Starting phenix.real_space_refine on Mon Sep 14 01:00:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kiu_9998/09_2026/6kiu_9998.cif" } 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-2.2.1-6174/lib/python3.11/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: 3.76, per 1000 atoms: 0.18 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: 1.55 Conformation dependent library (CDL) restraints added in 607.5 milliseconds 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: 2.75 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: 4.95 Time building geometry restraints manager: 2.07 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=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.435 1.492 -0.057 1.30e-02 5.92e+03 1.95e+01 bond pdb=" C3' DG J 95 " pdb=" C2' DG J 95 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.51e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.484 -0.049 1.30e-02 5.92e+03 1.44e+01 bond pdb=" C1' DT I 31 " pdb=" N1 DT I 31 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C3' DG I 55 " pdb=" C2' DG I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 28829 2.08 - 4.16: 1334 4.16 - 6.24: 95 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=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.83 -2.93 6.00e-01 2.78e+00 2.38e+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 ... (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 - 0.052: 2347 0.052 - 0.105: 842 0.105 - 0.157: 188 0.157 - 0.210: 23 0.210 - 0.262: 5 Chirality restraints: 3405 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.73 -2.47 -0.26 2.00e-01 2.50e+01 1.72e+00 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 ... (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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.900 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 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= 0.579 Angle : 0.949 10.396 30287 Z= 0.703 Chirality : 0.055 0.262 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 are 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/Z covalent geometry : bond 0.00790 / 0.57 (21495) covalent geometry : angle 0.94888 / 0.70 (30287) hydrogen bonds : bond 0.16115 / 10.43 ( 906) hydrogen bonds : angle 5.60495 / 4.03 ( 2292) metal coordination : bond 0.33911 / 22.61 ( 1) Misc. bond : bond 0.00151 / 0.10 ( 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 : 0.655 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: 0.7837 (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: 0.6968 (t) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2209 time to fit residues: 108.4493 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 20.0000 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: 20.0000 chunk 122 optimal weight: 6.9990 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 68 GLN G 84 GLN ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 GLN R 300 HIS T 376 GLN T 381 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.191889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141167 restraints weight = 28884.656| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 1.48 r_work: 0.3233 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21497 Z= 0.184 Angle : 0.709 10.207 30287 Z= 0.397 Chirality : 0.052 0.366 3405 Planarity : 0.006 0.100 2831 Dihedral : 27.395 171.549 5175 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.21 % Allowed : 7.19 % Favored : 91.60 % 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 are not related in a simple way. whole: -2.44 (0.18), residues: 1802 helix: 0.56 (0.21), residues: 582 sheet: -2.25 (0.29), residues: 275 loop : -2.98 (0.16), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 42 TYR 0.020 0.002 TYR B 51 PHE 0.017 0.002 PHE T 329 TRP 0.017 0.002 TRP N 279 HIS 0.010 0.001 HIS K3822 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (21495) covalent geometry : angle 0.70914 / 0.40 (30287) hydrogen bonds : bond 0.07876 / 5.18 ( 906) hydrogen bonds : angle 4.29893 / 3.08 ( 2292) metal coordination : bond 0.00767 / 0.51 ( 1) Misc. bond : bond 0.00047 / 0.03 ( 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 227 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 61 GLU cc_start: 0.7865 (tt0) cc_final: 0.7600 (mt-10) REVERT: G 87 VAL cc_start: 0.9385 (t) cc_final: 0.9138 (t) REVERT: H 56 MET cc_start: 0.8309 (tpp) cc_final: 0.8082 (tpp) REVERT: K 3884 MET cc_start: 0.6731 (mmm) cc_final: 0.5915 (mtm) REVERT: K 3919 ASN cc_start: 0.7874 (m-40) cc_final: 0.7479 (t0) REVERT: N 92 GLN cc_start: 0.6761 (tp40) cc_final: 0.6317 (tp40) REVERT: R 173 PRO cc_start: 0.5527 (Cg_exo) cc_final: 0.5248 (Cg_endo) outliers start: 19 outliers final: 13 residues processed: 