Starting phenix.real_space_refine on Sun Sep 13 09:34:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ud5_26454/09_2026/7ud5_26454_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ud5_26454/09_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_26454/09_2026/7ud5_26454_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ud5_26454/09_2026/7ud5_26454_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ud5_26454/09_2026/7ud5_26454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ud5_26454/09_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-2.2.1-6174/lib/python3.11/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: 5.51, 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: 1.62 Conformation dependent library (CDL) restraints added in 887.2 milliseconds 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: 2.94 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: 6.38 Time building geometry restraints manager: 2.32 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=" C3' DA I 8 " pdb=" C2' DA I 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT J 201 " pdb=" C2' DT J 201 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+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=" C3' DG I 37 " pdb=" C2' DG I 37 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.73e+00 ... (remaining 23766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 32912 2.35 - 4.71: 461 4.71 - 7.06: 21 7.06 - 9.42: 6 9.42 - 11.77: 2 Bond angle restraints: 33402 Sorted by residual: angle pdb=" O4' DA I 30 " pdb=" C4' DA I 30 " pdb=" C3' DA I 30 " ideal model delta sigma weight residual 106.00 102.51 3.49 6.00e-01 2.78e+00 3.39e+01 angle pdb=" O4' DC I 95 " pdb=" C4' DC I 95 " pdb=" C3' DC I 95 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.60e+01 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=" O4' DG I 102 " pdb=" C4' DG I 102 " pdb=" C3' DG I 102 " ideal model delta sigma weight residual 106.00 103.43 2.57 6.00e-01 2.78e+00 1.84e+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: 3397 0.077 - 0.154: 347 0.154 - 0.231: 4 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.030 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6003 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 : 0.004 0.059 23774 Z= 0.376 Angle : 0.692 11.770 33402 Z= 0.553 Chirality : 0.044 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/Z covalent geometry : bond 0.00429 / 0.38 (23771) covalent geometry : angle 0.69219 / 0.55 (33402) hydrogen bonds : bond 0.15621 / 10.34 ( 975) hydrogen bonds : angle 6.34440 / 4.49 ( 2459) metal coordination : bond 0.00168 / 0.12 ( 2) Misc. bond : bond 0.00063 / 0.04 ( 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 : 0.618 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: 0.7542 (p) REVERT: A 60 LEU cc_start: 0.6596 (tp) cc_final: 0.6271 (pt) REVERT: D 76 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.7603 (ttp80) REVERT: F 63 GLU cc_start: 0.8019 (pp20) cc_final: 0.7704 (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: 0.6476 (p90) REVERT: N 310 ILE cc_start: 0.7184 (pt) cc_final: 0.6261 (tt) outliers start: 26 outliers final: 0 residues processed: 295 average time/residue: 0.1967 time to fit residues: 83.4636 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 : 0.707 ------------------------------------------------------------------------------- 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: 30.0000 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 40.0000 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 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: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 38 ASN C 112 GLN K3779 ASN 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 ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.115808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100457 restraints weight = 224091.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.099075 restraints weight = 254578.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.097781 restraints weight = 173415.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.097324 restraints weight = 192168.