Starting phenix.real_space_refine on Mon Aug 25 09:43:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiu_9998/08_2025/6kiu_9998.map" } resolution = 3.2 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 8540 atoms to isotropic. 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 290 5.49 5 S 62 5.16 5 C 12025 2.51 5 N 3724 2.21 5 O 4401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20503 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 622 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 1, 'TRANS': 76} 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: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1436 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "N" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2768 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "R" Number of atoms: 2326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2326 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 8, 'TRANS': 291} Chain: "T" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1399 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 12, 'TRANS': 163} Chain breaks: 1 Chain: "O" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 45 Unusual residues: {' ZN': 1} Classifications: {'peptide': 3, 'undetermined': 1} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="SAH K4001 " pdbres=" ZN K4002 " Not linked: pdbres=" ZN K4002 " pdbres="LYS K4003 " List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13282 SG CYS K3959 91.570 70.702 20.892 1.00 54.95 S Time building chain proxies: 4.03, per 1000 atoms: 0.20 Number of scatterers: 20503 At special positions: 0 Unit cell: (158.05, 147.15, 129.71, 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 62 16.00 P 290 15.00 O 4401 8.00 N 3724 7.00 C 12025 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: 1.71 Conformation dependent library (CDL) restraints added in 603.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K4002 " pdb="ZN ZN K4002 " - pdb=" SG CYS K3959 " 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3434 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 32 sheets defined 32.1% alpha, 15.3% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.689A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.596A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.836A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.930A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.808A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.059A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.804A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.589A pdb=" N ASN C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.647A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 116 " --> pdb=" O SER C 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 112 through 116' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.569A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.854A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.689A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.596A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.835A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.578A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.055A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.804A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 removed outlier: 3.555A pdb=" N GLY G 37 " --> pdb=" O LEU G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.800A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.637A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.607A pdb=" N LEU G 115 " --> pdb=" O GLN G 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 3815 through 3830 removed outlier: 3.630A pdb=" N ARG K3819 " --> pdb=" O PRO K3815 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG K3821 " --> pdb=" O PRO K3817 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N HIS K3822 " --> pdb=" O MET K3818 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS K3824 " --> pdb=" O PHE K3820 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N LYS K3825 " --> pdb=" O ARG K3821 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS K3828 " --> pdb=" O LYS K3824 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU K3829 " --> pdb=" O LYS K3825 " (cutoff:3.500A) Processing helix chain 'K' and resid 3866 through 3878 removed outlier: 3.563A pdb=" N LYS K3870 " --> pdb=" O ILE K3866 " (cutoff:3.500A) Processing helix chain 'N' and resid 228 through 234 Processing helix chain 'O' and resid 23 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.037A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.606A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.152A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.822A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.803A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.169A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 3831 through 3835 removed outlier: 13.852A pdb=" N ARG K3841 " --> pdb=" O TYR K3942 " (cutoff:3.500A) removed outlier: 10.887A pdb=" N TYR K3942 " --> pdb=" O