Starting phenix.real_space_refine on Mon Jun 23 09:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.map" model { file = "/net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kiu_9998/06_2025/6kiu_9998.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'HIS:plan': 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: 13.60, per 1000 atoms: 0.66 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: 4.85 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 8.52 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: 9.43 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4596 1.33 - 1.45: 6066 1.45 - 1.58: 10165 1.58 - 1.70: 578 1.70 - 1.82: 90 Bond restraints: 21495 Sorted by residual: bond pdb=" C2 SAH K4001 " pdb=" N3 SAH K4001 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" C8 SAH K4001 " pdb=" N7 SAH K4001 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C2 SAH K4001 " pdb=" N1 SAH K4001 " ideal model delta sigma weight residual 1.330 1.378 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " ideal model delta sigma weight residual 1.422 1.492 -0.070 3.00e-02 1.11e+03 5.50e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.32e+00 ... (remaining 21490 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 29254 2.08 - 4.16: 917 4.16 - 6.24: 87 6.24 - 8.32: 23 8.32 - 10.40: 6 Bond angle restraints: 30287 Sorted by residual: angle pdb=" N VAL G 27 " pdb=" CA VAL G 27 " pdb=" C VAL G 27 " ideal model delta sigma weight residual 112.96 107.56 5.40 1.00e+00 1.00e+00 2.92e+01 angle pdb=" N VAL C 27 " pdb=" CA VAL C 27 " pdb=" C VAL C 27 " ideal model delta sigma weight residual 112.96 108.03 4.93 1.00e+00 1.00e+00 2.43e+01 angle pdb=" C ASN N 250 " pdb=" N ARG N 251 " pdb=" CA ARG N 251 " ideal model delta sigma weight residual 121.54 130.93 -9.39 1.91e+00 2.74e-01 2.42e+01 angle pdb=" C ASN N 12 " pdb=" N TYR N 13 " pdb=" CA TYR N 13 " ideal model delta sigma weight residual 120.51 127.38 -6.87 1.45e+00 4.76e-01 2.25e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 123.58 -10.40 2.37e+00 1.78e-01 1.92e+01 ... (remaining 30282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.07: 10714 35.07 - 70.15: 1410 70.15 - 105.22: 12 105.22 - 140.30: 2 140.30 - 175.37: 2 Dihedral angle restraints: 12140 sinusoidal: 6816 harmonic: 5324 Sorted by residual: dihedral pdb=" CA LYS B 31 " pdb=" C LYS B 31 " pdb=" N PRO B 32 " pdb=" CA PRO B 32 " ideal model delta harmonic sigma weight residual 180.00 135.05 44.95 0 5.00e+00 4.00e-02 8.08e+01 dihedral pdb=" CA ALA N 322 " pdb=" C ALA N 322 " pdb=" N GLN N 323 " pdb=" CA GLN N 323 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ARG N 251 " pdb=" C ARG N 251 " pdb=" N THR N 252 " pdb=" CA THR N 252 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2396 0.049 - 0.098: 770 0.098 - 0.147: 203 0.147 - 0.196: 32 0.196 - 0.245: 4 Chirality restraints: 3405 Sorted by residual: chirality pdb=" CB VAL D 45 " pdb=" CA VAL D 45 " pdb=" CG1 VAL D 45 " pdb=" CG2 VAL D 45 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA SER N 108 " pdb=" N SER N 108 " pdb=" C SER N 108 " pdb=" CB SER N 108 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE T 482 " pdb=" CA ILE T 482 " pdb=" CG1 ILE T 482 " pdb=" CG2 ILE T 482 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 3402 not shown) Planarity restraints: 2831 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " -0.081 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO B 32 " 0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 108 " 0.047 5.00e-02 4.00e+02 7.10e-02 8.07e+00 pdb=" N PRO N 109 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO N 109 