8942 (m-30) cc_final: 0.8730 (m-30) REVERT: B 26 ILE cc_start: 0.8623 (mm) cc_final: 0.8243 (pt) REVERT: B 44 LYS cc_start: 0.7697 (mtmt) cc_final: 0.7430 (mttt) REVERT: F 63 GLU cc_start: 0.8529 (pp20) cc_final: 0.8160 (pp20) REVERT: H 98 LEU cc_start: 0.8879 (tt) cc_final: 0.8669 (tt) REVERT: K 3854 MET cc_start: 0.7104 (tmm) cc_final: 0.6600 (tmm) REVERT: M 284 TYR cc_start: 0.3704 (m-10) cc_final: 0.2787 (m-80) REVERT: N 26 MET cc_start: 0.7708 (pmm) cc_final: 0.7194 (pmm) REVERT: N 310 ILE cc_start: 0.8063 (pt) cc_final: 0.7278 (tt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.1700 time to fit residues: 46.3624 Evaluate side-chains 120 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 69 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 215 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 220 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 23 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN N 65 HIS ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.117207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.102132 restraints weight = 169930.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.100578 restraints weight = 196954.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.099675 restraints weight = 148728.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.099234 restraints weight = 140880.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.098903 restraints weight = 126514.504| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6604 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 23774 Z= 0.199 Angle : 0.637 10.111 33402 Z= 0.354 Chirality : 0.041 0.210 3749 Planarity : 0.005 0.135 3230 Dihedral : 26.772 155.119 5509 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.06 % Allowed : 4.21 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.18), residues: 2061 helix: 0.64 (0.20), residues: 647 sheet: -1.90 (0.29), residues: 305 loop : -2.59 (0.17), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.033 0.001 ARG N 220 TYR 0.029 0.002 TYR G 50 PHE 0.012 0.002 PHE N 213 TRP 0.025 0.002 TRP N 35 HIS 0.007 0.001 HIS N 67 Details of bonding type rmsd covalent geometry : bond 0.00451 (23771) covalent geometry : angle 0.63694 (33402) hydrogen bonds : bond 0.05692 ( 975) hydrogen bonds : angle 4.69165 ( 2459) metal coordination : bond 0.00117 ( 2) Misc. bond : bond 0.00071 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8011 (p) cc_final: 0.7693 (p) REVERT: A 60 LEU cc_start: 0.7019 (tp) cc_final: 0.6400 (mt) REVERT: B 26 ILE cc_start: 0.8633 (mm) cc_final: 0.8277 (pt) REVERT: B 44 LYS cc_start: 0.7680 (mtmt) cc_final: 0.7359 (mttt) REVERT: E 97 GLU cc_start: 0.8407 (mp0) cc_final: 0.7999 (mp0) REVERT: F 63 GLU cc_start: 0.8483 (pp20) cc_final: 0.8219 (pp20) REVERT: G 50 TYR cc_start: 0.8159 (t80) cc_final: 0.7824 (t80) REVERT: H 122 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7370 (mttm) REVERT: K 3822 HIS cc_start: 0.6886 (t70) cc_final: 0.6664 (t-170) REVERT: M 284 TYR cc_start: 0.4246 (m-10) cc_final: 0.3418 (m-80) REVERT: N 26 MET cc_start: 0.7852 (pmm) cc_final: 0.7357 (pmm) REVERT: N 128 MET cc_start: 0.1007 (mmt) cc_final: 0.0766 (mmt) REVERT: N 310 ILE cc_start: 0.7984 (pt) cc_final: 0.7423 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1652 time to fit residues: 39.2084 Evaluate side-chains 121 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 119 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K3779 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 375 HIS ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.116377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.102182 restraints weight = 232427.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.101199 restraints weight = 244894.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.100480 restraints weight = 165473.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.100317 restraints weight = 159917.