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.097181 restraints weight = 153245.132| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3851 r_free = 0.3851 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 14 (21 function evaluations) r_final: 0.3851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 23774 Z= 0.323 Angle : 0.888 12.807 33402 Z= 0.477 Chirality : 0.054 0.283 3749 Planarity : 0.008 0.171 3230 Dihedral : 27.283 156.045 5509 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 0.39 % Allowed : 5.21 % Favored : 94.40 % 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: -2.65 (0.17), residues: 2061 helix: -0.33 (0.19), residues: 648 sheet: -1.96 (0.28), residues: 308 loop : -2.67 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 40 TYR 0.030 0.004 TYR F 98 PHE 0.035 0.003 PHE P 83 TRP 0.029 0.003 TRP N 35 HIS 0.013 0.003 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00701 / 0.32 (23771) covalent geometry : angle 0.88807 / 0.48 (33402) hydrogen bonds : bond 0.08694 / 5.84 ( 975) hydrogen bonds : angle 5.54167 / 3.99 ( 2459) metal coordination : bond 0.00103 / 0.07 ( 2) Misc. bond : bond 0.00008 / 0.01 ( 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 165 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8032 (p) cc_final: 0.7767 (p) REVERT: B 44 LYS cc_start: 0.7798 (mtmt) cc_final: 0.7244 (mttt) REVERT: B 84 MET cc_start: 0.7332 (tmm) cc_final: 0.7078 (tmm) REVERT: D 76 ARG cc_start: 0.8718 (ptm-80) cc_final: 0.8465 (ttm170) REVERT: E 97 GLU cc_start: 0.8535 (mp0) cc_final: 0.8223 (mp0) REVERT: E 105 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7765 (tm-30) REVERT: F 54 THR cc_start: 0.9027 (p) cc_final: 0.8814 (t) REVERT: F 63 GLU cc_start: 0.8696 (pp20) cc_final: 0.8365 (pp20) REVERT: H 122 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7531 (mttm) REVERT: K 3822 HIS cc_start: 0.6501 (OUTLIER) cc_final: 0.6020 (t-170) REVERT: K 3854 MET cc_start: 0.7105 (tmm) cc_final: 0.6365 (tmm) REVERT: L 197 ILE cc_start: 0.6179 (mm) cc_final: 0.5969 (mm) REVERT: M 284 TYR cc_start: 0.3689 (m-10) cc_final: 0.2526 (m-80) REVERT: M 382 TYR cc_start: 0.3598 (t80) cc_final: 0.3209 (t80) REVERT: N 26 MET cc_start: 0.7639 (pmm) cc_final: 0.7074 (pmm) REVERT: N 310 ILE cc_start: 0.7882 (pt) cc_final: 0.7496 (tt) outliers start: 6 outliers final: 1 residues processed: 164 average time/residue: 0.1759 time to fit residues: 43.3224 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 0.7980 chunk 223 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 192 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 143 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 108 ASN F 25 ASN K3906 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 ASN N 33 ASN ** N 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.119311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.105101 restraints weight = 233755.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.104023 restraints weight = 239515.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103236 restraints weight = 157762.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.103013 restraints weight = 157860.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.102281 restraints weight = 150051.197| |-----------------------------------------------------------------------------| r_work (final): 0.3952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23774 Z= 0.139 Angle : 0.631 10.061 33402 Z= 0.358 Chirality : 0.046 0.284 3749 Planarity : 0.005 0.145 3230 Dihedral : 27.106 154.345 5509 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.15 % Favored : 92.85 % Rotamer: Outliers : 0.17 % Allowed : 3.32 % Favored : 96.51 % 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: 0.68 (0.20), residues: 649 sheet: -1.93 (0.28), residues: 320 loop : -2.52 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 40 TYR 0.014 0.001 TYR B 98 PHE 0.013 0.001 PHE N 213 TRP 0.025 0.002 TRP N 35 HIS 0.005 0.001 HIS N 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (23771) covalent geometry : angle 0.63121 / 0.36 (33402) hydrogen bonds : bond 0.05770 / 3.81 ( 975) hydrogen bonds : angle 4.70558 / 3.38 ( 2459) metal coordination : bond 0.00070 / 0.05 ( 2) Misc. bond : bond 0.00018 / 0.01 ( 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 182 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 180 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7918 (p) cc_final: 0.7643 (p) REVERT: A 60 LEU cc_start: 0.6948 (tp) cc_final: 0.6351 (mt) REVERT: B 26 ILE cc_start: 0.8597 (mm) cc_final: 0.8212 (pt) REVERT: B 44 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7430 (mttt) REVERT: E 97 GLU cc_start: 0.8321 (mp0) cc_final: 0.7941 (mp0) REVERT: E 105 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7670 (tm-30) REVERT: F 25 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.6924 (t0) REVERT: F 54 THR cc_start: 0.8973 (p) cc_final: 0.8770 (t) REVERT: F 63 GLU cc_start: 0.8673 (pp20) cc_final: 0.8285 (pp20) REVERT: H 122 LYS cc_start: 0.7504 (mtmm) cc_final: 0.6719 (mmtt) REVERT: M 284 TYR cc_start: 0.3716 (m-10) cc_final: 0.2770 (m-80) REVERT: M 382 TYR cc_start: 0.3376 (t80) cc_final: 0.3062 (t80) REVERT: N 26 MET cc_start: 0.7631 (pmm) cc_final: 0.7102 (pmm) REVERT: N 310 ILE cc_start: 0.7888 (pt) cc_final: 0.7207 (tt) outliers start: 2 outliers final: 0 residues processed: 181 average time/residue: 0.1789 time to fit residues: 48.3973 Evaluate side-chains 123 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 122 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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: 5.9990 chunk 14 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 220 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 94 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 108 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 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 = 0.4214 r_free = 0.4214 target = 0.116910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.102450 restraints weight = 171263.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101213 restraints weight = 198981.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.099779 restraints weight = 148353.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.099288 restraints weight = 170473.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.098821 restraints weight = 150788.579| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 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 = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (11 function evaluations) r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6630 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23774 Z= 0.207 Angle : 0.703 12.176 33402 Z= 0.389 Chirality : 0.047 0.287 3749 Planarity : 0.006 0.113 3230 Dihedral : 27.082 156.001 5509 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.06 % Allowed : 5.15 % Favored : 94.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.40 (0.20), residues: 647 sheet: -1.98 (0.28), residues: 318 loop : -2.57 (0.17), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG F 40 TYR 0.019 0.002 TYR F 98 PHE 0.015 0.002 PHE E 84 TRP 0.026 0.002 TRP N 35 HIS 0.008 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.21 (23771) covalent geometry : angle 0.70282 / 0.39 (33402) hydrogen bonds : bond 0.06628 / 4.42 ( 975) hydrogen bonds : angle 4.90005 / 3.52 ( 2459) metal coordination : bond 0.00122 / 0.08 ( 2) Misc. bond : bond 0.00044 / 0.03 ( 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 151 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8021 (p) cc_final: 0.7758 (p) REVERT: A 60 LEU cc_start: 0.6928 (tp) cc_final: 0.6311 (mt) REVERT: B 26 ILE cc_start: 0.8656 (mm) cc_final: 0.8304 (pt) REVERT: B 44 LYS cc_start: 0.7743 (mtmt) cc_final: 0.7315 (mttt) REVERT: E 97 GLU cc_start: 0.8397 (mp0) cc_final: 0.8033 (mp0) REVERT: E 105 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7678 (tm-30) REVERT: F 63 GLU cc_start: 0.8593 (pp20) cc_final: 0.8205 (pp20) REVERT: H 122 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7353 (mttm) REVERT: L 197 ILE cc_start: 0.6230 (mm) cc_final: 0.6013 (mm) REVERT: M 284 TYR cc_start: 0.4151 (m-10) cc_final: 0.3074 (m-80) REVERT: M 382 TYR cc_start: 0.3506 (t80) cc_final: 0.3150 (t80) REVERT: N 26 MET cc_start: 0.7748 (pmm) cc_final: 0.7228 (pmm) REVERT: N 128 MET cc_start: 0.0928 (mmt) cc_final: 0.0710 (mmt) REVERT: N 310 ILE cc_start: 0.7668 (pt) cc_final: 0.7176 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1729 time to fit residues: 40.3504 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 : 0.736 ------------------------------------------------------------------------------- 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: 10.0000 chunk 35 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 126 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 108 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN ** N 116 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.117899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103753 restraints weight = 234175.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.102747 restraints weight = 245517.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.101489 restraints weight = 165359.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.101184 restraints weight = 181975.