Starting phenix.real_space_refine on Sat Jul 4 17:35:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ud5_26454/07_2026/7ud5_26454_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ud5_26454/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ud5_26454/07_2026/7ud5_26454.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ud5_26454/07_2026/7ud5_26454.map" model { file = "/net/cci-nas-00/data/ceres_data/7ud5_26454/07_2026/7ud5_26454_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ud5_26454/07_2026/7ud5_26454_neut.cif" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 292 5.49 5 S 60 5.16 5 C 13457 2.51 5 N 4083 2.21 5 O 4820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 5.13, per 1000 atoms: 0.23 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: 1.82 Conformation dependent library (CDL) restraints added in 797.0 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: 2.86 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 removed outlier: 4.014A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.647A pdb=" N ILE A 124 " --> pdb=" O NLE A 120 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 4.165A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.686A pdb=" N ILE B 34 " --> pdb=" O THR B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 76 removed outlier: 4.024A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.503A pdb=" N ALA C 21 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.541A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.693A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.807A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 4.157A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 4.004A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.779A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.572A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.670A pdb=" N NLE E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.043A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.595A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.893A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.380A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.758A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 35 through 46 removed outlier: 3.535A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.646A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.645A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 3816 through 3818 No H-bonds generated for 'chain 'K' and resid 3816 through 3818' Processing helix chain 'K' and resid 3819 through 3825 removed outlier: 4.064A pdb=" N LEU K3823 " --> pdb=" O ARG K3819 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) Processing helix chain 'K' and resid 3867 through 3879 Processing helix chain 'K' and resid 3901 through 3905 removed outlier: 3.698A pdb=" N PHE K3904 " --> pdb=" O ALA K3901 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE K3905 " --> pdb=" O ALA K3902 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 3901 through 3905' Processing helix chain 'M' and resid 202 through 211 removed outlier: 4.190A pdb=" N ARG M 206 " --> pdb=" O ARG M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 434 through 439 Processing helix chain 'M' and resid 504 through 526 removed outlier: 3.691A pdb=" N VAL M 508 " --> pdb=" O GLY M 504 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU M 521 " --> pdb=" O LEU M 517 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY M 526 " --> pdb=" O THR M 522 " (cutoff:3.500A) Processing helix chain 'N' and resid 229 through 234 Processing helix chain 'N' and resid 328 through 332 removed outlier: 3.922A pdb=" N PHE N 332 " --> pdb=" O TRP N 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 41 Processing helix chain 'O' and resid 55 through 60 removed outlier: 3.619A pdb=" N TYR O 59 " --> pdb=" O THR O 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 60 Processing helix chain 'P' and resid 61 through 75 removed outlier: 4.768A pdb=" N GLN P 67 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 Processing helix chain 'Q' and resid 52 through 60 Processing helix chain 'Q' and resid 64 through 74 Processing helix chain 'Q' and resid 79 through 91 removed outlier: 4.286A pdb=" N PHE Q 83 " --> pdb=" O ASN Q 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN Q 91 " --> pdb=" O TYR Q 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 97 through 98 removed outlier: 3.652A pdb=" N TYR B 98 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.376A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.697A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.045A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 3831 through 3835 Processing sheet with id=AA6, first strand: chain 'K' and resid 3854 through 3857 removed outlier: 6.730A pdb=" N ILE K3928 " --> pdb=" O VAL K3855 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU K3857 " --> pdb=" O ILE K3926 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K3926 " --> pdb=" O GLU K3857 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE K3929 " --> pdb=" O TYR K3914 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N TYR K3914 " --> pdb=" O PHE K3929 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 3854 through 3857 removed outlier: 6.730A pdb=" N ILE K3928 " --> pdb=" O VAL K3855 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N GLU K3857 " --> pdb=" O ILE K3926 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ILE K3926 " --> pdb=" O GLU K3857 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 3860 through 3864 Processing sheet with id=AA9, first strand: chain 'L' and resid 36 through 37 removed outlier: 4.541A pdb=" N LYS L 328 " --> pdb=" O SER L 318 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER L 318 " --> pdb=" O LYS L 328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 48 through 50 removed outlier: 3.682A pdb=" N SER L 50 " --> pdb=" O SER L 63 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS L 81 " --> pdb=" O ILE L 71 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 90 through 95 removed outlier: 4.687A pdb=" N ASP L 92 " --> pdb=" O ALA L 105 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 112 through 114 removed outlier: 6.482A pdb=" N ILE L 113 " --> pdb=" O LEU L 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 132 through 137 removed outlier: 4.409A pdb=" N ILE L 144 " --> pdb=" O TRP L 156 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP L 156 " --> pdb=" O ILE L 144 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE L 155 " --> pdb=" O LYS L 165 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS L 165 " --> pdb=" O ILE L 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 174 through 179 removed outlier: 7.295A pdb=" N SER L 189 " --> pdb=" O SER L 175 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL L 177 " --> pdb=" O VAL L 187 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL L 187 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N PHE L 179 " --> pdb=" O LEU L 185 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU L 185 " --> pdb=" O PHE L 179 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG L 196 " --> pdb=" O SER L 188 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N CYS L 195 " --> pdb=" O THR L 208 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR L 208 " --> pdb=" O CYS L 195 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE L 197 " --> pdb=" O LEU L 206 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 228 through 231 removed outlier: 3.871A pdb=" N ALA L 231 " --> pdb=" O LYS L 239 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS L 239 " --> pdb=" O ALA L 231 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ASP L 242 " --> pdb=" O LYS L 247 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LYS L 247 " --> pdb=" O ASP L 242 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 264 through 267 removed outlier: 3.788A pdb=" N GLN L 295 " --> pdb=" O ILE L 285 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 247 through 250 removed outlier: 3.531A pdb=" N ILE M 250 " --> pdb=" O PHE M 426 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 299 through 300 Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 Processing sheet with id=AC2, first strand: chain 'M' and resid 391 through 394 Processing sheet with id=AC3, first strand: chain 'M' and resid 373 through 375 Processing sheet with id=AC4, first strand: chain 'M' and resid 450 through 451 removed outlier: 4.032A pdb=" N VAL M 454 " --> pdb=" O LYS M 451 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 16 through 18 removed outlier: 3.941A pdb=" N ILE N 320 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ALA N 311 " --> pdb=" O VAL N 301 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL N 301 " --> pdb=" O ALA N 311 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE N 313 " --> pdb=" O LEU N 299 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 38 through 42 removed outlier: 6.493A pdb=" N ILE N 48 " --> pdb=" O ILE N 61 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE N 61 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE N 50 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'N' and resid 73 through 74 removed outlier: 3.937A pdb=" N TRP N 93 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN N 102 " --> pdb=" O GLN N 92 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP N 94 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS N 100 " --> pdb=" O ASP N 94 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 114 through 116 removed outlier: 3.672A pdb=" N GLN N 114 " --> pdb=" O LEU N 124 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N HIS N 116 " --> pdb=" O LYS N 122 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LYS N 122 " --> pdb=" O HIS N 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 133 through 136 removed outlier: 3.591A pdb=" N LYS N 141 " --> pdb=" O THR N 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.690A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 201 through 206 Processing sheet with id=AD3, first strand: chain 'N' and