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099661 restraints weight = 140809.835| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3897 r_free = 0.3897 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 23774 Z= 0.236 Angle : 0.679 10.434 33402 Z= 0.376 Chirality : 0.043 0.211 3749 Planarity : 0.006 0.147 3230 Dihedral : 26.873 156.857 5509 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.18), residues: 2061 helix: 0.42 (0.20), residues: 643 sheet: -2.00 (0.29), residues: 298 loop : -2.66 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 40 TYR 0.033 0.002 TYR F 88 PHE 0.015 0.002 PHE E 104 TRP 0.027 0.002 TRP N 35 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00534 (23771) covalent geometry : angle 0.67911 (33402) hydrogen bonds : bond 0.06090 ( 975) hydrogen bonds : angle 4.85517 ( 2459) metal coordination : bond 0.00150 ( 2) Misc. bond : bond 0.00126 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8045 (p) cc_final: 0.7777 (p) REVERT: A 60 LEU cc_start: 0.6944 (tp) cc_final: 0.6381 (mt) REVERT: B 44 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7442 (mttt) REVERT: B 63 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8154 (mm-30) REVERT: E 97 GLU cc_start: 0.8351 (mp0) cc_final: 0.7915 (mp0) REVERT: F 63 GLU cc_start: 0.8686 (pp20) cc_final: 0.8277 (pp20) REVERT: G 50 TYR cc_start: 0.8208 (t80) cc_final: 0.7834 (t80) REVERT: H 122 LYS cc_start: 0.7980 (mtpt) cc_final: 0.7376 (mttm) REVERT: N 26 MET cc_start: 0.8019 (pmm) cc_final: 0.7512 (pmm) REVERT: N 128 MET cc_start: 0.1101 (mmt) cc_final: 0.0862 (mmt) REVERT: N 310 ILE cc_start: 0.8141 (pt) cc_final: 0.7308 (tt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1637 time to fit residues: 39.3053 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 36 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 216 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 199 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 213 optimal weight: 20.0000 chunk 52 optimal weight: 0.0070 overall best weight: 3.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.116279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.101446 restraints weight = 190217.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.100090 restraints weight = 223802.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.098873 restraints weight = 168555.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.098587 restraints weight = 177634.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.098136 restraints weight = 150319.928| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3858 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3858 r_free = 0.3858 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| r_final: 0.3858 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23774 Z= 0.215 Angle : 0.665 9.789 33402 Z= 0.369 Chirality : 0.042 0.275 3749 Planarity : 0.005 0.146 3230 Dihedral : 26.888 157.347 5509 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 0.06 % Allowed : 3.27 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.18), residues: 2061 helix: 0.42 (0.20), residues: 645 sheet: -1.97 (0.29), residues: 298 loop : -2.70 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 40 TYR 0.031 0.002 TYR M 284 PHE 0.017 0.002 PHE N 259 TRP 0.028 0.002 TRP N 35 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00486 (23771) covalent geometry : angle 0.66456 (33402) hydrogen bonds : bond 0.05828 ( 975) hydrogen bonds : angle 4.81042 ( 2459) metal coordination : bond 0.00117 ( 2) Misc. bond : bond 0.00537 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7866 (p) cc_final: 0.7579 (p) REVERT: A 60 LEU cc_start: 0.7099 (tp) cc_final: 0.6491 (mt) REVERT: B 26 ILE cc_start: 0.8735 (mm) cc_final: 0.8415 (pt) REVERT: B 44 LYS cc_start: 0.7719 (mtmt) cc_final: 0.7440 (mttt) REVERT: B 63 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8004 (mm-30) REVERT: F 59 LYS cc_start: 0.8623 (tppt) cc_final: 0.8414 (tppt) REVERT: F 63 GLU cc_start: 0.8719 (pp20) cc_final: 0.8254 (pp20) REVERT: G 50 TYR cc_start: 0.8250 (t80) cc_final: 0.7727 (t80) REVERT: H 122 LYS cc_start: 0.7942 (mtpt) cc_final: 0.7359 (mttm) REVERT: N 26 MET cc_start: 0.8061 (pmm) cc_final: 0.7539 (pmm) REVERT: N 310 ILE cc_start: 0.8060 (pt) cc_final: 0.7476 (tt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.1565 time to fit residues: 36.7758 Evaluate side-chains 115 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 224 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 172 optimal weight: 0.5980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.104113 restraints weight = 203590.