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.100842 restraints weight = 149186.559| |-----------------------------------------------------------------------------| r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6566 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23774 Z= 0.162 Angle : 0.646 9.446 33402 Z= 0.363 Chirality : 0.046 0.290 3749 Planarity : 0.005 0.137 3230 Dihedral : 27.028 155.878 5509 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % 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: -2.09 (0.18), residues: 2061 helix: 0.69 (0.20), residues: 647 sheet: -1.92 (0.29), residues: 300 loop : -2.63 (0.17), residues: 1114 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.018 0.002 TYR F 98 PHE 0.012 0.001 PHE D 67 TRP 0.027 0.002 TRP N 35 HIS 0.005 0.001 HIS N 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.16 (23771) covalent geometry : angle 0.64600 / 0.36 (33402) hydrogen bonds : bond 0.05646 / 3.76 ( 975) hydrogen bonds : angle 4.68429 / 3.35 ( 2459) metal coordination : bond 0.00097 / 0.07 ( 2) Misc. bond : bond 0.00061 / 0.04 ( 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 162 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7995 (p) cc_final: 0.7701 (p) REVERT: A 60 LEU cc_start: 0.6940 (tp) cc_final: 0.6338 (mt) REVERT: B 26 ILE cc_start: 0.8653 (mm) cc_final: 0.8293 (pt) REVERT: B 44 LYS cc_start: 0.7803 (mtmt) cc_final: 0.7501 (mttt) REVERT: E 97 GLU cc_start: 0.8473 (mp0) cc_final: 0.7973 (mp0) REVERT: E 105 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7915 (tm-30) REVERT: F 63 GLU cc_start: 0.8604 (pp20) cc_final: 0.8237 (pp20) REVERT: M 284 TYR cc_start: 0.3950 (m-10) cc_final: 0.3277 (m-80) REVERT: M 382 TYR cc_start: 0.3535 (t80) cc_final: 0.3205 (t80) REVERT: N 26 MET cc_start: 0.7858 (pmm) cc_final: 0.7342 (pmm) REVERT: N 310 ILE cc_start: 0.7990 (pt) cc_final: 0.7318 (tt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1648 time to fit residues: 41.3739 Evaluate side-chains 118 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.655 ------------------------------------------------------------------------------- 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: 6.9990 chunk 216 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 83 optimal weight: 30.0000 chunk 199 optimal weight: 6.9990 chunk 85 optimal weight: 40.0000 chunk 18 optimal weight: 0.9980 chunk 213 optimal weight: 30.0000 chunk 52 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN M 229 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.117462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.101645 restraints weight = 190724.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.099980 restraints weight = 207976.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.098478 restraints weight = 164093.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.097972 restraints weight = 184123.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.097720 restraints weight = 148535.812| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23774 Z= 0.174 Angle : 0.658 9.576 33402 Z= 0.367 Chirality : 0.046 0.288 3749 Planarity : 0.005 0.133 3230 Dihedral : 27.014 156.667 5509 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 0.06 % Allowed : 2.77 % Favored : 97.17 % 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: 0.73 (0.20), residues: 646 sheet: -1.98 (0.30), residues: 285 loop : -2.61 (0.17), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.040 0.002 TYR G 50 PHE 0.011 0.002 PHE N 213 TRP 0.028 0.002 TRP N 35 HIS 0.005 0.001 HIS M 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (23771) covalent geometry : angle 0.65754 / 0.37 (33402) hydrogen bonds : bond 0.05774 / 3.85 ( 975) hydrogen bonds : angle 4.67011 / 3.34 ( 2459) metal coordination : bond 0.00110 / 0.08 ( 2) Misc. bond : bond 0.00075 / 0.05 ( 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 156 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.706 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: 0.7988 (p) cc_final: 0.7715 (p) REVERT: A 60 LEU cc_start: 0.6914 (tp) cc_final: 0.6346 (mt) REVERT: B 26 ILE cc_start: 0.8656 (mm) cc_final: 0.8312 (pt) REVERT: B 44 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7435 (mttt) REVERT: E 97 GLU cc_start: 0.8386 (mp0) cc_final: 0.8042 (mp0) REVERT: E 105 GLU cc_start: 0.8035 (tm-30) cc_final: 0.7644 (tm-30) REVERT: F 63 GLU cc_start: 0.8596 (pp20) cc_final: 0.8269 (pp20) REVERT: M 382 TYR cc_start: 0.3684 (t80) cc_final: 0.3317 (t80) REVERT: N 26 MET cc_start: 0.7892 (pmm) cc_final: 0.7374 (pmm) REVERT: N 310 ILE cc_start: 0.7768 (pt) cc_final: 0.7282 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1631 time to fit residues: 39.2521 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 : 0.719 ------------------------------------------------------------------------------- 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: 0.9990 chunk 101 optimal weight: 3.9990 chunk 192 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 18 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 69 optimal weight: 0.0170 chunk 113 optimal weight: 3.9990 chunk 172 optimal weight: 5.