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 109 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 51 " 0.017 2.00e-02 2.50e+03 1.96e-02 7.67e+00 pdb=" CG TYR B 51 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 51 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR B 51 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR B 51 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 51 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 51 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 51 " -0.002 2.00e-02 2.50e+03 ... (remaining 2828 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1219 2.72 - 3.27: 16732 3.27 - 3.81: 33632 3.81 - 4.36: 43392 4.36 - 4.90: 65991 Nonbonded interactions: 160966 Sorted by model distance: nonbonded pdb=" O CYS K3957 " pdb="ZN ZN K4002 " model vdw 2.178 2.230 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.241 3.040 nonbonded pdb=" O ILE K3905 " pdb=" OH TYR K3944 " model vdw 2.280 3.040 nonbonded pdb=" O TYR K3874 " pdb=" OG SER K3877 " model vdw 2.291 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.295 3.040 ... (remaining 160961 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 59.210 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.339 21497 Z= 0.320 Angle : 0.863 10.396 30287 Z= 0.494 Chirality : 0.052 0.245 3405 Planarity : 0.007 0.123 2831 Dihedral : 22.068 175.371 8706 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.029 0.002 TRP N 303 HIS 0.022 0.002 HIS C 82 PHE 0.041 0.003 PHE C 25 TYR 0.049 0.003 TYR B 51 ARG 0.015 0.002 ARG H 69 Details of bonding type rmsd hydrogen bonds : bond 0.16115 ( 906) hydrogen bonds : angle 5.60495 ( 2292) metal coordination : bond 0.33911 ( 1) covalent geometry : bond 0.00718 (21495) covalent geometry : angle 0.86255 (30287) Misc. bond : bond 0.00151 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3604 Ramachandran restraints generated. 1802 Oldfield, 0 Emsley, 1802 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.739 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: 0.7578 (mt0) REVERT: D 73 GLU cc_start: 0.8064 (tp30) cc_final: 0.7838 (tp30) REVERT: F 74 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7149 (mt-10) REVERT: G 73 ASN cc_start: 0.8264 (m110) cc_final: 0.8049 (m110) REVERT: H 56 MET cc_start: 0.7950 (tpp) cc_final: 0.7695 (tpp) REVERT: K 3849 ILE cc_start: 0.7903 (mt) cc_final: 0.7668 (mt) REVERT: K 3892 VAL cc_start: 0.7279 (t) cc_final: 0.6968 (t) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.4691 time to fit residues: 228.0631 Evaluate side-chains 190 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 6.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 53 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 8.9990 chunk 160 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 119 optimal weight: 10.0000 chunk 186 optimal weight: 0.0000 overall best weight: 3.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 73 ASN E 68 GLN F 75 HIS G 84 GLN K3822 HIS ** N 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 300 HIS T 376 GLN T 381 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.189663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138872 restraints weight = 28780.554| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.44 r_work: 0.3191 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21497 Z= 0.249 Angle : 0.687 11.757 30287 Z= 0.388 Chirality : 0.044 0.190 3405 Planarity : 0.006 0.108 2831 Dihedral : 27.276 176.635 5175 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.21 % Allowed : 7.45 % Favored : 91.