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.102832 restraints weight = 236536.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.102024 restraints weight = 174490.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.101562 restraints weight = 177680.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.100954 restraints weight = 167909.172| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 26 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23774 Z= 0.152 Angle : 0.616 9.733 33402 Z= 0.342 Chirality : 0.041 0.213 3749 Planarity : 0.005 0.121 3230 Dihedral : 26.735 156.553 5509 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.06 % Allowed : 2.33 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.18), residues: 2061 helix: 0.88 (0.21), residues: 645 sheet: -1.82 (0.30), residues: 280 loop : -2.67 (0.17), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 40 TYR 0.023 0.002 TYR M 284 PHE 0.024 0.001 PHE K3820 TRP 0.030 0.002 TRP N 303 HIS 0.004 0.001 HIS N 304 Details of bonding type rmsd covalent geometry : bond 0.00334 (23771) covalent geometry : angle 0.61640 (33402) hydrogen bonds : bond 0.04716 ( 975) hydrogen bonds : angle 4.48818 ( 2459) metal coordination : bond 0.00065 ( 2) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7967 (p) cc_final: 0.7674 (p) REVERT: A 60 LEU cc_start: 0.6794 (tp) cc_final: 0.6222 (mt) REVERT: B 26 ILE cc_start: 0.8650 (mm) cc_final: 0.8289 (pt) REVERT: B 44 LYS cc_start: 0.7721 (mtmt) cc_final: 0.7285 (mttt) REVERT: C 56 GLU cc_start: 0.7935 (tp30) cc_final: 0.7586 (tt0) REVERT: C 87 VAL cc_start: 0.9171 (t) cc_final: 0.8960 (t) REVERT: C 89 ASN cc_start: 0.8461 (p0) cc_final: 0.8261 (t0) REVERT: E 97 GLU cc_start: 0.8520 (mp0) cc_final: 0.8009 (mp0) REVERT: F 63 GLU cc_start: 0.8775 (pp20) cc_final: 0.8423 (pp20) REVERT: G 50 TYR cc_start: 0.8072 (t80) cc_final: 0.7779 (t80) REVERT: N 26 MET cc_start: 0.8033 (pmm) cc_final: 0.7513 (pmm) REVERT: N 310 ILE cc_start: 0.8113 (pt) cc_final: 0.7314 (tt) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.1487 time to fit residues: 35.4121 Evaluate side-chains 117 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 219 optimal weight: 20.0000 chunk 62 optimal weight: 4.9990 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 chunk 190 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 49 optimal weight: 0.0980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.117038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.100035 restraints weight = 162688.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.098674 restraints weight = 210579.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.097771 restraints weight = 159559.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097329 restraints weight = 156471.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.096946 restraints weight = 140645.622| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3837 r_free = 0.3837 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 23774 Z= 0.183 Angle : 0.644 12.284 33402 Z= 0.356 Chirality : 0.041 0.203 3749 Planarity : 0.005 0.113 3230 Dihedral : 26.715 157.242 5509 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 0.06 % Allowed : 1.16 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.18), residues: 2061 helix: 0.63 (0.20), residues: 651 sheet: -1.89 (0.30), residues: 286 loop : -2.67 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 40 TYR 0.025 0.002 TYR M 284 PHE 0.013 0.001 PHE A 104 TRP 0.031 0.001 TRP N 303 HIS 0.008 0.001 HIS N 67 Details of bonding type rmsd covalent geometry : bond 0.00410 (23771) covalent geometry : angle 0.64388 (33402) hydrogen bonds : bond 0.05321 ( 975) hydrogen bonds : angle 4.62685 ( 2459) metal coordination : bond 0.00094 ( 2) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7972 (p) cc_final: 0.7662 (p) REVERT: A 60 LEU cc_start: 0.6910 (tp) cc_final: 0.6402 (mt) REVERT: B 26 ILE cc_start: 0.8668 (mm) cc_final: 0.8351 (pt) REVERT: B 44 LYS cc_start: 0.7630 (mtmt) cc_final: 0.7257 (mttt) REVERT: C 87 VAL cc_start: 0.9112 (t) cc_final: 0.8893 (t) REVERT: C 89 ASN cc_start: 0.8519 (p0) cc_final: 0.8217 (t0) REVERT: E 97 GLU cc_start: 0.8624 (mp0) cc_final: 0.8160 (mp0) REVERT: F 63 GLU cc_start: 0.8796 (pp20) cc_final: 0.8466 (pp20) REVERT: N 26 MET cc_start: 0.8076 (pmm) cc_final: 0.7506 (pmm) REVERT: N 310 ILE cc_start: 0.7947 (pt) cc_final: 0.7332 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1462 time to fit residues: 34.3788 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 221 optimal weight: 0.5980 chunk 78 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 147 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 219 optimal weight: 20.0000 chunk 199 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 101 optimal weight: 8.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN K3822 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.116524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.100477 restraints weight = 182699.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.099415 restraints weight = 237159.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.098585 restraints weight = 182178.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.098616 restraints weight = 158962.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.098596 restraints weight = 128873.769| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3871 r_free = 0.3871 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23774 Z= 0.201 Angle : 0.661 11.558 33402 Z= 0.365 Chirality : 0.042 0.203 3749 Planarity : 0.005 0.117 3230 Dihedral : 26.762 157.721 5509 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.11 % Allowed : 1.05 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.18), residues: 2061 helix: 0.50 (0.20), residues: 652 sheet: -1.87 (0.30), residues: 282 loop : -2.70 (0.17), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 40 TYR 0.016 0.002 TYR H 80 PHE 0.034 0.002 PHE E 104 TRP 0.035 0.002 TRP N 303 HIS 0.006 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00454 (23771) covalent geometry : angle 0.66071 (33402) hydrogen bonds : bond 0.05516 ( 975) hydrogen bonds : angle 4.67336 ( 2459) metal coordination : bond 0.00114 ( 2) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 144 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8049 (p) cc_final: 0.7799 (p) REVERT: A 60 LEU cc_start: 0.6906 (tp) cc_final: 0.6376 (mt) REVERT: B 26 ILE cc_start: 0.8761 (mm) cc_final: 0.8331 (pt) REVERT: B 44 LYS cc_start: 0.7732 (mtmt) cc_final: 0.7276 (mttt) REVERT: E 97 GLU cc_start: 0.8691 (mp0) cc_final: 0.8238 (mp0) REVERT: F 63 GLU cc_start: 0.8683 (pp20) cc_final: 0.8367 (pp20) REVERT: H 122 LYS cc_start: 0.7948 (mtpt) cc_final: 0.7382 (mttm) REVERT: K 3854 MET cc_start: 0.7400 (tmm) cc_final: 0.7164 (tmm) REVERT: K 3931 MET cc_start: 0.5193 (pmm) cc_final: 0.4518 (tpp) REVERT: N 26 MET cc_start: 0.8189 (pmm) cc_final: 0.7668 (pmm) REVERT: N 310 ILE cc_start: 0.8054 (pt) cc_final: 0.7189 (tt) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.1603 time to fit residues: 35.3193 Evaluate side-chains 114 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 203 optimal weight: 5.9990 chunk 28 optimal weight: 0.0870 chunk 128 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 0.0050 chunk 150 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 overall best weight: 1.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN K3822 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.117596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.102011 restraints weight = 149302.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101681 restraints weight = 260925.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100926 restraints weight = 149838.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.100914 restraints weight = 122345.