ARG K3841 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N LEU K3843 " --> pdb=" O LEU K3940 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASN K3906 " --> pdb=" O TYR K3942 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 3856 through 3857 removed outlier: 3.733A pdb=" N ILE K3856 " --> pdb=" O ILE K3928 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN K3923 " --> pdb=" O ILE K3920 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL K3927 " --> pdb=" O ARG K3916 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 3884 through 3886 Processing sheet with id=AB3, first strand: chain 'K' and resid 3898 through 3899 removed outlier: 3.682A pdb=" N GLY K3899 " --> pdb=" O LYS N 337 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'N' and resid 20 through 21 removed outlier: 4.385A pdb=" N VAL N 318 " --> pdb=" O LEU N 21 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP N 300 " --> pdb=" O ILE N 313 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 31 through 32 removed outlier: 3.515A pdb=" N THR N 31 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU N 39 " --> pdb=" O TRP N 51 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP N 52 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE N 58 " --> pdb=" O ASP N 52 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 69 through 74 removed outlier: 3.900A pdb=" N SER N 71 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA N 84 " --> pdb=" O SER N 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 110 through 112 removed outlier: 3.635A pdb=" N LYS N 112 " --> pdb=" O CYS N 126 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 156 through 159 removed outlier: 3.976A pdb=" N ALA N 187 " --> pdb=" O VAL N 177 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 201 through 206 removed outlier: 6.915A pdb=" N ASN N 216 " --> pdb=" O LYS N 202 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ILE N 204 " --> pdb=" O LEU N 214 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N LEU N 214 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE N 213 " --> pdb=" O TYR N 225 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR N 217 " --> pdb=" O ILE N 221 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ILE N 221 " --> pdb=" O THR N 217 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 254 through 259 removed outlier: 3.992A pdb=" N LYS N 256 " --> pdb=" O GLY N 269 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS N 288 " --> pdb=" O ILE N 278 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU N 280 " --> pdb=" O LEU N 286 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU N 286 " --> pdb=" O GLU N 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'R' and resid 36 through 42 removed outlier: 7.161A pdb=" N LEU R 329 " --> pdb=" O LYS R 38 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N THR R 40 " --> pdb=" O ILE R 327 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ILE R 327 " --> pdb=" O THR R 40 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER R 318 " --> pdb=" O LYS R 328 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA R 308 " --> pdb=" O ALA R 317 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER R 306 " --> pdb=" O ALA R 319 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'R' and resid 69 through 72 removed outlier: 3.893A pdb=" N LYS R 81 " --> pdb=" O ILE R 71 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'R' and resid 90 through 93 removed outlier: 3.877A pdb=" N LYS R 112 " --> pdb=" O SER R 104 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS R 123 " --> pdb=" O ILE R 113 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'R' and resid 132 through 137 removed outlier: 3.889A pdb=" N ARG R 154 " --> pdb=" O SER R 146 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N SER R 148 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N SER R 152 " --> pdb=" O SER R 148 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL R 153 " --> pdb=" O THR R 166 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR R 166 " --> pdb=" O VAL R 153 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE R 155 " --> pdb=" O LEU R 164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'R' and resid 176 through 179 removed outlier: 4.050A pdb=" N ALA R 176 " --> pdb=" O SER R 189 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS R 178 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS R 195 " --> pdb=" O LEU R 209 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS R 207 " --> pdb=" O ILE R 197 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ASP R 199 " --> pdb=" O CYS R 205 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N CYS R 205 " --> pdb=" O ASP R 199 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 221 through 222 removed outlier: 3.560A pdb=" N ILE R 229 " --> pdb=" O TRP R 241 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR R 233 " --> pdb=" O THR R 237 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N THR R 237 " --> pdb=" O THR R 233 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU R 238 " --> pdb=" O THR R 251 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N THR R 251 " --> pdb=" O LEU R 238 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU R 240 " --> pdb=" O LEU R 249 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 273 through 276 removed outlier: 3.611A pdb=" N LEU R 297 " --> pdb=" O VAL R 283 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'T' and resid 299 through 300 Processing sheet with id=AD1, first strand: chain 'T' and resid 316 through 317 removed outlier: 3.671A pdb=" N ALA T 471 " --> pdb=" O GLY T 345 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLY T 345 " --> pdb=" O ALA T 471 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER T 473 " --> pdb=" O ARG T 343 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'T' and resid 373 through 374 removed outlier: 3.711A pdb=" N LYS T 380 " --> pdb=" O LYS T 373 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 448 through 451 removed outlier: 4.354A pdb=" N GLY T 457 " --> pdb=" O PHE T 449 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LYS T 451 " --> pdb=" O ASN T 455 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ASN T 455 " --> pdb=" O LYS T 451 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 12 through 14 removed outlier: 3.948A pdb=" N VAL O 5 " --> pdb=" O ILE O 13 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE O 4 " --> pdb=" O LEU O 67 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 48 through 49 removed outlier: 4.532A pdb=" N ARG O 42 " --> pdb=" O VAL O 70 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL O 70 " --> pdb=" O ARG O 42 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 369 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4596 1.33 - 1.45: 6066 1.45 - 1.58: 10165 1.58 - 1.70: 578 1.70 - 1.82: 90 Bond restraints: 21495 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 29254 2.08 - 4.16: 917 4.16 - 6.24: 87 6.24 - 8.32: 23 8.32 - 10.40: 6 Bond angle restraints: 30287 Sorted by residual: angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 107.56 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 112.96 108.03 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" C ASN N 250 " pdb=" N ARG N 251 " pdb=" CA ARG N 251 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C ASN N 12 " pdb=" N TYR N 13 " pdb=" CA TYR N 13 " ideal model delta sigma weight residual 120.51 127.38 -6.87 1.45e+00 4.76e-01 2.25e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 123.58 -10.40 2.37e+00 1.78e-01 1.92e+01 ... (remaining 30282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 10714 35.07 - 70.15: 1410 70.15 - 105.22: 12 105.22 - 140.30: 2 140.30 - 175.37: 2 Dihedral angle restraints: 12140 sinusoidal: 6816 harmonic: 5324 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 135.05 44.95 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ALA N 322 " pdb=" C ALA N 322 " pdb=" N GLN N 323 " pdb=" CA GLN N 323 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG N 251 " pdb=" C ARG N 251 " pdb=" N THR N 252 " pdb=" CA THR N 252 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2396 0.049 - 0.098: 770 0.098 - 0.147: 203 0.147 - 0.196: 32 0.196 - 0.245: 4 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA SER N 108 " pdb=" N SER N 108 " pdb=" C SER N 108 " pdb=" CB SER N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE T 482 " pdb=" CA ILE T 482 " pdb=" CG1 ILE T 482 " pdb=" CG2 ILE T 482 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3402 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO B 32 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 108 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO N 109 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 109 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 109 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " 0.017 2.00e-02 2.50e+03 1.96e-02 7.67e+00 pdb=" CG TYR B 51 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " -0.002 2.00e-02 2.50e+03 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1219 2.72 - 3.27: 16732 3.27 - 3.81: 33632 3.81 - 4.36: 43392 4.36 - 4.90: 65991 Nonbonded interactions: 160966 Sorted by model distance: nonbonded pdb=" O CYS K3957 " pdb="ZN ZN K4002 " model vdw 2.178 2.230 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.241 3.040 nonbonded pdb=" O ILE K3905 " pdb=" OH TYR K3944 " model vdw 2.280 3.040 nonbonded pdb=" O TYR K3874 " pdb=" OG SER K3877 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.295 3.040 ... (remaining 160961 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 21.590 Find NCS groups from input model: 0.110 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:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.008 0.339 21497 Z= 0.320 Angle : 0.863 10.396 30287 Z= 0.494 Chirality : 0.052 0.245 3405 Planarity : 0.007 0.123 2831 Dihedral : 22.068 175.371 8706 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -3.67 (0.16), residues: 1802 helix: -1.23 (0.18), residues: 582 sheet: -2.84 (0.28), residues: 270 loop : -3.19 (0.16), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG H 69 TYR 0.049 0.003 TYR B 51 PHE 0.041 0.003 PHE C 25 TRP 0.029 0.002 TRP N 303 HIS 0.022 0.002 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00718 (21495) covalent geometry : angle 0.86255 (30287) hydrogen bonds : bond 0.16115 ( 906) hydrogen bonds : angle 5.60495 ( 2292) metal coordination : bond 0.33911 ( 1) Misc. bond : bond 0.00151 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 44 GLN cc_start: 0.7789 (mt0) cc_final: 0.7577 (mt0) REVERT: D 73 GLU cc_start: 0.8064 (tp30) cc_final: 0.7838 (tp30) REVERT: F 74 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7149 (mt-10) REVERT: G 73 ASN cc_start: 0.8264 (m110) cc_final: 0.8049 (m110) REVERT: H 56 MET cc_start: 0.7950 (tpp) cc_final: 0.7695 (tpp) REVERT: K 3849 ILE cc_start: 0.7903 (mt) cc_final: 0.7668 (mt) REVERT: K 3892 VAL cc_start: 0.7279 (t) cc_final: 0.6966 (t) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1865 time to fit residues: 90.8811 Evaluate side-chains 189 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 30.0000 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.0060 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.1980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 68 GLN F 75 HIS G 84 GLN K3822 HIS N 65 HIS ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 HIS T 376 GLN T 381 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.191973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142311 restraints weight = 29110.569| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.42 r_work: 0.3252 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 21497 Z= 0.193 Angle : 0.638 11.757 30287 Z= 0.364 Chirality : 0.042 0.190 3405 Planarity : 0.006 0.101 2831 Dihedral : 27.147 175.690 5175 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.15 % Allowed : 7.19 % Favored : 91.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -2.39 (0.18), residues: 1802 helix: 0.61 (0.21), residues: 584 sheet: -2.38 (0.28), residues: 278 loop : -2.90 (0.17), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.021 0.002 TYR B 51 PHE 0.017 0.002 PHE N 104 TRP 0.019 0.002 TRP N 279 HIS 0.008 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00438 (21495) covalent geometry : angle 0.63761 (30287) hydrogen bonds : bond 0.07082 ( 906) hydrogen bonds : angle 4.06568 ( 2292) metal coordination : bond 0.00203 ( 1) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 206 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 GLU cc_start: 0.8165 (tt0) cc_final: 0.7859 (mt-10) REVERT: G 87 VAL cc_start: 0.9422 (t) cc_final: 0.9180 (t) REVERT: K 3884 MET cc_start: 0.6720 (mmm) cc_final: 0.6181 (mtm) REVERT: K 3919 ASN cc_start: 0.7761 (m-40) cc_final: 0.7476 (t0) REVERT: K 3939 GLU cc_start: 0.7269 (tt0) cc_final: 0.6998 (tt0) REVERT: N 92 GLN cc_start: 0.6878 (tp40) cc_final: 0.6515 (tp40) REVERT: N 183 GLN cc_start: 0.6000 (mp10) cc_final: 0.5751 (mp10) REVERT: N 233 CYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5293 (m) REVERT: R 129 SER cc_start: 0.4199 (p) cc_final: 0.3878 (m) REVERT: R 173 PRO cc_start: 0.5515 (Cg_exo) cc_final: 0.5189 (Cg_endo) REVERT: T 500 MET cc_start: 0.2322 (mtm) cc_final: 0.1985 (mtp) outliers start: 18 outliers final: 11 residues processed: 218 average time/residue: 0.1825 time to fit residues: 58.4603 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 233 CYS Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 157 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 169 optimal weight: 20.0000 chunk 61 optimal weight: 0.9990 chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 127 optimal weight: 0.0670 chunk 189 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 186 optimal weight: 0.0020 overall best weight: 0.6730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS H 46 HIS H 81 ASN ** K3861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 GLN ** R 86 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 = 0.4285 r_free = 0.4285 target = 0.195505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147271 restraints weight = 29403.203| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 1.53 r_work: 0.3309 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21497 Z= 0.132 Angle : 0.549 11.192 30287 Z= 0.315 Chirality : 0.039 0.158 3405 Planarity : 0.004 0.091 2831 Dihedral : 26.793 171.545 5175 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.95 % Allowed : 9.04 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -1.59 (0.19), residues: 1802 helix: 1.61 (0.22), residues: 584 sheet: -2.14 (0.29), residues: 286 loop : -2.59 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.015 0.001 TYR K3834 PHE 0.015 0.001 PHE K3904 TRP 0.017 0.001 TRP N 279 HIS 0.005 0.001 HIS R 86 Details of bonding type rmsd covalent geometry : bond 0.00274 (21495) covalent geometry : angle 0.54886 (30287) hydrogen bonds : bond 0.04667 ( 906) hydrogen bonds : angle 3.49183 ( 2292) metal coordination : bond 0.00012 ( 1) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 222 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 