resid 265 through 268 Processing sheet with id=AD4, first strand: chain 'O' and resid 12 through 15 612 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 2.46 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: 32913 2.35 - 4.71: 460 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: 2.160 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 26.880 Find NCS groups from input model: 0.220 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: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- 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 : 0.688 11.770 33402 Z= 0.549 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 0.68829 / 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 : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7817 (p) cc_final: 0.7541 (p) REVERT: A 60 LEU cc_start: 0.6596 (tp) cc_final: 0.6272 (pt) REVERT: D 76 ARG cc_start: 0.8540 (ptm-80) cc_final: 0.7605 (ttp80) REVERT: F 63 GLU cc_start: 0.8019 (pp20) cc_final: 0.7706 (pp20) REVERT: M 410 ASP cc_start: 0.1510 (OUTLIER) cc_final: 0.0899 (t0) REVERT: N 13 TYR cc_start: 0.6773 (p90) cc_final: 0.6474 (p90) REVERT: N 310 ILE cc_start: 0.7184 (pt) cc_final: 0.6259 (tt) outliers start: 26 outliers final: 0 residues processed: 295 average time/residue: 0.2115 time to fit residues: 89.0668 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 : 0.762 ------------------------------------------------------------------------------- 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** N 250 ASN ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.115939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.099320 restraints weight = 222985.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.097599 restraints weight = 244087.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.096055 restraints weight = 187439.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.095955 restraints weight = 188784.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.095466 restraints weight = 157394.213| |-----------------------------------------------------------------------------| r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3818 r_free = 0.3818 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 15 (21 function evaluations) r_final: 0.3818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 23774 Z= 0.315 Angle : 0.853 12.597 33402 Z= 0.464 Chirality : 0.052 0.258 3749 Planarity : 0.008 0.170 3230 Dihedral : 27.306 157.010 5509 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % Rotamer: Outliers : 0.39 % Allowed : 4.82 % 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: -2.57 (0.17), residues: 2061 helix: -0.22 (0.19), residues: 648 sheet: -1.95 (0.28), residues: 308 loop : -2.65 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG F 40 TYR 0.029 0.003 TYR F 98 PHE 0.026 0.003 PHE P 83 TRP 0.032 0.002 TRP N 35 HIS 0.014 0.002 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.31 (23771) covalent geometry : angle 0.85295 / 0.46 (33402) hydrogen bonds : bond 0.08446 / 5.67 ( 975) hydrogen bonds : angle 5.51910 / 3.98 ( 2459) metal coordination : bond 0.00226 / 0.16 ( 2) Misc. bond : bond 0.00075 / 0.05 ( 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 166 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 160 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8009 (p) cc_final: 0.7759 (p) REVERT: B 44 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7241 (mttt) REVERT: D 76 ARG cc_start: 0.8765 (ptm-80) cc_final: 0.8497 (ttm170) REVERT: E 97 GLU cc_start: 0.8547 (mp0) cc_final: 0.8182 (mp0) REVERT: F 63 GLU cc_start: 0.8715 (pp20) cc_final: 0.8399 (pp20) REVERT: F 84 MET cc_start: 0.6972 (tpp) cc_final: 0.6691 (tpp) REVERT: H 68 GLU cc_start: 0.7468 (mp0) cc_final: 0.7216 (mp0) REVERT: H 76 ARG cc_start: 0.8363 (ttp-110) cc_final: 0.8065 (ttm110) REVERT: H 122 LYS cc_start: 0.7785 (mtmm) cc_final: 0.7565 (mttm) REVERT: K 3854 MET cc_start: 0.7080 (tmm) cc_final: 0.6799 (tmm) REVERT: L 197 ILE cc_start: 0.6240 (mm) cc_final: 0.6025 (mm) REVERT: M 284 TYR cc_start: 0.3707 (m-10) cc_final: 0.2508 (m-80) REVERT: M 382 TYR cc_start: 0.3743 (t80) cc_final: 0.3368 (t80) REVERT: N 26 MET cc_start: 0.7583 (pmm) cc_final: 0.7012 (pmm) REVERT: N 310 ILE cc_start: 0.7958 (pt) cc_final: 0.7559 (tt) outliers start: 6 outliers final: 1 residues processed: 165 average time/residue: 0.1835 time to fit residues: 45.4381 Evaluate side-chains 113 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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: 3.9990 chunk 53 optimal weight: 1.9990 chunk 223 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 chunk 192 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 143 optimal weight: 40.0000 chunk 62 optimal weight: 3.9990 chunk 227 optimal weight: 0.0030 chunk 18 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 108 ASN F 25 ASN K3822 HIS K3906 ASN ** M 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 397 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 = 0.4261 r_free = 0.4261 target = 0.119598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.106504 restraints weight = 234148.