221 average time/residue: 0.1802 time to fit residues: 58.5208 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 209 LYS Chi-restraints excluded: chain R residue 45 THR 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 157 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 chunk 61 optimal weight: 3.9990 chunk 171 optimal weight: 9.9990 chunk 94 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 189 optimal weight: 30.0000 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 0.0980 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 31 HIS C 73 ASN F 75 HIS ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 323 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.189600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138751 restraints weight = 28940.926| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.47 r_work: 0.3174 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 21497 Z= 0.243 Angle : 0.737 11.352 30287 Z= 0.405 Chirality : 0.054 0.397 3405 Planarity : 0.006 0.108 2831 Dihedral : 27.564 171.946 5175 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 1.34 % Allowed : 9.23 % Favored : 89.43 % 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 are not related in a simple way. whole: -2.25 (0.18), residues: 1802 helix: 0.81 (0.21), residues: 583 sheet: -2.14 (0.29), residues: 290 loop : -2.94 (0.17), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 83 TYR 0.025 0.002 TYR B 51 PHE 0.021 0.003 PHE C 25 TRP 0.020 0.002 TRP R 198 HIS 0.011 0.002 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (21495) covalent geometry : angle 0.73687 / 0.41 (30287) hydrogen bonds : bond 0.08762 / 5.79 ( 906) hydrogen bonds : angle 4.15091 / 2.98 ( 2292) metal coordination : bond 0.00187 / 0.12 ( 1) Misc. bond : bond 0.00054 / 0.04 ( 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 217 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9085 (m-80) cc_final: 0.8817 (m-80) REVERT: G 61 GLU cc_start: 0.7878 (tt0) cc_final: 0.7540 (mt-10) REVERT: K 3884 MET cc_start: 0.6649 (mmm) cc_final: 0.5739 (mtm) REVERT: K 3919 ASN cc_start: 0.7685 (m-40) cc_final: 0.7328 (t0) REVERT: N 26 MET cc_start: 0.6651 (mmt) cc_final: 0.6291 (mpp) REVERT: N 183 GLN cc_start: 0.5918 (mp10) cc_final: 0.5624 (mp10) REVERT: R 173 PRO cc_start: 0.5477 (Cg_exo) cc_final: 0.5248 (Cg_endo) REVERT: R 242 ASP cc_start: 0.6693 (t0) cc_final: 0.6478 (t0) REVERT: T 380 LYS cc_start: 0.5264 (mtpt) cc_final: 0.4672 (ptpp) outliers start: 21 outliers final: 13 residues processed: 210 average time/residue: 0.1767 time to fit residues: 55.3294 Evaluate side-chains 194 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 181 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 49 THR 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 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 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 130 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 172 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 chunk 26 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 190 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS N 65 HIS N 323 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 = 0.4242 r_free = 0.4242 target = 0.191819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141396 restraints weight = 29057.309| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 1.55 r_work: 0.3214 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21497 Z= 0.157 Angle : 0.640 11.645 30287 Z= 0.358 Chirality : 0.049 0.372 3405 Planarity : 0.005 0.098 2831 Dihedral : 27.463 171.280 5175 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.46 % Allowed : 10.06 % Favored : 88.48 % 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 are not related in a simple way. whole: -1.81 (0.19), residues: 1802 helix: 1.35 (0.22), residues: 584 sheet: -2.09 (0.29), residues: 272 loop : -2.74 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 83 TYR 0.014 0.001 TYR B 88 PHE 0.012 0.002 PHE T 329 TRP 0.019 0.001 TRP N 279 HIS 0.005 0.001 HIS R 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (21495) covalent geometry : angle 0.64048 / 0.36 (30287) hydrogen bonds : bond 0.06863 / 4.49 ( 906) hydrogen bonds : angle 3.86037 / 2.79 ( 2292) metal coordination : bond 0.00122 / 0.08 ( 1) Misc. bond : bond 0.00063 / 0.04 ( 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 217 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 61 GLU cc_start: 0.7833 (tt0) cc_final: 0.7485 (mt-10) REVERT: G 87 VAL cc_start: 0.9397 (t) cc_final: 0.9107 (t) REVERT: H 103 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8582 (mp) REVERT: K 3874 TYR cc_start: 0.8126 (t80) cc_final: 0.7781 (t80) REVERT: K 3884 MET cc_start: 