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.18), residues: 1802 helix: 0.43 (0.21), residues: 582 sheet: -2.49 (0.28), residues: 288 loop : -2.95 (0.17), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 279 HIS 0.009 0.001 HIS C 82 PHE 0.019 0.003 PHE N 104 TYR 0.024 0.002 TYR B 51 ARG 0.008 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.08105 ( 906) hydrogen bonds : angle 4.14454 ( 2292) metal coordination : bond 0.00606 ( 1) covalent geometry : bond 0.00580 (21495) covalent geometry : angle 0.68686 (30287) Misc. bond : bond 0.00031 ( 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 221 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 2.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.9032 (m-80) cc_final: 0.8778 (m-80) REVERT: G 61 GLU cc_start: 0.7852 (tt0) cc_final: 0.7554 (mt-10) REVERT: K 3884 MET cc_start: 0.6443 (mmm) cc_final: 0.5876 (mtm) REVERT: K 3919 ASN cc_start: 0.7730 (m-40) cc_final: 0.7472 (t0) REVERT: K 3939 GLU cc_start: 0.7509 (tt0) cc_final: 0.7291 (tt0) REVERT: N 92 GLN cc_start: 0.6680 (tp40) cc_final: 0.6340 (tp40) REVERT: N 183 GLN cc_start: 0.5940 (mp10) cc_final: 0.5681 (mp10) REVERT: R 101 LEU cc_start: 0.7617 (tp) cc_final: 0.7348 (tp) REVERT: R 129 SER cc_start: 0.4212 (p) cc_final: 0.3884 (m) REVERT: R 173 PRO cc_start: 0.5540 (Cg_exo) cc_final: 0.5226 (Cg_endo) REVERT: R 198 TRP cc_start: 0.7192 (m100) cc_final: 0.6936 (m100) REVERT: T 500 MET cc_start: 0.2327 (mtm) cc_final: 0.1999 (mtp) outliers start: 19 outliers final: 11 residues processed: 214 average time/residue: 0.4553 time to fit residues: 145.4419 Evaluate side-chains 191 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 120 SER Chi-restraints excluded: chain K residue 3777 MET Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 124 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 105 optimal weight: 9.9990 chunk 203 optimal weight: 0.7980 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 165 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 46 HIS H 81 ASN N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.194684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.145971 restraints weight = 29086.767| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.52 r_work: 0.3294 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21497 Z= 0.133 Angle : 0.555 10.739 30287 Z= 0.319 Chirality : 0.039 0.154 3405 Planarity : 0.004 0.094 2831 Dihedral : 26.871 171.852 5175 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.02 % Allowed : 9.04 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.19), residues: 1802 helix: 1.49 (0.22), residues: 584 sheet: -2.18 (0.28), residues: 289 loop : -2.65 (0.17), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 279 HIS 0.009 0.001 HIS K3898 PHE 0.013 0.001 PHE K3904 TYR 0.013 0.001 TYR B 51 ARG 0.006 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 906) hydrogen bonds : angle 3.59893 ( 2292) metal coordination : bond 0.00136 ( 1) covalent geometry : bond 0.00277 (21495) covalent geometry : angle 0.55461 (30287) Misc. bond : bond 0.00052 ( 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 239 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 223 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 105 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7875 (tttm) REVERT: G 87 VAL cc_start: 0.9347 (t) cc_final: 0.9127 (t) REVERT: K 3874 TYR cc_start: 0.8115 (t80) cc_final: 0.7847 (t80) REVERT: K 3884 MET cc_start: 0.6447 (mmm) cc_final: 0.5853 (mtm) REVERT: K 3919 ASN cc_start: 0.7418 (m-40) cc_final: 0.7097 (t0) REVERT: K 3939 GLU cc_start: 0.7449 (tt0) cc_final: 0.7205 (tt0) REVERT: N 26 MET cc_start: 0.6283 (mmt) cc_final: 0.6030 (mpp) REVERT: N 183 GLN cc_start: 