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.104698 restraints weight = 209621.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.103809 restraints weight = 152214.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.103581 restraints weight = 156854.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.103036 restraints weight = 139604.058| |-----------------------------------------------------------------------------| r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3963 r_free = 0.3963 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 10 (26 function evaluations) r_final: 0.3963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 23774 Z= 0.139 Angle : 0.624 10.067 33402 Z= 0.355 Chirality : 0.045 0.258 3749 Planarity : 0.005 0.142 3230 Dihedral : 27.120 154.988 5509 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 0.17 % Allowed : 3.93 % Favored : 95.90 % 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: -1.97 (0.18), residues: 2061 helix: 0.75 (0.20), residues: 649 sheet: -1.87 (0.28), residues: 317 loop : -2.53 (0.17), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 40 TYR 0.015 0.001 TYR B 98 PHE 0.014 0.001 PHE N 213 TRP 0.026 0.002 TRP N 35 HIS 0.006 0.001 HIS N 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.14 (23771) covalent geometry : angle 0.62377 / 0.35 (33402) hydrogen bonds : bond 0.05694 / 3.75 ( 975) hydrogen bonds : angle 4.65939 / 3.35 ( 2459) metal coordination : bond 0.00104 / 0.07 ( 2) Misc. bond : bond 0.00075 / 0.05 ( 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 189 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 187 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7835 (p) cc_final: 0.7558 (p) REVERT: A 60 LEU cc_start: 0.6916 (tp) cc_final: 0.6340 (mt) REVERT: A 123 ASP cc_start: 0.8668 (m-30) cc_final: 0.8416 (m-30) REVERT: B 26 ILE cc_start: 0.8580 (mm) cc_final: 0.8167 (pt) REVERT: B 44 LYS cc_start: 0.7790 (mtmt) cc_final: 0.7248 (mttt) REVERT: E 97 GLU cc_start: 0.8342 (mp0) cc_final: 0.7922 (mp0) REVERT: F 25 ASN cc_start: 0.7646 (OUTLIER) cc_final: 0.6886 (t0) REVERT: F 63 GLU cc_start: 0.8542 (pp20) cc_final: 0.8264 (pp20) REVERT: H 122 LYS cc_start: 0.7497 (mtmm) cc_final: 0.6697 (mmtt) REVERT: K 3854 MET cc_start: 0.6939 (tmm) cc_final: 0.6565 (tmm) REVERT: M 284 TYR cc_start: 0.3589 (m-10) cc_final: 0.2739 (m-80) REVERT: M 382 TYR cc_start: 0.3326 (t80) cc_final: 0.3010 (t80) REVERT: N 26 MET cc_start: 0.7590 (pmm) cc_final: 0.7062 (pmm) REVERT: N 310 ILE cc_start: 0.7940 (pt) cc_final: 0.7229 (tt) outliers start: 2 outliers final: 0 residues processed: 188 average time/residue: 0.1866 time to fit residues: 52.3088 Evaluate side-chains 128 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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: 6.9990 chunk 147 optimal weight: 7.9990 chunk 197 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 7 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 chunk 94 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 GLN 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 33 ASN ** N 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.116522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.101813 restraints weight = 170923.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.100335 restraints weight = 201287.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.098947 restraints weight = 166759.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.098275 restraints weight = 182826.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.098032 restraints weight = 157313.649| |-----------------------------------------------------------------------------| r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3865 r_free = 0.3865 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (17 function evaluations) r_final: 0.3865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 23774 Z= 0.225 Angle : 0.716 12.204 33402 Z= 0.396 Chirality : 0.048 0.259 3749 Planarity : 0.007 0.164 3230 Dihedral : 27.162 157.479 5509 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 0.06 % Allowed : 5.21 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.25 (0.18), residues: 2061 helix: 0.37 (0.20), residues: 646 sheet: -1.92 (0.28), residues: 313 loop : -2.61 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 40 TYR 0.028 0.002 TYR B 88 PHE 0.018 0.002 PHE E 104 TRP 0.027 0.002 TRP N 35 HIS 0.009 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.23 (23771) covalent geometry : angle 0.71647 / 0.40 (33402) hydrogen bonds : bond 0.07037 / 4.70 ( 975) hydrogen bonds : angle 4.96242 / 3.56 ( 2459) metal coordination : bond 0.00137 / 0.09 ( 2) Misc. bond : bond 0.00061 / 0.04 ( 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 : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8021 (p) cc_final: 0.7755 (p) REVERT: A 60 LEU cc_start: 0.7019 (tp) cc_final: 0.6395 (mt) REVERT: B 26 ILE cc_start: 0.8643 (mm) cc_final: 0.8288 (pt) REVERT: B 44 LYS cc_start: 0.7742 (mtmt) cc_final: 0.7216 (mttt) REVERT: E 97 GLU cc_start: 0.8534 (mp0) cc_final: 0.8075 (mp0) REVERT: F 63 GLU cc_start: 0.8574 (pp20) cc_final: 0.8195 (pp20) REVERT: F 84 MET cc_start: 0.7614 (tpp) cc_final: 0.7410 (tpp) REVERT: H 68 GLU cc_start: 0.7487 (mp0) cc_final: 0.7269 (mp0) REVERT: H 122 LYS cc_start: 0.7637 (mtmm) cc_final: 0.7364 (mttm) REVERT: M 284 TYR cc_start: 0.4354 (m-10) cc_final: 0.3206 (m-80) REVERT: M 382 TYR cc_start: 0.3613 (t80) cc_final: 0.3290 (t80) REVERT: N 26 MET cc_start: 0.7791 (pmm) cc_final: 0.7272 (pmm) REVERT: N 310 ILE cc_start: 0.7766 (pt) cc_final: 0.7323 (tt) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.1665 time to fit residues: 38.6165 Evaluate side-chains 111 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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: 5.9990 chunk 35 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 70 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 50 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN E 108 ASN K3906 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.116807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.102676 restraints weight = 233608.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.101681 restraints weight = 248642.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.100138 restraints weight = 171077.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.099584 restraints weight = 193504.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.099452 restraints weight = 151637.934| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3891 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3891 r_free = 0.3891 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 = 0.3891 r_free = 0.3891 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (10 function evaluations) r_final: 0.3891 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 23774 Z= 0.200 Angle : 0.682 9.445 33402 Z= 0.382 Chirality : 0.047 0.264 3749 Planarity : 0.005 0.122 3230 Dihedral : 27.157 157.781 5509 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 0.11 % Allowed : 3.27 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.17), residues: 2061 helix: 0.49 (0.20), residues: 645 sheet: -1.85 (0.31), residues: 258 loop : -2.71 (0.16), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 29 TYR 0.024 0.002 TYR F 98 PHE 0.015 0.002 PHE D 67 TRP 0.027 0.002 TRP N 35 HIS 0.006 0.001 HIS D 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (23771) covalent geometry : angle 0.68188 / 0.38 (33402) hydrogen bonds : bond 0.06145 / 4.10 ( 975) hydrogen bonds : angle 4.85729 / 3.47 ( 2459) metal coordination : bond 0.00144 / 0.10 ( 2) Misc. bond : bond 0.00095 / 0.06 ( 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 158 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 157 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8045 (p) cc_final: 0.7756 (p) REVERT: A 60 LEU cc_start: 0.6939 (tp) cc_final: 0.6338 (mt) REVERT: B 26 ILE cc_start: 0.8695 (mm) cc_final: 0.8359 (pt) REVERT: B 44 LYS cc_start: 0.7795 (mtmt) cc_final: 0.7380 (mttt) REVERT: E 97 GLU cc_start: 0.8454 (mp0) cc_final: 0.7938 (mp0) REVERT: F 63 GLU cc_start: 0.8596 (pp20) cc_final: 0.8323 (pp20) REVERT: H 32 GLU cc_start: 0.8323 (tp30) cc_final: 0.8057 (tp30) REVERT: K 3854 MET cc_start: 0.7159 (tmm) cc_final: 0.6897 (tmm) REVERT: M 284 TYR cc_start: 0.4105 (m-10) cc_final: 0.3380 (m-80) REVERT: M 382 TYR cc_start: 0.3529 (t80) cc_final: 0.3134 (t80) REVERT: N 26 MET cc_start: 0.7897 (pmm) cc_final: 0.7383 (pmm) REVERT: N 310 ILE cc_start: 0.8000 (pt) cc_final: 0.7287 (tt) outliers start: 1 outliers final: 0 residues processed: 158 average time/residue: 0.1791 time to fit residues: 42.8993 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 : 0.690 ------------------------------------------------------------------------------- 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: 10.0000 chunk 194 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 199 optimal weight: 5.9990 chunk 85 optimal weight: 40.0000 chunk 18 optimal weight: 1.9990 chunk 213 optimal weight: 30.0000 chunk 52 optimal weight: 0.0670 overall best weight: 3.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** L 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 229 GLN ** 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** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.116781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.102301 restraints weight = 190927.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.101211 restraints weight = 223427.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.100056 restraints weight = 157523.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.099652 restraints weight = 171096.