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.118336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.103924 restraints weight = 203819.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.102600 restraints weight = 225004.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101561 restraints weight = 161414.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.101258 restraints weight = 159326.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.100681 restraints weight = 143257.057| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3910 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3910 r_free = 0.3910 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (14 function evaluations) r_final: 0.3910 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23774 Z= 0.145 Angle : 0.635 13.040 33402 Z= 0.355 Chirality : 0.045 0.288 3749 Planarity : 0.005 0.126 3230 Dihedral : 26.951 156.570 5509 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 0.06 % Allowed : 1.94 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.00 (0.18), residues: 2061 helix: 0.82 (0.20), residues: 645 sheet: -1.86 (0.29), residues: 299 loop : -2.61 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 40 TYR 0.024 0.001 TYR D 80 PHE 0.013 0.001 PHE N 332 TRP 0.030 0.002 TRP N 35 HIS 0.004 0.001 HIS N 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.15 (23771) covalent geometry : angle 0.63462 / 0.36 (33402) hydrogen bonds : bond 0.05272 / 3.51 ( 975) hydrogen bonds : angle 4.56655 / 3.27 ( 2459) metal coordination : bond 0.00083 / 0.06 ( 2) Misc. bond : bond 0.00072 / 0.05 ( 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 164 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.627 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: 0.8001 (p) cc_final: 0.7709 (p) REVERT: A 60 LEU cc_start: 0.6976 (tp) cc_final: 0.6361 (mt) REVERT: B 26 ILE cc_start: 0.8610 (mm) cc_final: 0.8247 (pt) REVERT: B 44 LYS cc_start: 0.7722 (mtmt) cc_final: 0.7415 (mttt) REVERT: E 105 GLU cc_start: 0.7968 (tm-30) cc_final: 0.7414 (tm-30) REVERT: F 63 GLU cc_start: 0.8568 (pp20) cc_final: 0.8263 (pp20) REVERT: M 382 TYR cc_start: 0.3394 (t80) cc_final: 0.3090 (t80) REVERT: N 26 MET cc_start: 0.7891 (pmm) cc_final: 0.7364 (pmm) REVERT: N 310 ILE cc_start: 0.7940 (pt) cc_final: 0.7301 (tt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1683 time to fit residues: 42.4358 Evaluate side-chains 126 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.687 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 30.0000 chunk 210 optimal weight: 6.9990 chunk 219 optimal weight: 0.0870 chunk 62 optimal weight: 0.0870 chunk 141 optimal weight: 0.7980 chunk 55 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 190 optimal weight: 10.0000 chunk 135 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.119965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.106738 restraints weight = 163266.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.105517 restraints weight = 276929.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.105077 restraints weight = 159365.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.105083 restraints weight = 127293.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.105112 restraints weight = 109700.867| |-----------------------------------------------------------------------------| r_work (final): 0.3991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6413 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 23774 Z= 0.127 Angle : 0.618 11.053 33402 Z= 0.345 Chirality : 0.044 0.288 3749 Planarity : 0.004 0.098 3230 Dihedral : 26.784 156.039 5509 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % 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: -1.76 (0.18), residues: 2061 helix: 1.11 (0.21), residues: 653 sheet: -1.79 (0.29), residues: 295 loop : -2.52 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 40 TYR 0.029 0.001 TYR G 50 PHE 0.012 0.001 PHE M 426 TRP 0.031 0.002 TRP N 35 HIS 0.005 0.001 HIS N 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.13 (23771) covalent geometry : angle 0.61784 / 0.35 (33402) hydrogen bonds : bond 0.04563 / 3.02 ( 975) hydrogen bonds : angle 4.30183 / 3.07 ( 