0.6177 (mp10) cc_final: 0.5813 (mp10) REVERT: R 198 TRP cc_start: 0.7106 (m100) cc_final: 0.5595 (m100) REVERT: T 380 LYS cc_start: 0.5129 (mtpt) cc_final: 0.4549 (ptpp) REVERT: T 500 MET cc_start: 0.2827 (mtm) cc_final: 0.2500 (mtp) outliers start: 16 outliers final: 11 residues processed: 233 average time/residue: 0.3753 time to fit residues: 128.0336 Evaluate side-chains 202 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR 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 183 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 153 optimal weight: 0.0060 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 HIS N 323 GLN ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.192436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.142696 restraints weight = 29078.078| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 1.53 r_work: 0.3252 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21497 Z= 0.164 Angle : 0.568 10.090 30287 Z= 0.325 Chirality : 0.040 0.146 3405 Planarity : 0.004 0.094 2831 Dihedral : 26.903 172.328 5175 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.21 % Allowed : 9.42 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.19), residues: 1802 helix: 1.67 (0.22), residues: 584 sheet: -1.99 (0.29), residues: 287 loop : -2.59 (0.17), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 279 HIS 0.006 0.001 HIS C 82 PHE 0.013 0.001 PHE N 104 TYR 0.019 0.001 TYR B 88 ARG 0.005 0.000 ARG T 367 Details of bonding type rmsd hydrogen bonds : bond 0.05820 ( 906) hydrogen bonds : angle 3.53559 ( 2292) metal coordination : bond 0.00091 ( 1) covalent geometry : bond 0.00365 (21495) covalent geometry : angle 0.56804 (30287) Misc. bond : bond 0.00048 ( 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 212 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.984 Fit side-chains revert: symmetry clash REVERT: G 61 GLU cc_start: 0.7741 (tt0) cc_final: 0.7459 (mt-10) REVERT: G 87 VAL cc_start: 0.9390 (t) cc_final: 0.9151 (t) REVERT: K 3874 TYR cc_start: 0.8076 (t80) cc_final: 0.7836 (t80) REVERT: K 3884 MET cc_start: 0.6579 (mmm) cc_final: 0.6084 (mtm) REVERT: K 3919 ASN cc_start: 0.7445 (m-40) cc_final: 0.7107 (t0) REVERT: K 3939 GLU cc_start: 0.7572 (tt0) cc_final: 0.7325 (tt0) REVERT: N 183 GLN cc_start: 0.6240 (mp10) cc_final: 0.5862 (mp10) REVERT: R 198 TRP cc_start: 0.7030 (m100) cc_final: 0.5738 (m100) REVERT: T 369 LYS cc_start: 0.1252 (tmtt) cc_final: 0.0499 (tptm) REVERT: T 373 LYS cc_start: 0.0689 (ttpt) cc_final: 0.0469 (mtpt) REVERT: T 380 LYS cc_start: 0.4928 (mtpt) cc_final: 0.4591 (ptpp) REVERT: T 500 MET cc_start: 0.2875 (mtm) cc_final: 0.2534 (mtp) outliers start: 19 outliers final: 15 residues processed: 208 average time/residue: 0.3640 time to fit residues: 113.0244 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 : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3828 LYS Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 323 GLN Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 59 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 4 optimal weight: 0.0470 chunk 87 optimal weight: 8.9990 chunk 113 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 153 optimal weight: 2.9990 chunk 186 optimal weight: 0.2980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.196137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.148639 restraints weight = 29506.818| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.54 r_work: 0.3323 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21497 Z= 0.125 Angle : 0.529 9.643 30287 Z= 0.305 Chirality : 0.038 0.230 3405 Planarity : 0.004 0.086 2831 Dihedral : 26.696 171.148 5175 