0.6577 (mmm) cc_final: 0.6114 (mtm) REVERT: K 3919 ASN cc_start: 0.7503 (m-40) cc_final: 0.7065 (t0) REVERT: N 183 GLN cc_start: 0.6069 (mp10) cc_final: 0.5699 (mp10) REVERT: N 238 GLU cc_start: 0.5612 (tp30) cc_final: 0.5400 (mt-10) REVERT: T 369 LYS cc_start: 0.1233 (tmtt) cc_final: 0.0559 (tptm) REVERT: T 373 LYS cc_start: 0.0686 (ttpt) cc_final: 0.0001 (ttpt) REVERT: T 380 LYS cc_start: 0.5049 (mtpt) cc_final: 0.4658 (ptpp) REVERT: T 500 MET cc_start: 0.2490 (mtm) cc_final: 0.2116 (mtp) outliers start: 23 outliers final: 13 residues processed: 209 average time/residue: 0.1719 time to fit residues: 53.1166 Evaluate side-chains 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 103 LEU 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 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 287 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 197 optimal weight: 3.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.0070 chunk 43 optimal weight: 5.9990 chunk 103 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 159 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 323 GLN N 325 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4258 r_free = 0.4258 target = 0.193180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.143797 restraints weight = 29022.261| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 1.65 r_work: 0.3248 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21497 Z= 0.138 Angle : 0.595 10.816 30287 Z= 0.337 Chirality : 0.046 0.351 3405 Planarity : 0.004 0.092 2831 Dihedral : 27.359 171.583 5175 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.46 % Allowed : 10.69 % Favored : 87.84 % 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 are not related in a simple way. whole: -1.47 (0.19), residues: 1802 helix: 1.75 (0.22), residues: 584 sheet: -1.84 (0.29), residues: 292 loop : -2.63 (0.18), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 228 TYR 0.025 0.001 TYR B 88 PHE 0.014 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/Z covalent geometry : bond 0.00259 / 0.14 (21495) covalent geometry : angle 0.59514 / 0.34 (30287) hydrogen bonds : bond 0.05894 / 3.85 ( 906) hydrogen bonds : angle 3.61574 / 2.62 ( 2292) metal coordination : bond 0.00165 / 0.11 ( 1) Misc. bond : bond 0.00058 / 0.04 ( 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 228 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 43 LYS cc_start: 0.9211 (mmtm) cc_final: 0.9000 (mmtm) REVERT: G 61 GLU cc_start: 0.7777 (tt0) cc_final: 0.7466 (mt-10) REVERT: G 71 ARG cc_start: 0.8686 (ttm-80) cc_final: 0.8394 (ttp80) REVERT: G 87 VAL cc_start: 0.9333 (t) cc_final: 0.9081 (t) REVERT: H 31 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7902 (tptm) REVERT: K 3874 TYR cc_start: 0.8074 (t80) cc_final: 0.7825 (t80) REVERT: K 3884 MET cc_start: 0.6756 (mmm) cc_final: 0.5899 (mtm) REVERT: K 3891 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6897 (mm-30) REVERT: K 3919 ASN cc_start: 0.7309 (m-40) cc_final: 0.7082 (t0) REVERT: K 3923 GLN cc_start: 0.8325 (mm-40) cc_final: 0.8116 (mm-40) REVERT: N 183 GLN cc_start: 0.6263 (mp10) cc_final: 0.5848 (mp10) REVERT: N 238 GLU cc_start: 0.5570 (tp30) cc_final: 0.5334 (mt-10) REVERT: T 369 LYS cc_start: 0.1319 (tmtt) cc_final: 0.0696 (tptm) REVERT: T 380 LYS cc_start: 0.4978 (mtpt) cc_final: 0.4612 (ptpp) REVERT: T 500 MET cc_start: 0.2775 (mtm) cc_final: 0.2415 (mtp) outliers start: 23 outliers final: 15 residues processed: 222 average time/residue: 0.1650 time to fit residues: 54.4534 Evaluate side-chains 203 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 188 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 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 287 VAL Chi-restraints excluded: chain R residue 45 THR 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 315 MET 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: 4.9990 chunk 163 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 122 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 20 optimal weight: 0.9990 chunk 195 optimal weight: 8.9990 chunk 187 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 123 optimal weight: 20.0000 chunk 146 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS G 84 GLN N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4232 r_free = 0.4232 target = 0.190796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140210 restraints weight = 28764.917| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.56 r_work: 0.3191 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2622 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= 0.198 Angle : 0.659 9.949 30287 Z= 0.365 Chirality : 0.050 0.364 3405 Planarity : 0.005 0.098 2831 Dihedral : 27.445 173.067 5175 