2459) metal coordination : bond 0.00047 / 0.03 ( 2) Misc. bond : bond 0.00794 / 0.53 ( 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 173 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7668 (p) cc_final: 0.7322 (p) REVERT: A 60 LEU cc_start: 0.6554 (tp) cc_final: 0.6078 (mt) REVERT: A 123 ASP cc_start: 0.8302 (m-30) cc_final: 0.8041 (m-30) REVERT: B 26 ILE cc_start: 0.8431 (mm) cc_final: 0.8101 (pt) REVERT: B 44 LYS cc_start: 0.7546 (mtmt) cc_final: 0.7314 (mttt) REVERT: C 56 GLU cc_start: 0.7804 (tp30) cc_final: 0.7381 (tt0) REVERT: E 97 GLU cc_start: 0.8224 (mp0) cc_final: 0.7915 (mp0) REVERT: E 105 GLU cc_start: 0.7914 (tm-30) cc_final: 0.7411 (tm-30) REVERT: F 63 GLU cc_start: 0.8700 (pp20) cc_final: 0.8461 (pp20) REVERT: H 32 GLU cc_start: 0.8232 (tp30) cc_final: 0.7874 (tp30) REVERT: N 26 MET cc_start: 0.7826 (pmm) cc_final: 0.7330 (pmm) REVERT: N 310 ILE cc_start: 0.7640 (pt) cc_final: 0.7285 (tt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1613 time to fit residues: 43.2035 Evaluate side-chains 132 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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: 0.0980 chunk 78 optimal weight: 30.0000 chunk 195 optimal weight: 20.0000 chunk 147 optimal weight: 20.0000 chunk 159 optimal weight: 4.9990 chunk 96 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 199 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 overall best weight: 6.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K3906 ASN ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 240 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 67 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.114539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099625 restraints weight = 183072.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.098081 restraints weight = 212521.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.097197 restraints weight = 191743.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.096429 restraints weight = 183152.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.095748 restraints weight = 187969.315| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3813 r_free = 0.3813 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (8 function evaluations) r_final: 0.3813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 23774 Z= 0.333 Angle : 0.863 12.094 33402 Z= 0.466 Chirality : 0.053 0.287 3749 Planarity : 0.007 0.125 3230 Dihedral : 27.171 158.862 5509 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.90 % Favored : 89.10 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % 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: -2.58 (0.17), residues: 2061 helix: -0.12 (0.19), residues: 652 sheet: -2.02 (0.30), residues: 277 loop : -2.71 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG H 76 TYR 0.032 0.003 TYR F 98 PHE 0.029 0.003 PHE K3820 TRP 0.046 0.002 TRP N 303 HIS 0.017 0.003 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00735 / 0.33 (23771) covalent geometry : angle 0.86338 / 0.47 (33402) hydrogen bonds : bond 0.08258 / 5.52 ( 975) hydrogen bonds : angle 5.30993 / 3.81 ( 2459) metal coordination : bond 0.00194 / 0.13 ( 2) Misc. bond : bond 0.00376 / 0.25 ( 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 142 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8082 (p) cc_final: 0.7769 (p) REVERT: A 60 LEU cc_start: 0.7027 (tp) cc_final: 0.6465 (mt) REVERT: B 44 LYS cc_start: 0.7601 (mtmt) cc_final: 0.7207 (mttt) REVERT: F 63 GLU cc_start: 0.8680 (pp20) cc_final: 0.8362 (pp20) REVERT: H 32 GLU cc_start: 0.8622 (tp30) cc_final: 0.8217 (tp30) REVERT: H 122 LYS cc_start: 0.7736 (mtmm) cc_final: 0.7482 (mttm) REVERT: K 3854 MET cc_start: 0.7270 (tmm) cc_final: 0.6953 (tmm) REVERT: N 26 MET cc_start: 0.8078 (pmm) cc_final: 0.7529 (pmm) REVERT: N 310 ILE cc_start: 0.8033 (pt) cc_final: 0.7655 (tt) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1646 time to fit residues: 36.1709 Evaluate side-chains 109 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.693 ------------------------------------------------------------------------------- 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: 10.0000 chunk 28 optimal weight: 0.8980 chunk 128 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 113 optimal weight: 0.0050 chunk 150 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 126 optimal weight: 7.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K3906 ASN N 33 ASN N 65 HIS ** N 67 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.118613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.102716 restraints weight = 152125.