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.34 % Allowed : 10.18 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.20), residues: 1802 helix: 2.14 (0.22), residues: 585 sheet: -1.72 (0.30), residues: 280 loop : -2.41 (0.18), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 321 HIS 0.003 0.001 HIS R 86 PHE 0.010 0.001 PHE K3904 TYR 0.010 0.001 TYR B 51 ARG 0.004 0.000 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 906) hydrogen bonds : angle 3.24953 ( 2292) metal coordination : bond 0.00096 ( 1) covalent geometry : bond 0.00258 (21495) covalent geometry : angle 0.52866 (30287) Misc. bond : bond 0.00036 ( 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 218 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: D 105 LYS cc_start: 0.8203 (ttmt) cc_final: 0.7990 (tttm) REVERT: G 71 ARG cc_start: 0.8569 (ttm-80) cc_final: 0.8355 (ttm110) REVERT: G 87 VAL cc_start: 0.9347 (t) cc_final: 0.9057 (t) REVERT: K 3884 MET cc_start: 0.6641 (mmm) cc_final: 0.5989 (mtm) REVERT: K 3891 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6764 (mm-30) REVERT: K 3939 GLU cc_start: 0.7608 (tt0) cc_final: 0.7359 (tt0) REVERT: N 26 MET cc_start: 0.6170 (mpp) cc_final: 0.5294 (ptp) REVERT: N 183 GLN cc_start: 0.6166 (mp10) cc_final: 0.5749 (mp10) REVERT: R 78 LYS cc_start: 0.7622 (tppt) cc_final: 0.7244 (tptp) REVERT: R 198 TRP cc_start: 0.7042 (m100) cc_final: 0.6841 (m100) REVERT: T 369 LYS cc_start: 0.1177 (tmtt) cc_final: 0.0525 (tptm) REVERT: T 380 LYS cc_start: 0.5010 (mtpt) cc_final: 0.4629 (ptpp) REVERT: T 500 MET cc_start: 0.3097 (mtm) cc_final: 0.2855 (mtp) outliers start: 21 outliers final: 13 residues processed: 213 average time/residue: 0.5883 time to fit residues: 187.7584 Evaluate side-chains 206 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 85 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 188 optimal weight: 0.4980 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 129 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS G 84 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 = 0.4247 r_free = 0.4247 target = 0.192096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142250 restraints weight = 28906.874| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.55 r_work: 0.3224 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21497 Z= 0.178 Angle : 0.574 9.288 30287 Z= 0.327 Chirality : 0.040 0.147 3405 Planarity : 0.005 0.092 2831 Dihedral : 26.877 172.988 5175 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.46 % Allowed : 10.76 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.59 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1802 helix: 1.89 (0.22), residues: 590 sheet: -1.65 (0.31), residues: 268 loop : -2.41 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 303 HIS 0.007 0.001 HIS C 82 PHE 0.013 0.002 PHE N 104 TYR 0.015 0.001 TYR B 51 ARG 0.004 0.000 ARG E 83 Details of bonding type rmsd hydrogen bonds : bond 0.06227 ( 906) hydrogen bonds : angle 3.35884 ( 2292) metal coordination : bond 0.00083 ( 1) covalent geometry : bond 0.00403 (21495) covalent geometry : angle 0.57414 (30287) Misc. bond : bond 0.00033 ( 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 214 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.674 Fit side-chains revert: symmetry clash REVERT: G 71 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8443 (ttm110) REVERT: K 3822 HIS cc_start: 0.7317 (m-70) cc_final: 0.7102 (m90) REVERT: K 3884 MET cc_start: 0.6803 (mmm) cc_final: 0.6006 (mtm) REVERT: K 3939 GLU cc_start: 0.7642 (tt0) cc_final: 0.7389 (tt0) REVERT: N 26 MET cc_start: 0.6237 (mpp) cc_final: 0.5448 (ptp) REVERT: N 183 GLN