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.85 % Allowed : 10.88 % Favored : 87.27 % 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 are not related in a simple way. whole: -1.62 (0.19), residues: 1802 helix: 1.46 (0.22), residues: 585 sheet: -1.78 (0.30), residues: 287 loop : -2.66 (0.17), residues: 930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K3821 TYR 0.020 0.002 TYR R 191 PHE 0.016 0.002 PHE R 219 TRP 0.017 0.002 TRP N 279 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (21495) covalent geometry : angle 0.65924 / 0.37 (30287) hydrogen bonds : bond 0.07430 / 4.88 ( 906) hydrogen bonds : angle 3.71650 / 2.69 ( 2292) metal coordination : bond 0.00065 / 0.04 ( 1) Misc. bond : bond 0.00062 / 0.04 ( 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 216 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7991 (mtp85) REVERT: E 133 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7523 (mt-10) REVERT: G 71 ARG cc_start: 0.8693 (ttm-80) cc_final: 0.8416 (ttp80) REVERT: K 3874 TYR cc_start: 0.8083 (t80) cc_final: 0.7796 (t80) REVERT: K 3891 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6808 (mm-30) REVERT: K 3919 ASN cc_start: 0.7457 (m-40) cc_final: 0.7159 (t0) REVERT: N 183 GLN cc_start: 0.6233 (mp10) cc_final: 0.5778 (mp10) REVERT: R 78 LYS cc_start: 0.7631 (tppt) cc_final: 0.7235 (tptp) REVERT: T 369 LYS cc_start: 0.1267 (tmtt) cc_final: 0.0640 (tptm) REVERT: T 380 LYS cc_start: 0.5077 (mtpt) cc_final: 0.4666 (ptpp) REVERT: T 476 LYS cc_start: 0.5469 (pttt) cc_final: 0.4075 (mtpt) REVERT: T 500 MET cc_start: 0.2851 (mtm) cc_final: 0.2484 (mtp) outliers start: 29 outliers final: 21 residues processed: 208 average time/residue: 0.1683 time to fit residues: 52.1453 Evaluate side-chains 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 287 VAL Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 315 MET 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: 7.9990 chunk 39 optimal weight: 0.9980 chunk 136 optimal weight: 0.0570 chunk 25 optimal weight: 0.9980 chunk 179 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN H 46 HIS ** N 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4262 r_free = 0.4262 target = 0.193613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145086 restraints weight = 29128.588| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.47 r_work: 0.3274 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21497 Z= 0.124 Angle : 0.589 9.736 30287 Z= 0.333 Chirality : 0.046 0.346 3405 Planarity : 0.004 0.091 2831 Dihedral : 27.338 172.062 5175 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.21 % Allowed : 12.03 % Favored : 86.76 % 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 are not related in a simple way. whole: -1.17 (0.20), residues: 1802 helix: 1.98 (0.22), residues: 584 sheet: -1.59 (0.31), residues: 273 loop : -2.46 (0.18), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.016 0.001 TYR N 345 PHE 0.010 0.001 PHE R 137 TRP 0.017 0.001 TRP N 279 HIS 0.003 0.001 HIS R 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.12 (21495) covalent geometry : angle 0.58867 / 0.33 (30287) hydrogen bonds : bond 0.05656 / 3.70 ( 906) hydrogen bonds : angle 3.48953 / 2.54 ( 2292) metal coordination : bond 0.00007 / 0.00 ( 1) Misc. bond : bond 0.00056 / 0.04 ( 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 213 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 194 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: E 133 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: G 71 ARG cc_start: 0.8610 (ttm-80) cc_final: 0.8378 (ttp80) REVERT: G 87 VAL cc_start: 0.9339 (t) cc_final: 0.9078 (t) REVERT: K 3874 TYR cc_start: 0.8056 (t80) cc_final: 0.7821 (t80) REVERT: K 3891 GLU cc_start: 0.7164 (mm-30) cc_final: 0.6873 (mm-30) REVERT: R 78 LYS cc_start: 0.7515 (tppt) cc_final: 0.7160 (tptp) REVERT: T 369 LYS cc_start: 0.1286 (tmtt) cc_final: 0.0681 (tptm) REVERT: T 380 LYS cc_start: 0.5021 (mtpt) cc_final: 0.4603 (ptpp) REVERT: T 476 LYS cc_start: 0.5186 (pttt) cc_final: 0.4088 (mtpt) REVERT: T 500 MET cc_start: 0.2774 (mtm) cc_final: 0.2432 (mtp) outliers start: 19 outliers final: 14 residues processed: 207 average time/residue: 0.1787 time to fit residues: 54.4914 Evaluate side-chains 199 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 184 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 109 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 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 315 MET 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: 7.9990 chunk 21 optimal weight: 0.8980 chunk 180 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 199 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 158 optimal weight: 