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.099341 restraints weight = 141083.586| |-----------------------------------------------------------------------------| r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3888 r_free = 0.3888 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 = 0.3888 r_free = 0.3888 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 23774 Z= 0.196 Angle : 0.680 9.600 33402 Z= 0.379 Chirality : 0.047 0.261 3749 Planarity : 0.006 0.143 3230 Dihedral : 27.149 158.767 5509 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.27 (0.18), residues: 2061 helix: 0.52 (0.20), residues: 645 sheet: -1.94 (0.29), residues: 296 loop : -2.75 (0.17), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 40 TYR 0.042 0.002 TYR G 50 PHE 0.015 0.002 PHE N 259 TRP 0.029 0.002 TRP N 35 HIS 0.008 0.001 HIS M 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.20 (23771) covalent geometry : angle 0.68027 / 0.38 (33402) hydrogen bonds : bond 0.06216 / 4.15 ( 975) hydrogen bonds : angle 4.82082 / 3.45 ( 2459) metal coordination : bond 0.00124 / 0.08 ( 2) Misc. bond : bond 0.00093 / 0.06 ( 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 : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8044 (p) cc_final: 0.7764 (p) REVERT: A 60 LEU cc_start: 0.6981 (tp) cc_final: 0.6435 (mt) REVERT: B 26 ILE cc_start: 0.8736 (mm) cc_final: 0.8374 (pt) REVERT: B 44 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7406 (mttt) REVERT: E 97 GLU cc_start: 0.8315 (mp0) cc_final: 0.7931 (mp0) REVERT: F 63 GLU cc_start: 0.8599 (pp20) cc_final: 0.8318 (pp20) REVERT: H 32 GLU cc_start: 0.8365 (tp30) cc_final: 0.8120 (tp30) REVERT: H 122 LYS cc_start: 0.7609 (mtmm) cc_final: 0.7358 (mttm) REVERT: N 26 MET cc_start: 0.7993 (pmm) cc_final: 0.7480 (pmm) REVERT: N 310 ILE cc_start: 0.7802 (pt) cc_final: 0.7298 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1743 time to fit residues: 41.7066 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 : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 192 optimal weight: 10.0000 chunk 224 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 69 optimal weight: 0.3980 chunk 113 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN K3906 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 = 0.4245 r_free = 0.4245 target = 0.118908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.104298 restraints weight = 203706.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.102964 restraints weight = 214045.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.101382 restraints weight = 142305.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.101066 restraints weight = 170969.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100437 restraints weight = 142353.764| |-----------------------------------------------------------------------------| r_work (final): 0.3910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6599 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23774 Z= 0.134 Angle : 0.627 13.500 33402 Z= 0.352 Chirality : 0.045 0.261 3749 Planarity : 0.005 0.121 3230 Dihedral : 27.001 157.966 5509 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.06 % Allowed : 1.77 % Favored : 98.17 % 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: -1.97 (0.18), residues: 2061 helix: 0.95 (0.21), residues: 645 sheet: -1.80 (0.29), residues: 294 loop : -2.68 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 40 TYR 0.023 0.002 TYR G 50 PHE 0.011 0.001 PHE D 67 TRP 0.032 0.002 TRP N 303 HIS 0.006 0.001 HIS M 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (23771) covalent geometry : angle 0.62676 / 0.35 (33402) hydrogen bonds : bond 0.05036 / 3.34 ( 975) hydrogen bonds : angle 4.49073 / 3.20 ( 2459) metal coordination : bond 0.00068 / 0.05 ( 2) Misc. bond : bond 0.00192 / 0.13 ( 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 169 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8001 (p) cc_final: 0.7689 (p) REVERT: A 60 LEU cc_start: 0.6945 (tp) cc_final: 0.6347 (mt) REVERT: B 26 ILE cc_start: 0.8607 (mm) cc_final: 0.8252 (pt) REVERT: B 44 LYS cc_start: 0.7716 (mtmt) cc_final: 0.7341 (mttt) REVERT: C 56 GLU cc_start: 0.7640 (tp30) cc_final: 0.7435 (tt0) REVERT: F 63 GLU cc_start: 0.8523 (pp20) cc_final: 0.8178 (pp20) REVERT: H 32 GLU cc_start: 0.8392 (tp30) cc_final: 0.8078 (tp30) REVERT: H 68 GLU cc_start: 0.7392 (mp0) cc_final: 0.7102 (mp0) REVERT: H 122 LYS cc_start: 0.7436 (mtmm) cc_final: 0.7157 (mttm) REVERT: L 197 ILE cc_start: 0.6236 (mm) cc_final: 0.6012 (mm) REVERT: N 26 MET cc_start: 0.7884 (pmm) cc_final: 0.7343 (pmm) REVERT: N 310 ILE cc_start: 0.8033 (pt) cc_final: 0.7343 (tt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.1896 time to fit residues: 48.4334 Evaluate side-chains 127 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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: 0.7980 chunk 77 optimal weight: 30.0000 chunk 210 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 151 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 overall best weight: 1.1982 ------------------------------------------------------------------------------- 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 = 0.4245 r_free = 0.4245 target = 0.118805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.103162 restraints weight = 163184.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.101796 restraints weight = 199143.