cc_start: 0.6121 (mp10) cc_final: 0.5654 (mp10) REVERT: R 78 LYS cc_start: 0.7543 (tppt) cc_final: 0.7166 (tptp) REVERT: R 198 TRP cc_start: 0.7101 (m100) cc_final: 0.6863 (m100) REVERT: T 369 LYS cc_start: 0.1295 (tmtt) cc_final: 0.0603 (tptm) REVERT: T 380 LYS cc_start: 0.4990 (mtpt) cc_final: 0.4615 (ptpp) REVERT: T 476 LYS cc_start: 0.5512 (pttt) cc_final: 0.4405 (mtpt) REVERT: T 500 MET cc_start: 0.3073 (mtm) cc_final: 0.2860 (mtp) outliers start: 23 outliers final: 18 residues processed: 210 average time/residue: 0.3502 time to fit residues: 109.6724 Evaluate side-chains 200 residues out of total 1574 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain H residue 82 LYS Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 3827 SER Chi-restraints excluded: chain K residue 3863 ILE Chi-restraints excluded: chain K residue 3866 ILE Chi-restraints excluded: chain N residue 28 LEU Chi-restraints excluded: chain N residue 135 LEU Chi-restraints excluded: chain N residue 168 THR Chi-restraints excluded: chain N residue 236 ASP Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 103 VAL Chi-restraints excluded: chain R residue 111 LEU Chi-restraints excluded: chain R residue 124 THR Chi-restraints excluded: chain R residue 187 VAL Chi-restraints excluded: chain T residue 384 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.5349 > 50: distance: 55 - 234: 29.744 distance: 58 - 231: 27.456 distance: 123 - 242: 36.710 distance: 148 - 211: 31.642 distance: 151 - 208: 36.211 distance: 191 - 196: 23.167 distance: 196 - 197: 25.728 distance: 197 - 198: 24.842 distance: 197 - 200: 4.838 distance: 198 - 199: 38.797 distance: 200 - 201: 18.964 distance: 201 - 203: 56.675 distance: 202 - 204: 22.575 distance: 203 - 205: 30.700 distance: 204 - 206: 4.676 distance: 205 - 206: 41.245 distance: 206 - 207: 36.538 distance: 209 - 210: 56.019 distance: 209 - 212: 37.089 distance: 210 - 211: 7.558 distance: 210 - 219: 40.913 distance: 212 - 213: 25.052 distance: 213 - 214: 16.780 distance: 213 - 215: 43.883 distance: 214 - 216: 27.519 distance: 215 - 217: 30.852 distance: 216 - 218: 7.580 distance: 217 - 218: 19.153 distance: 219 - 220: 14.546 distance: 219 - 225: 30.025 distance: 220 - 221: 50.664 distance: 220 - 223: 10.289 distance: 221 - 222: 52.801 distance: 221 - 226: 42.580 distance: 223 - 224: 41.859 distance: 224 - 225: 9.464 distance: 226 - 227: 31.117 distance: 227 - 228: 7.689 distance: 227 - 230: 43.531 distance: 228 - 229: 14.611 distance: 228 - 231: 30.243 distance: 231 - 232: 22.138 distance: 232 - 233: 42.911 distance: 232 - 235: 24.222 distance: 233 - 234: 25.471 distance: 233 - 239: 16.554 distance: 235 - 236: 17.777 distance: 235 - 237: 43.586 distance: 236 - 238: 56.132 distance: 239 - 240: 36.930 distance: 240 - 241: 16.137 distance: 240 - 243: 55.859 distance: 241 - 242: 14.199 distance: 241 - 245: 14.975 distance: 246 - 247: 39.567 distance: 246 - 249: 40.181 distance: 247 - 253: 56.515 distance: 250 - 251: 38.518 distance: 250 - 252: 56.278 distance: 254 - 255: 56.484 distance: 254 - 257: 12.658 distance: 255 - 256: 41.130 distance: 255 - 265: 54.530 distance: 257 - 258: 11.184 distance: 258 - 259: 55.387 distance: 258 - 260: 53.890 distance: 259 - 261: 14.588 distance: 260 - 262: 34.602 distance: 261 - 263: 30.154 distance: 262 - 263: 43.386 distance: 265 - 266: 51.876 distance: 266 - 267: 53.162 distance: 266 - 269: 42.344 distance: 267 - 268: 16.557 distance: 269 - 270: 42.450 distance: 270 - 271: 39.503 distance: 271 - 272: 39.391 distance: 272 - 273: 30.927 distance: 275 - 276: 40.061 distance: 275 - 278: 6.396 distance: 276 - 280: 34.835 distance: 278 - 279: 41.666