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.101609 restraints weight = 215337.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.100745 restraints weight = 155227.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.100191 restraints weight = 170223.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099692 restraints weight = 158580.284| |-----------------------------------------------------------------------------| r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3893 r_free = 0.3893 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 23774 Z= 0.141 Angle : 0.656 11.952 33402 Z= 0.366 Chirality : 0.046 0.291 3749 Planarity : 0.005 0.108 3230 Dihedral : 26.976 157.189 5509 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.06 % Allowed : 0.28 % Favored : 99.67 % 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: -2.03 (0.18), residues: 2061 helix: 0.78 (0.20), residues: 650 sheet: -1.91 (0.29), residues: 298 loop : -2.62 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 40 TYR 0.032 0.002 TYR F 88 PHE 0.014 0.001 PHE A 104 TRP 0.038 0.002 TRP N 35 HIS 0.006 0.001 HIS N 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (23771) covalent geometry : angle 0.65587 / 0.37 (33402) hydrogen bonds : bond 0.05225 / 3.46 ( 975) hydrogen bonds : angle 4.54200 / 3.25 ( 2459) metal coordination : bond 0.00062 / 0.04 ( 2) Misc. bond : bond 0.00150 / 0.10 ( 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 157 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7972 (p) cc_final: 0.7667 (p) REVERT: A 60 LEU cc_start: 0.6735 (tp) cc_final: 0.6298 (mt) REVERT: B 26 ILE cc_start: 0.8647 (mm) cc_final: 0.8356 (pt) REVERT: B 44 LYS cc_start: 0.7512 (mtmt) cc_final: 0.7139 (mttt) REVERT: E 97 GLU cc_start: 0.8391 (mp0) cc_final: 0.7895 (mp0) REVERT: F 59 LYS cc_start: 0.8621 (tppt) cc_final: 0.8147 (tppt) REVERT: F 63 GLU cc_start: 0.8769 (pp20) cc_final: 0.8413 (pp20) REVERT: F 88 TYR cc_start: 0.7409 (m-80) cc_final: 0.7013 (m-80) REVERT: H 32 GLU cc_start: 0.8569 (tp30) cc_final: 0.7936 (tp30) REVERT: H 80 TYR cc_start: 0.7700 (m-10) cc_final: 0.7339 (m-80) REVERT: H 122 LYS cc_start: 0.7570 (mtmm) cc_final: 0.7328 (mttm) REVERT: L 197 ILE cc_start: 0.6140 (mm) cc_final: 0.5939 (mm) REVERT: N 26 MET cc_start: 0.7922 (pmm) cc_final: 0.7392 (pmm) REVERT: N 310 ILE cc_start: 0.8039 (pt) cc_final: 0.7629 (tt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1617 time to fit residues: 39.0752 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 : 0.673 ------------------------------------------------------------------------------- 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: 10.0000 chunk 139 optimal weight: 20.0000 chunk 163 optimal weight: 0.1980 chunk 173 optimal weight: 30.0000 chunk 12 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 81 optimal weight: 30.0000 chunk 82 optimal weight: 20.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN N 33 ASN N 65 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.118034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.102571 restraints weight = 197656.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.101133 restraints weight = 218890.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.100257 restraints weight = 168579.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.100188 restraints weight = 171561.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.099847 restraints weight = 134692.118| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3899 r_free = 0.3899 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6600 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23774 Z= 0.150 Angle : 0.651 12.140 33402 Z= 0.361 Chirality : 0.045 0.288 3749 Planarity : 0.005 0.104 3230 Dihedral : 26.911 157.553 5509 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.56 % 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: -2.00 (0.18), residues: 2061 helix: 0.79 (0.20), residues: 651 sheet: -1.84 (0.29), residues: 293 loop : -2.62 (0.17), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.022 0.002 TYR F 88 PHE 0.030 0.001 PHE K3820 TRP 0.016 0.001 TRP N 303 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.15 (23771) covalent geometry : angle 0.65093 / 0.36 (33402) hydrogen bonds : bond 0.05290 / 3.51 ( 975) hydrogen bonds : angle 4.53317 / 3.24 ( 2459) metal coordination : bond 0.00074 / 0.05 ( 2) Misc. bond : bond 0.00019 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3047.16 seconds wall clock time: 53 minutes 58.86 seconds (3238.86 seconds total)