7.9990 chunk 182 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 323 ASN ** 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 = 0.4221 r_free = 0.4221 target = 0.189781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.139080 restraints weight = 28976.530| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.52 r_work: 0.3178 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 21497 Z= 0.230 Angle : 0.692 9.465 30287 Z= 0.381 Chirality : 0.051 0.367 3405 Planarity : 0.006 0.098 2831 Dihedral : 27.485 173.808 5175 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.78 % Allowed : 11.65 % Favored : 86.57 % 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 are not related in a simple way. whole: -1.59 (0.19), residues: 1802 helix: 1.36 (0.21), residues: 585 sheet: -1.64 (0.30), residues: 290 loop : -2.60 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K3821 TYR 0.020 0.002 TYR A 54 PHE 0.019 0.002 PHE N 104 TRP 0.023 0.002 TRP N 303 HIS 0.007 0.001 HIS C 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (21495) covalent geometry : angle 0.69223 / 0.38 (30287) hydrogen bonds : bond 0.08106 / 5.34 ( 906) hydrogen bonds : angle 3.73836 / 2.71 ( 2292) metal coordination : bond 0.00029 / 0.02 ( 1) Misc. bond : bond 0.00076 / 0.05 ( 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 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 177 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.7912 (mtp85) REVERT: E 133 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7526 (mt-10) REVERT: G 71 ARG cc_start: 0.8655 (ttm-80) cc_final: 0.8407 (ttp80) REVERT: K 3874 TYR cc_start: 0.8056 (t80) cc_final: 0.7817 (t80) REVERT: R 78 LYS cc_start: 0.7703 (tppt) cc_final: 0.7300 (tptp) REVERT: T 369 LYS cc_start: 0.1357 (tmtt) cc_final: 0.0708 (tptm) REVERT: T 380 LYS cc_start: 0.5313 (mtpt) cc_final: 0.4798 (ptpp) REVERT: T 476 LYS cc_start: 0.5396 (pttt) cc_final: 0.4123 (mtpt) REVERT: T 500 MET cc_start: 0.2861 (mtm) cc_final: 0.2648 (mtp) outliers start: 28 outliers final: 21 residues processed: 196 average time/residue: 0.1735 time to fit residues: 50.4484 Evaluate side-chains 197 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain H residue 98 LEU 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 287 VAL Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 129 SER Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain T residue 315 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 129 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 180 optimal weight: 5.9990 chunk 142 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 352 ASN ** 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 = 0.4252 r_free = 0.4252 target = 0.192742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.145379 restraints weight = 28875.345| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 1.63 r_work: 0.3242 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21497 Z= 0.136 Angle : 0.606 9.608 30287 Z= 0.338 Chirality : 0.047 0.351 3405 Planarity : 0.004 0.094 2831 Dihedral : 27.382 172.690 5175 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.34 % Allowed : 12.16 % Favored : 86.51 % 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 are not related in a simple way. whole: -1.19 (0.20), residues: 1802 helix: 1.89 (0.22), residues: 584 sheet: -1.56 (0.31), residues: 271 loop : -2.43 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K3821 TYR 0.012 0.001 TYR N 345 PHE 0.011 0.001 PHE R 137 TRP 0.018 0.002 TRP N 279 HIS 0.010 0.001 HIS T 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (21495) covalent geometry : angle 0.60648 / 0.34 (30287) hydrogen bonds : bond 0.06086 / 3.98 ( 906) hydrogen bonds : angle 3.46525 / 2.51 ( 2292) metal coordination : bond 0.00086 / 0.06 ( 1) Misc. bond : bond 0.00059 / 0.04 ( 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 207 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 186 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7940 (mtp85) REVERT: E 133 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7490 (mt-10) REVERT: G 71 ARG cc_start: 0.8674 (ttm-80) cc_final: 0.8472 (ttp80) REVERT: G 87 VAL cc_start: 0.9369 (t) cc_final: 0.9116 (t) REVERT: K 3874 TYR cc_start: 0.8050 (t80) cc_final: 0.7839 (t80) REVERT: K 3891 GLU cc_start: 0.6997 (mm-30) cc_final: 0.6491 (mm-30) REVERT: R 35 TYR cc_start: 0.4890 (m-10) cc_final: 0.4639 (m-10) REVERT: R 78 LYS cc_start: 0.7497 (tppt) cc_final: 0.7135 (tptp) REVERT: T 369 LYS cc_start: 0.1313 (tmtt) cc_final: 0.0675 (tptm) REVERT: T 380 LYS cc_start: 0.5220 (mtpt) cc_final: 0.4732 (ptpp) REVERT: T 476 LYS cc_start: 0.5216 (pttt) cc_final: 0.4105 (mtpt) REVERT: T 500 MET cc_start: 0.3474 (mtm) cc_final: 0.3157 (mtp) outliers