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.100380 restraints weight = 150086.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.099595 restraints weight = 169635.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.099505 restraints weight = 161525.660| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3890 r_free = 0.3890 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 = 0.3890 r_free = 0.3890 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23774 Z= 0.135 Angle : 0.623 11.057 33402 Z= 0.349 Chirality : 0.044 0.259 3749 Planarity : 0.005 0.111 3230 Dihedral : 26.921 158.363 5509 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 0.06 % Allowed : 1.16 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.18), residues: 2061 helix: 1.00 (0.21), residues: 651 sheet: -1.84 (0.29), residues: 294 loop : -2.61 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG H 76 TYR 0.014 0.001 TYR N 165 PHE 0.030 0.001 PHE K3820 TRP 0.032 0.002 TRP N 303 HIS 0.004 0.001 HIS N 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (23771) covalent geometry : angle 0.62282 / 0.35 (33402) hydrogen bonds : bond 0.04958 / 3.30 ( 975) hydrogen bonds : angle 4.43191 / 3.16 ( 2459) metal coordination : bond 0.00048 / 0.03 ( 2) Misc. bond : bond 0.00074 / 0.05 ( 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 160 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7906 (p) cc_final: 0.7619 (p) REVERT: A 60 LEU cc_start: 0.6623 (tp) cc_final: 0.6151 (mt) REVERT: B 26 ILE cc_start: 0.8526 (mm) cc_final: 0.8183 (pt) REVERT: B 44 LYS cc_start: 0.7650 (mtmt) cc_final: 0.7390 (mttt) REVERT: E 97 GLU cc_start: 0.8222 (mp0) cc_final: 0.7778 (mp0) REVERT: F 59 LYS cc_start: 0.8566 (tppt) cc_final: 0.8105 (tppt) REVERT: H 32 GLU cc_start: 0.8461 (tp30) cc_final: 0.8067 (tp30) REVERT: H 122 LYS cc_start: 0.7432 (mtmm) cc_final: 0.6660 (mmtt) REVERT: L 197 ILE cc_start: 0.6201 (mm) cc_final: 0.5989 (mm) REVERT: N 26 MET cc_start: 0.7876 (pmm) cc_final: 0.7331 (pmm) REVERT: N 310 ILE cc_start: 0.7738 (pt) cc_final: 0.7255 (tt) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1788 time to fit residues: 43.8971 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 : 0.708 ------------------------------------------------------------------------------- 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: 0.0000 chunk 78 optimal weight: 20.0000 chunk 195 optimal weight: 20.0000 chunk 147 optimal weight: 8.9990 chunk 159 optimal weight: 1.9990 chunk 96 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 219 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 93 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.115707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.100748 restraints weight = 182949.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.099466 restraints weight = 215602.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.097936 restraints weight = 164861.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.097505 restraints weight = 185604.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.097002 restraints weight = 148751.724| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 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 = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (8 function evaluations) r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.2991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23774 Z= 0.241 Angle : 0.747 11.967 33402 Z= 0.409 Chirality : 0.048 0.260 3749 Planarity : 0.006 0.124 3230 Dihedral : 27.127 159.971 5509 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.78 % Favored : 90.22 % Rotamer: Outliers : 0.06 % Allowed : 0.83 % Favored : 99.11 % 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: -2.42 (0.17), residues: 2061 helix: 0.18 (0.19), residues: 653 sheet: -1.86 (0.30), residues: 276 loop : -2.75 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG F 40 TYR 0.034 0.003 TYR G 50 PHE 0.020 0.002 PHE E 104 TRP 0.044 0.002 TRP N 303 HIS 0.012 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.24 (23771) covalent geometry : angle 0.74730 / 0.41 (33402) hydrogen bonds : bond 0.07003 / 4.69 ( 975) hydrogen bonds : angle 4.95959 / 3.55 ( 2459) metal coordination : bond 0.00171 / 0.12 ( 2) Misc. bond : bond 0.00051 / 0.03 ( 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 146 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8012 (p) cc_final: 0.7709 (p) REVERT: A 60 LEU cc_start: 0.6844 (tp) cc_final: 0.6365 (mt) REVERT: B 26 ILE cc_start: 0.8717 (mm) cc_final: 0.8354 (pt) REVERT: B 44 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7415 (mttt) REVERT: F 63 GLU cc_start: 0.8709 (pp20) cc_final: 0.8298 (pp20) REVERT: H 32 GLU cc_start: 0.8545 (tp30) cc_final: 0.8148 (tp30) REVERT: H 122 LYS cc_start: 0.7687 (mtmm) cc_final: 0.7428 (mttm) REVERT: K 3854 MET cc_start: 0.7225 (tmm) cc_final: 0.6975 (tmm) REVERT: N 26 MET cc_start: 0.8073 (pmm) cc_final: 0.7527 (pmm) REVERT: N 310 ILE cc_start: 0.8053 (pt) cc_final: 0.7657 (tt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1783 time to fit residues: 40.1539 Evaluate side-chains 112 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.705 ------------------------------------------------------------------------------- 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: 8.9990 chunk 28 optimal weight: 0.9980 chunk 128 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 187 optimal weight: 8.9990 chunk 177 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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** ** O 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.118167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.103288 restraints weight = 153320.