105 LYS cc_start: 0.8054 (ttmt) cc_final: 0.7854 (tttm) REVERT: G 87 VAL cc_start: 0.9336 (t) cc_final: 0.9116 (t) REVERT: K 3874 TYR cc_start: 0.8088 (t80) cc_final: 0.7815 (t80) REVERT: K 3884 MET cc_start: 0.6455 (mmm) cc_final: 0.5966 (mtm) REVERT: K 3888 ASP cc_start: 0.6410 (p0) cc_final: 0.5967 (t0) REVERT: K 3919 ASN cc_start: 0.7287 (m-40) cc_final: 0.7043 (t0) REVERT: K 3939 GLU cc_start: 0.7429 (tt0) cc_final: 0.7177 (tt0) REVERT: N 51 TRP cc_start: 0.7905 (m-90) cc_final: 0.6983 (m-90) REVERT: N 183 GLN cc_start: 0.6030 (mp10) cc_final: 0.5709 (mp10) REVERT: N 323 GLN cc_start: 0.5763 (OUTLIER) cc_final: 0.4995 (mm-40) REVERT: T 380 LYS cc_start: 0.5201 (mtpt) cc_final: 0.4585 (ptpp) REVERT: T 500 MET cc_start: 0.2885 (mtm) cc_final: 0.2581 (mtp) outliers start: 15 outliers final: 10 residues processed: 231 average time/residue: 0.1811 time to fit residues: 61.3859 Evaluate side-chains 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 193 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 20.0000 chunk 70 optimal weight: 5.9990 chunk 145 optimal weight: 0.0060 chunk 14 optimal weight: 4.9990 chunk 172 optimal weight: 0.0040 chunk 138 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 190 optimal weight: 2.9990 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** N 323 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 = 0.4277 r_free = 0.4277 target = 0.194846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147200 restraints weight = 29397.453| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.64 r_work: 0.3296 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21497 Z= 0.135 Angle : 0.543 10.437 30287 Z= 0.313 Chirality : 0.039 0.187 3405 Planarity : 0.004 0.089 2831 Dihedral : 26.774 171.605 5175 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.53 % Allowed : 9.23 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -1.25 (0.20), residues: 1802 helix: 1.99 (0.22), residues: 584 sheet: -1.83 (0.31), residues: 273 loop : -2.50 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 367 TYR 0.020 0.001 TYR B 88 PHE 0.012 0.001 PHE K3904 TRP 0.016 0.001 TRP N 321 HIS 0.010 0.001 HIS T 320 Details of bonding type rmsd covalent geometry : bond 0.00287 (21495) covalent geometry : angle 0.54350 (30287) hydrogen bonds : bond 0.04757 ( 906) hydrogen bonds : angle 3.33870 ( 2292) metal coordination : bond 0.00086 ( 1) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 39 TYR cc_start: 0.8672 (t80) cc_final: 0.8455 (t80) REVERT: G 87 VAL cc_start: 0.9355 (t) cc_final: 0.9116 (t) REVERT: H 31 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7912 (tptm) REVERT: K 3874 TYR cc_start: 0.8034 (t80) cc_final: 0.7819 (t80) REVERT: K 3884 MET cc_start: 0.6694 (mmm) cc_final: 0.6159 (mtm) REVERT: K 3891 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6893 (mm-30) REVERT: K 3919 ASN cc_start: 0.7335 (m-40) cc_final: 0.7085 (t0) REVERT: K 3939 GLU cc_start: 0.7462 (tt0) cc_final: 0.7244 (tt0) REVERT: N 51 TRP cc_start: 0.7834 (m-90) cc_final: 0.6938 (m-90) REVERT: N 183 GLN cc_start: 0.6200 (mp10) cc_final: 0.5805 (mp10) REVERT: N 233 CYS cc_start: 0.5988 (m) cc_final: 0.5707 (m) REVERT: T 369 LYS cc_start: 0.1173 (tmtt) cc_final: 0.0470 (tptm) REVERT: T 373 LYS cc_start: 0.0592 (ttpt) cc_final: -0.0171 (tmtt) REVERT: T 380 LYS cc_start: 0.4764 (mtpt) cc_final: 0.4385 (ptpp) REVERT: T 500 MET cc_start: 0.2903 (mtm) cc_final: 0.2664 (mtp) outliers start: 24 outliers final: 18 residues processed: 215 average time/residue: 0.1714 time to fit residues: 55.4402 Evaluate side-chains 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 122 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 197 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN T 320 HIS ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.195632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147880 restraints weight = 29196.281| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 1.60 r_work: 0.3303 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21497 Z= 0.130 Angle : 0.527 9.567 30287 Z= 0.303 Chirality : 0.038 0.150 3405 Planarity : 0.004 0.087 2831 Dihedral : 26.705 171.659 5175 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.65 % Allowed : 10.06 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.92 (0.20), residues: 1802 helix: 2.19 (0.22), residues: 590 sheet: -1.42 (0.32), residues: 282 loop : -2.36 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.013 0.001 TYR B 51 PHE 0.013 0.001 PHE K3904 TRP 0.014 0.001 TRP N 279 HIS 0.004 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00277 (21495) covalent geometry : angle 0.52684 (30287) hydrogen bonds : bond 0.04588 ( 906) hydrogen bonds : angle 3.18895 ( 2292) metal coordination : bond 0.00066 ( 1) Misc. bond : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 0.666 Fit side-chains REVERT: D 39 TYR cc_start: 0.8715 (t80) cc_final: 0.8470 (t80) REVERT: G 71 ARG cc_start: 0.8661 (ttm-80) cc_final: 0.8447 (ttm110) REVERT: G 87 VAL cc_start: 0.9348 (t) cc_final: 0.9102 (t) REVERT: K 3884 MET cc_start: 