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.100896 restraints weight = 106602.740| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3913 r_free = 0.3913 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6558 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23774 Z= 0.158 Angle : 0.630 12.140 33402 Z= 0.346 Chirality : 0.041 0.234 3749 Planarity : 0.005 0.102 3230 Dihedral : 26.683 157.258 5509 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 0.11 % Allowed : 0.28 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.02 (0.18), residues: 2061 helix: 0.78 (0.21), residues: 651 sheet: -1.81 (0.30), residues: 280 loop : -2.64 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG F 40 TYR 0.024 0.002 TYR G 50 PHE 0.023 0.001 PHE E 104 TRP 0.038 0.001 TRP N 303 HIS 0.005 0.001 HIS N 304 Details of bonding type rmsd covalent geometry : bond 0.00349 (23771) covalent geometry : angle 0.63045 (33402) hydrogen bonds : bond 0.04868 ( 975) hydrogen bonds : angle 4.48905 ( 2459) metal coordination : bond 0.00066 ( 2) Misc. bond : bond 0.00079 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4122 Ramachandran restraints generated. 2061 Oldfield, 0 Emsley, 2061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7844 (p) cc_final: 0.7548 (p) REVERT: A 60 LEU cc_start: 0.6684 (tp) cc_final: 0.6140 (mt) REVERT: B 26 ILE cc_start: 0.8639 (mm) cc_final: 0.8237 (pt) REVERT: B 44 LYS cc_start: 0.7668 (mtmt) cc_final: 0.7184 (mttt) REVERT: C 87 VAL cc_start: 0.9135 (t) cc_final: 0.8904 (t) REVERT: C 89 ASN cc_start: 0.8471 (p0) cc_final: 0.8226 (t0) REVERT: E 97 GLU cc_start: 0.8492 (mp0) cc_final: 0.8027 (mp0) REVERT: F 63 GLU cc_start: 0.8822 (pp20) cc_final: 0.8557 (pp20) REVERT: F 67 ARG cc_start: 0.8370 (ttm-80) cc_final: 0.7800 (ttt180) REVERT: G 115 LEU cc_start: 0.7775 (tp) cc_final: 0.7548 (tp) REVERT: K 3931 MET cc_start: 0.5257 (pmm) cc_final: 0.4520 (tpp) REVERT: M 284 TYR cc_start: 0.3350 (m-10) cc_final: 0.2954 (m-80) REVERT: M 315 MET cc_start: -0.0085 (mtp) cc_final: -0.0468 (mtp) REVERT: N 26 MET cc_start: 0.8149 (pmm) cc_final: 0.7615 (pmm) REVERT: N 310 ILE cc_start: 0.7785 (pt) cc_final: 0.7128 (tt) outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.1674 time to fit residues: 37.8852 Evaluate side-chains 116 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 176 optimal weight: 7.9990 chunk 139 optimal weight: 0.0980 chunk 163 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 12 optimal weight: 0.5980 chunk 161 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 54 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN K3822 HIS ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.118081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.105153 restraints weight = 197842.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.104535 restraints weight = 275066.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.104072 restraints weight = 139341.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.104264 restraints weight = 109335.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.104449 restraints weight = 89993.376| |-----------------------------------------------------------------------------| r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 29 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23774 Z= 0.153 Angle : 0.622 12.195 33402 Z= 0.342 Chirality : 0.041 0.224 3749 Planarity : 0.004 0.090 3230 Dihedral : 26.602 157.043 5509 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 0.11 % Allowed : 0.66 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.18), residues: 2061 helix: 0.87 (0.21), residues: 650 sheet: -1.83 (0.30), residues: 279 loop : -2.61 (0.17), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 40 TYR 0.025 0.002 TYR D 80 PHE 0.033 0.001 PHE K3820 TRP 0.035 0.001 TRP N 303 HIS 0.005 0.001 HIS D 79 Details of bonding type rmsd covalent geometry : bond 0.00339 (23771) covalent geometry : angle 0.62250 (33402) hydrogen bonds : bond 0.04704 ( 975) hydrogen bonds : angle 4.39241 ( 2459) metal coordination : bond 0.00065 ( 2) Misc. bond : bond 0.00073 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2927.95 seconds wall clock time: 51 minutes 51.30 seconds (3111.30 seconds total)