start: 21 outliers final: 18 residues processed: 201 average time/residue: 0.1769 time to fit residues: 52.6955 Evaluate side-chains 205 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 41 GLU 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 193 THR 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 R residue 144 ILE Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain R residue 209 LEU Chi-restraints excluded: chain T residue 315 MET 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: 0.8980 chunk 111 optimal weight: 0.1980 chunk 193 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 204 optimal weight: 30.0000 chunk 57 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 186 optimal weight: 0.0020 chunk 71 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 overall best weight: 1.0192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4257 r_free = 0.4257 target = 0.193260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.144184 restraints weight = 28968.187| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 1.47 r_work: 0.3269 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21497 Z= 0.129 Angle : 0.585 12.032 30287 Z= 0.330 Chirality : 0.046 0.344 3405 Planarity : 0.004 0.093 2831 Dihedral : 27.330 172.505 5175 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.27 % Allowed : 12.29 % Favored : 86.44 % 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 are not related in a simple way. whole: -1.05 (0.20), residues: 1802 helix: 2.04 (0.22), residues: 584 sheet: -1.48 (0.32), residues: 271 loop : -2.37 (0.18), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 83 TYR 0.012 0.001 TYR N 345 PHE 0.010 0.001 PHE R 137 TRP 0.018 0.001 TRP N 51 HIS 0.006 0.001 HIS T 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.13 (21495) covalent geometry : angle 0.58545 / 0.33 (30287) hydrogen bonds : bond 0.05698 / 3.72 ( 906) hydrogen bonds : angle 3.40344 / 2.47 ( 2292) metal coordination : bond 0.00047 / 0.03 ( 1) Misc. bond : bond 0.00053 / 0.04 ( 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 207 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: E 133 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7452 (mt-10) REVERT: G 87 VAL cc_start: 0.9343 (t) cc_final: 0.9095 (t) REVERT: K 3891 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6614 (mm-30) REVERT: R 35 TYR cc_start: 0.4921 (m-10) cc_final: 0.4685 (m-10) REVERT: R 78 LYS cc_start: 0.7560 (tppt) cc_final: 0.7185 (tptp) REVERT: T 369 LYS cc_start: 0.1204 (tmtt) cc_final: 0.0560 (tptm) REVERT: T 380 LYS cc_start: 0.5269 (mtpt) cc_final: 0.4763 (ptpp) REVERT: T 476 LYS cc_start: 0.5404 (pttt) cc_final: 0.4300 (mtpt) REVERT: T 500 MET cc_start: 0.3321 (mtm) cc_final: 0.3026 (mtp) outliers start: 20 outliers final: 18 residues processed: 200 average time/residue: 0.1711 time to fit residues: 51.3037 Evaluate side-chains 201 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain G residue 41 GLU 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 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 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 R residue 209 LEU Chi-restraints excluded: chain T residue 315 MET 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: 0.6980 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 129 optimal weight: 0.0270 chunk 91 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 84 GLN H 81 ASN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4277 r_free = 0.4277 target = 0.195121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146856 restraints weight = 29157.332| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.46 r_work: 0.3307 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21497 Z= 0.122 Angle : 0.567 12.707 30287 Z= 0.321 Chirality : 0.044 0.334 3405 Planarity : 0.004 0.091 2831 Dihedral : 27.202 172.516 5175 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.34 % Allowed : 12.29 % Favored : 86.38 % 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 are not related in a simple way. whole: -0.79 (0.20), residues: 1802 helix: 2.20 (0.22), residues: 590 sheet: -1.29 (0.32), residues: 271 loop : -2.21 (0.18), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 71 TYR 0.023 0.001 TYR K3874 PHE 0.026 0.001 PHE K3780 TRP 0.018 0.001 TRP N 51 HIS 0.004 0.001 HIS N 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.12 (21495) covalent geometry : angle 0.56716 / 0.32 (30287) hydrogen bonds : bond 0.04962 / 3.23 ( 906) hydrogen bonds : angle 3.22597 / 2.34 ( 2292) metal coordination : bond 0.00104 / 0.07 ( 1) Misc. bond : bond 0.00052 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4800.73 seconds wall clock time: 82 minutes 52.87 seconds (4972.87 seconds total)