0.6803 (mmm) cc_final: 0.6008 (mtm) REVERT: K 3891 GLU cc_start: 0.7205 (mm-30) cc_final: 0.7005 (mm-30) REVERT: K 3939 GLU cc_start: 0.7577 (tt0) cc_final: 0.7337 (tt0) REVERT: K 3942 TYR cc_start: 0.7563 (p90) cc_final: 0.7244 (p90) REVERT: N 51 TRP cc_start: 0.7787 (m-90) cc_final: 0.6952 (m-90) REVERT: N 183 GLN cc_start: 0.6258 (mp10) cc_final: 0.5862 (mp10) REVERT: N 233 CYS cc_start: 0.6032 (m) cc_final: 0.5687 (m) REVERT: N 273 GLN cc_start: 0.7797 (pt0) cc_final: 0.7571 (pt0) REVERT: R 198 TRP cc_start: 0.7057 (m100) cc_final: 0.6331 (m100) REVERT: T 369 LYS cc_start: 0.1172 (tmtt) cc_final: 0.0539 (tptm) REVERT: T 373 LYS cc_start: 0.0767 (ttpt) cc_final: -0.0399 (tmtt) REVERT: T 380 LYS cc_start: 0.4978 (mtpt) cc_final: 0.4619 (ptpp) REVERT: T 500 MET cc_start: 0.3150 (mtm) cc_final: 0.2883 (mtp) outliers start: 26 outliers final: 16 residues processed: 217 average time/residue: 0.1754 time to fit residues: 56.6040 Evaluate side-chains 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 188 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 26 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 chunk 69 optimal weight: 0.0060 chunk 122 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 20 optimal weight: 0.5980 chunk 195 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 123 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 overall best weight: 1.9202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN G 73 ASN N 323 GLN R 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.193156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143658 restraints weight = 28924.831| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 1.55 r_work: 0.3248 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21497 Z= 0.165 Angle : 0.555 8.182 30287 Z= 0.317 Chirality : 0.040 0.148 3405 Planarity : 0.004 0.090 2831 Dihedral : 26.794 172.682 5175 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.65 % Allowed : 9.99 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -1.00 (0.20), residues: 1802 helix: 2.03 (0.22), residues: 590 sheet: -1.47 (0.32), residues: 271 loop : -2.32 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 307 TYR 0.021 0.001 TYR B 88 PHE 0.012 0.001 PHE N 104 TRP 0.014 0.001 TRP N 303 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00371 (21495) covalent geometry : angle 0.55451 (30287) hydrogen bonds : bond 0.05731 ( 906) hydrogen bonds : angle 3.25321 ( 2292) metal coordination : bond 0.00041 ( 1) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: G 71 ARG cc_start: 0.8607 (ttm-80) cc_final: 0.8386 (ttm110) REVERT: G 87 VAL cc_start: 0.9394 (t) cc_final: 0.9117 (t) REVERT: K 3884 MET cc_start: 0.6815 (mmm) cc_final: 0.6013 (mtm) REVERT: K 3939 GLU cc_start: 0.7602 (tt0) cc_final: 0.7357 (tt0) REVERT: K 3942 TYR cc_start: 0.7624 (p90) cc_final: 0.7417 (p90) REVERT: N 26 MET cc_start: 0.5851 (mmt) cc_final: 0.5172 (ptp) REVERT: N 51 TRP cc_start: 0.7832 (m-90) cc_final: 0.6979 (m-90) REVERT: N 183 GLN cc_start: 0.6126 (mp10) cc_final: 0.5699 (mp10) REVERT: N 233 CYS cc_start: 0.6104 (m) cc_final: 0.5795 (m) REVERT: N 273 GLN cc_start: 0.7888 (pt0) cc_final: 0.7639 (pt0) REVERT: R 198 TRP cc_start: 0.6968 (m100) cc_final: 0.6407 (m100) REVERT: T 369 LYS cc_start: 0.1191 (tmtt) cc_final: 0.0533 (tptm) REVERT: T 373 LYS cc_start: 0.0805 (ttpt) cc_final: -0.0354 (tmtt) REVERT: T 380 LYS cc_start: 0.4975 (mtpt) cc_final: 0.4601 (ptpp) REVERT: T 476 LYS cc_start: 0.5672 (pttt) cc_final: 0.4535 (mtpt) REVERT: T 500 MET cc_start: 0.3281 (mtm) cc_final: 0.2968 (mtp) outliers start: 26 outliers final: 19 residues processed: 214 average time/residue: 0.1775 time to fit residues: 56.4038 Evaluate side-chains 204 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 186 optimal weight: 30.0000 chunk 39 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 168 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN G 73 ASN G 84 GLN ** T 352 ASN ** 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 = 0.4282 r_free = 0.4282 target = 0.195380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.147459 restraints weight = 29283.019| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.54 r_work: 0.3315 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 21497 Z= 0.132 Angle : 0.527 8.198 30287 Z= 0.303 Chirality : 0.038 0.170 3405 Planarity : 0.004 0.087 2831 Dihedral : 26.690 171.939 5175 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.40 % Allowed : 10.57 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.76 (0.20), residues: 1802 helix: 2.27 (0.22), residues: 590 sheet: -1.22 (0.32), residues: 277 loop : -2.25 (0.18), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.012 0.001 TYR K3874 PHE 0.010 0.001 PHE R 137 TRP 0.015 0.001 TRP N 321 HIS 0.004 0.001 HIS K3907 Details of bonding type rmsd covalent geometry : bond 0.00280 (21495) covalent geometry : angle 0.52696 (30287) hydrogen bonds : bond 0.04710 ( 906) hydrogen bonds : angle 3.10530 ( 2292) metal coordination : bond 0.00012 ( 1) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: G 71 ARG cc_start: 0.8601 (ttm-80) cc_final: 0.8388 (ttm110) REVERT: G 87 VAL cc_start: 0.9307 (t) cc_final: 0.9048 (t) REVERT: K 3822 HIS cc_start: 0.7187 (m-70) cc_final: 0.6973 (m90) REVERT: K 3891 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6861 (mm-30) REVERT: K 3939 GLU cc_start: 0.7512 (tt0) cc_final: 0.7246 (tt0) REVERT: K 3942 TYR cc_start: 0.7581 (p90) cc_final: 0.7361 (p90) REVERT: N 51 TRP cc_start: 0.7807 (m-90) cc_final: 0.7047 (m-90) REVERT: N 183 GLN cc_start: 0.6179 (mp10) cc_final: 0.5682 (mp10) REVERT: N 233 CYS cc_start: 0.6110 (m) cc_final: 0.5782 (m) REVERT: N 273 GLN cc_start: 0.7856 (pt0) cc_final: 0.7590 (pt0) REVERT: R 78 LYS cc_start: 0.7486 (tppt) cc_final: 0.7142 (tptp) REVERT: R 198 TRP cc_start: 0.6853 (m100) cc_final: 0.6416 (m100) REVERT: T 369 LYS cc_start: 0.1132 (tmtt) cc_final: 0.0514 (tptm) REVERT: T 380 LYS cc_start: 0.4920 (mtpt) cc_final: 0.4578 (ptpp) REVERT: T 476 LYS cc_start: 0.5502 (pttt) cc_final: 0.4505 (mtpt) REVERT: T 500 MET cc_start: 0.3277 (mtm) cc_final: 0.2967 (mtp) outliers start: 22 outliers final: 19 residues processed: 211 average time/residue: 0.1689 time to fit residues: 53.6472 Evaluate side-chains 203 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 114 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 30.0000 chunk 58 optimal weight: 0.7980 chunk 199 optimal weight: 9.9990 chunk 101 optimal weight: 0.7980 chunk 132 optimal weight: 20.0000 chunk 158 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 127 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 73 ASN N 325 GLN ** T 352 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.192512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.143057 restraints weight = 29084.359| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.60 r_work: 0.3235 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21497 Z= 0.170 Angle : 0.564 8.727 30287 Z= 0.322 Chirality : 0.040 0.156 3405 Planarity : 0.004 0.090 2831 Dihedral : 26.815 173.087 5175 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.53 % Allowed : 11.27 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.88 (0.20), residues: 1802 helix: 2.05 (0.22), residues: 589 sheet: -1.24 (0.32), residues: 283 loop : -2.25 (0.18), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 42 TYR 0.015 0.001 TYR B 51 PHE 0.011 0.001 PHE N 104 TRP 0.018 0.001 TRP N 303 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00385 (21495) covalent geometry : angle 0.56415 (30287) hydrogen bonds : bond 0.06069 ( 906) hydrogen bonds : angle 3.22118 ( 2292) metal coordination : bond 0.00028 ( 1) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 184 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: G 87 VAL cc_start: 0.9368 (t) cc_final: 0.9131 (t) REVERT: K 3822 HIS cc_start: 0.7336 (m-70) cc_final: 0.7122 (m90) REVERT: K 3939 GLU cc_start: 0.7589 (tt0) cc_final: 0.7321 (tt0) REVERT: N 26 MET cc_start: 0.6009 (mmt) cc_final: 0.5314 (ptp) REVERT: N 51 TRP cc_start: 0.7787 (m-90) cc_final: 0.6925 (m-90) REVERT: N 102 GLN cc_start: 0.5692 (mp10) cc_final: 0.5426 (mp10) REVERT: N 183 GLN cc_start: 0.6075 (mp10) cc_final: 0.5589 (mp10) REVERT: N 233 CYS cc_start: 0.6178 (m) cc_final: 0.5890 (m) REVERT: R 78 LYS cc_start: 0.7573 (tppt) cc_final: 0.7200 (tptp) REVERT: R 198 TRP cc_start: 0.7027 (m100) cc_final: 0.6535 (m100) REVERT: T 369 LYS cc_start: 0.1197 (tmtt) cc_final: 0.0521 (tptm) REVERT: T 373 LYS cc_start: 0.0768 (ttpt) cc_final: -0.0291 (tmtt) REVERT: T 380 LYS cc_start: 0.5011 (mtpt) cc_final: 0.4594 (ptpp) REVERT: T 476 LYS cc_start: 0.5696 (pttt) cc_final: 0.4678 (mtpt) REVERT: T 500 MET cc_start: 0.3334 (mtm) cc_final: 0.3037 (mtp) outliers start: 24 outliers final: 20 residues processed: 202 average time/residue: 0.1787 time to fit residues: 53.5004 Evaluate side-chains 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 129 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 180 optimal weight: 30.0000 chunk 142 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 40 optimal weight: 0.0870 chunk 104 optimal weight: 0.1980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 73 ASN G 84 GLN N 323 GLN ** T 352 ASN ** 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 = 0.4269 r_free = 0.4269 target = 0.194110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145537 restraints weight = 28964.031| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.59 r_work: 0.3275 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21497 Z= 0.132 Angle : 0.548 9.758 30287 Z= 0.314 Chirality : 0.039 0.152 3405 Planarity : 0.004 0.088 2831 Dihedral : 26.783 172.930 5175 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.15 % Allowed : 11.84 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.74 (0.20), residues: 1802 helix: 2.19 (0.22), residues: 590 sheet: -1.18 (0.32), residues: 283 loop : -2.19 (0.18), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG R 196 TYR 0.018 0.001 TYR R 35 PHE 0.010 0.001 PHE K3904 TRP 0.013 0.001 TRP N 279 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00269 (21495) covalent geometry : angle 0.54784 (30287) hydrogen bonds : bond 0.05166 ( 906) hydrogen bonds : angle 3.20979 ( 2292) metal coordination : bond 0.00033 ( 1) Misc. bond : bond 0.00052 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 181 time to evaluate : 0.693 Fit side-chains revert: symmetry clash REVERT: G 87 VAL cc_start: 0.9338 (t) cc_final: 0.9102 (t) REVERT: K 3822 HIS cc_start: 0.7265 (m-70) cc_final: 0.7054 (m90) REVERT: K 3939 GLU cc_start: 0.7554 (tt0) cc_final: 0.7285 (tt0) REVERT: K 3942 TYR cc_start: 0.7677 (p90) cc_final: 0.7459 (p90) REVERT: N 26 MET cc_start: 0.6025 (mmt) cc_final: 0.5406 (ptp) REVERT: N 51 TRP cc_start: 0.7835 (m-90) cc_final: 0.7001 (m-90) REVERT: N 233 CYS cc_start: 0.6178 (m) cc_final: 0.5885 (m) REVERT: R 78 LYS cc_start: 0.7567 (tppt) cc_final: 0.7192 (tptp) REVERT: R 198 TRP cc_start: 0.6864 (m100) cc_final: 0.6476 (m100) REVERT: T 369 LYS cc_start: 0.1140 (tmtt) cc_final: 0.0477 (tptm) REVERT: T 380 LYS cc_start: 0.5007 (mtpt) cc_final: 0.4596 (ptpp) REVERT: T 476 LYS cc_start: 0.5756 (pttt) cc_final: 0.4745 (mtpt) REVERT: T 500 MET cc_start: 0.3278 (mtm) cc_final: 0.3008 (mtp) outliers start: 18 outliers final: 16 residues processed: 196 average time/residue: 0.1748 time to fit residues: 51.4192 Evaluate side-chains 196 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 193 optimal weight: 20.0000 chunk 53 optimal weight: 0.6980 chunk 204 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 186 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 31 HIS G 73 ASN G 84 GLN N 323 GLN ** T 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.191526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141486 restraints weight = 28923.144| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.48 r_work: 0.3218 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21497 Z= 0.191 Angle : 0.587 13.027 30287 Z= 0.333 Chirality : 0.041 0.156 3405 Planarity : 0.005 0.091 2831 Dihedral : 26.864 173.532 5175 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.27 % Allowed : 11.84 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.95 (0.20), residues: 1802 helix: 1.87 (0.22), residues: 591 sheet: -1.17 (0.32), residues: 283 loop : -2.25 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 83 TYR 0.015 0.001 TYR B 51 PHE 0.012 0.002 PHE C 25 TRP 0.025 0.002 TRP N 303 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00439 (21495) covalent geometry : angle 0.58671 (30287) hydrogen bonds : bond 0.06587 ( 906) hydrogen bonds : angle 3.28127 ( 2292) metal coordination : bond 0.00051 ( 1) Misc. bond : bond 0.00054 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: K 3822 HIS cc_start: 0.7329 (m-70) cc_final: 0.7114 (m90) REVERT: K 3891 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6412 (mm-30) REVERT: K 3939 GLU cc_start: 0.7692 (tt0) cc_final: 0.7406 (tt0) REVERT: N 26 MET cc_start: 0.6027 (mmt) cc_final: 0.5334 (ptp) REVERT: N 233 CYS cc_start: 0.5817 (m) cc_final: 0.5584 (m) REVERT: R 78 LYS cc_start: 0.7699 (tppt) cc_final: 0.7299 (tptp) REVERT: T 369 LYS cc_start: 0.1267 (tmtt) cc_final: 0.0672 (tptm) REVERT: T 380 LYS cc_start: 0.5279 (mtpt) cc_final: 0.4791 (ptpp) REVERT: T 476 LYS cc_start: 0.5737 (pttt) cc_final: 0.4864 (mtpp) REVERT: T 500 MET cc_start: 0.3491 (mtm) cc_final: 0.3213 (mtp) outliers start: 20 outliers final: 19 residues processed: 196 average time/residue: 0.1768 time to fit residues: 51.7065 Evaluate side-chains 198 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 45 optimal weight: 0.0050 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 141 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 53 optimal weight: 0.4980 chunk 14 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN G 73 ASN G 104 GLN ** T 352 ASN ** 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 = 0.4244 r_free = 0.4244 target = 0.191788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142017 restraints weight = 28943.943| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.49 r_work: 0.3213 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.117 21497 Z= 0.196 Angle : 0.729 59.200 30287 Z= 0.433 Chirality : 0.040 0.154 3405 Planarity : 0.005 0.092 2831 Dihedral : 26.866 173.470 5175 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.15 % Allowed : 12.29 % Favored : 86.57 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % 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 aren not related in a simple way. whole: -0.94 (0.20), residues: 1802 helix: 1.87 (0.22), residues: 591 sheet: -1.17 (0.32), residues: 283 loop : -2.24 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.014 0.001 TYR B 51 PHE 0.011 0.001 PHE D 62 TRP 0.021 0.001 TRP N 303 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00404 (21495) covalent geometry : angle 0.72892 (30287) hydrogen bonds : bond 0.06333 ( 906) hydrogen bonds : angle 3.28116 ( 2292) metal coordination : bond 0.00034 ( 1) Misc. bond : bond 0.00058 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.76 seconds wall clock time: 85 minutes 22.07 seconds (5122.07 seconds total)