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.103190 restraints weight = 286028.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.102463 restraints weight = 152282.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.102516 restraints weight = 124948.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.102706 restraints weight = 102846.508| |-----------------------------------------------------------------------------| r_work (final): 0.3945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 25 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 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: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 23774 Z= 0.140 Angle : 0.645 11.975 33402 Z= 0.360 Chirality : 0.045 0.262 3749 Planarity : 0.005 0.112 3230 Dihedral : 27.009 159.166 5509 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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: -2.07 (0.18), residues: 2061 helix: 0.75 (0.20), residues: 652 sheet: -1.81 (0.29), residues: 287 loop : -2.70 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 40 TYR 0.026 0.002 TYR H 80 PHE 0.030 0.001 PHE K3820 TRP 0.032 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 0.64516 / 0.36 (33402) hydrogen bonds : bond 0.05279 / 3.52 ( 975) hydrogen bonds : angle 4.55698 / 3.25 ( 2459) metal coordination : bond 0.00073 / 0.05 ( 2) Misc. bond : bond 0.00034 / 0.02 ( 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 156 residues out of total 1798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.7882 (p) cc_final: 0.7551 (p) REVERT: A 60 LEU cc_start: 0.6666 (tp) cc_final: 0.6239 (mt) REVERT: B 26 ILE cc_start: 0.8547 (mm) cc_final: 0.8251 (pt) REVERT: B 44 LYS cc_start: 0.7553 (mtmt) cc_final: 0.7315 (mttt) REVERT: C 56 GLU cc_start: 0.7832 (tp30) cc_final: 0.7476 (tt0) REVERT: F 63 GLU cc_start: 0.8689 (pp20) cc_final: 0.8401 (pp20) REVERT: H 32 GLU cc_start: 0.8523 (tp30) cc_final: 0.8024 (tp30) REVERT: N 26 MET cc_start: 0.8002 (pmm) cc_final: 0.7464 (pmm) REVERT: N 310 ILE cc_start: 0.7973 (pt) cc_final: 0.7580 (tt) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1795 time to fit residues: 42.7068 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 : 0.734 ------------------------------------------------------------------------------- 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: 6.9990 chunk 173 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 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: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN ** E 93 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** M 375 HIS 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 = 0.4190 r_free = 0.4190 target = 0.115690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.099842 restraints weight = 198408.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.098654 restraints weight = 236035.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.097711 restraints weight = 170465.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.097259 restraints weight = 161209.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.096963 restraints weight = 151895.224| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3839 r_free = 0.3839 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 = 0.3839 r_free = 0.3839 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 22 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (10 function evaluations) r_final: 0.3839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 23774 Z= 0.235 Angle : 0.744 11.986 33402 Z= 0.407 Chirality : 0.048 0.263 3749 Planarity : 0.006 0.129 3230 Dihedral : 27.123 160.598 5509 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.12 % Favored : 89.88 % 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: -2.45 (0.17), residues: 2061 helix: 0.16 (0.20), residues: 652 sheet: -1.98 (0.29), residues: 277 loop : -2.75 (0.16), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG F 40 TYR 0.029 0.002 TYR F 88 PHE 0.018 0.002 PHE E 104 TRP 0.019 0.002 TRP N 303 HIS 0.012 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00506 / 0.24 (23771) covalent geometry : angle 0.74376 / 0.41 (33402) hydrogen bonds : bond 0.06842 / 4.57 ( 975) hydrogen bonds : angle 4.95876 / 3.53 ( 2459) metal coordination : bond 0.00146 / 0.10 ( 2) Misc. bond : bond 0.00078 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3211.02 seconds wall clock time: 57 minutes 1.96 seconds (3421.96 seconds total)