Starting phenix.real_space_refine on Wed Apr 8 03:08:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.map" model { file = "/net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z19_14445/04_2026/7z19_14445.cif" } resolution = 2.57 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= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 2 5.49 5 S 81 5.16 5 C 10607 2.51 5 N 2989 2.21 5 O 3705 1.98 5 H 16717 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34105 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2178 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 2, 'TRANS': 139} Chain: "B" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2950 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 177} Chain breaks: 1 Chain: "C" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5408 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 4331 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 20, 'TRANS': 255} Chain: "E" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2194 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 2955 Classifications: {'peptide': 192} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 177} Chain: "G" Number of atoms: 5408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5408 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 4317 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 20, 'TRANS': 254} Chain: "I" Number of atoms: 3873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3873 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 11, 'TRANS': 236} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "C" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 110 Classifications: {'water': 110} Link IDs: {None: 109} Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "F" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 114 Classifications: {'water': 114} Link IDs: {None: 113} Chain: "H" Number of atoms: 68 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 68 Classifications: {'water': 68} Link IDs: {None: 67} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14330 SG CYS D 241 89.302 39.075 41.502 1.00 80.25 S ATOM 14369 SG CYS D 244 88.990 38.847 38.062 1.00 82.43 S ATOM 14689 SG CYS D 266 86.972 41.042 39.840 1.00 79.72 S ATOM 14769 SG CYS D 272 86.753 36.919 40.189 1.00 81.84 S ATOM 29204 SG CYS H 241 27.503 65.764 101.278 1.00 79.62 S ATOM 29243 SG CYS H 244 28.037 66.742 104.649 1.00 83.62 S ATOM 29563 SG CYS H 266 30.491 66.907 102.398 1.00 79.59 S ATOM 29643 SG CYS H 272 28.987 63.217 103.464 1.00 81.82 S Residues with excluded nonbonded symmetry interactions: 115 residue: pdb="ZN ZN C 401 " occ=0.51 residue: pdb="ZN ZN G 401 " occ=0.54 residue: pdb=" O HOH A 202 " occ=0.95 residue: pdb=" O HOH A 205 " occ=0.92 residue: pdb=" O HOH A 212 " occ=0.86 residue: pdb=" O HOH A 215 " occ=0.96 residue: pdb=" O HOH A 216 " occ=0.99 residue: pdb=" O HOH A 217 " occ=0.99 residue: pdb=" O HOH A 218 " occ=0.88 residue: pdb=" O HOH A 222 " occ=0.75 residue: pdb=" O HOH A 227 " occ=0.86 residue: pdb=" O HOH A 233 " occ=0.89 ... (remaining 103 not shown) Time building chain proxies: 5.77, per 1000 atoms: 0.17 Number of scatterers: 34105 At special positions: 0 Unit cell: (109.56, 126.16, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 81 16.00 P 2 15.00 O 3705 8.00 N 2989 7.00 C 10607 6.00 H 16717 1.00 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=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 333 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 266 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 272 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 241 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 244 " pdb=" ZN G 401 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G 401 " - pdb=" NE2 HIS G 333 " pdb=" ZN H 301 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 244 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 272 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 266 " pdb="ZN ZN H 301 " - pdb=" SG CYS H 241 " Number of angles added : 12 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4042 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 45.7% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 88 through 103 removed outlier: 3.653A pdb=" N GLN A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 removed outlier: 4.288A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU A 113 " --> pdb=" O GLN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 136 removed outlier: 3.763A pdb=" N ALA A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 27 Processing helix chain 'B' and resid 46 through 56 Processing helix chain 'B' and resid 66 through 69 Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 88 through 92 Processing helix chain 'B' and resid 102 through 109 removed outlier: 3.556A pdb=" N LEU B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'C' and resid 7 through 25 Processing helix chain 'C' and resid 33 through 41 Processing helix chain 'C' and resid 41 through 53 Processing helix chain 'C' and resid 56 through 67 Processing helix chain 'C' and resid 70 through 85 removed outlier: 3.579A pdb=" N THR C 83 " --> pdb=" O ARG C 79 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 85 " --> pdb=" O TYR C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 99 Processing helix chain 'C' and resid 130 through 135 Processing helix chain 'C' and resid 154 through 162 Processing helix chain 'C' and resid 188 through 198 Processing helix chain 'C' and resid 200 through 213 Processing helix chain 'C' and resid 280 through 295 removed outlier: 4.245A pdb=" N ALA C 284 " --> pdb=" O SER C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 300 removed outlier: 3.650A pdb=" N TYR C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 308 Processing helix chain 'C' and resid 309 through 316 removed outlier: 3.617A pdb=" N HIS C 316 " --> pdb=" O PHE C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 329 through 331 No H-bonds generated for 'chain 'C' and resid 329 through 331' Processing helix chain 'C' and resid 333 through 352 Processing helix chain 'D' and resid 13 through 30 Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 76 through 91 Processing helix chain 'D' and resid 137 through 147 removed outlier: 4.080A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 165 removed outlier: 3.758A pdb=" N GLN D 154 " --> pdb=" O TYR D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 268 through 277 Processing helix chain 'E' and resid 4 through 18 Processing helix chain 'E' and resid 19 through 31 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 88 through 103 removed outlier: 3.556A pdb=" N ALA E 92 " --> pdb=" O ASP E 88 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN E 103 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 115 removed outlier: 4.541A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 136 removed outlier: 3.713A pdb=" N ALA E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 27 Processing helix chain 'F' and resid 45 through 56 Processing helix chain 'F' and resid 66 through 69 Processing helix chain 'F' and resid 70 through 80 Processing helix chain 'F' and resid 88 through 92 Processing helix chain 'F' and resid 102 through 109 Processing helix chain 'F' and resid 116 through 120 removed outlier: 3.814A pdb=" N GLY F 120 " --> pdb=" O PRO F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 164 Processing helix chain 'G' and resid 8 through 25 Processing helix chain 'G' and resid 33 through 41 Processing helix chain 'G' and resid 41 through 53 Processing helix chain 'G' and resid 56 through 67 Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.605A pdb=" N THR G 83 " --> pdb=" O ARG G 79 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 99 Processing helix chain 'G' and resid 130 through 135 removed outlier: 3.590A pdb=" N ALA G 135 " --> pdb=" O THR G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 162 Processing helix chain 'G' and resid 188 through 199 Processing helix chain 'G' and resid 200 through 213 Processing helix chain 'G' and resid 280 through 295 removed outlier: 3.896A pdb=" N ALA G 284 " --> pdb=" O SER G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 300 Processing helix chain 'G' and resid 305 through 308 Processing helix chain 'G' and resid 309 through 316 removed outlier: 3.662A pdb=" N HIS G 316 " --> pdb=" O PHE G 312 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 328 Processing helix chain 'G' and resid 329 through 331 No H-bonds generated for 'chain 'G' and resid 329 through 331' Processing helix chain 'G' and resid 333 through 351 removed outlier: 3.520A pdb=" N GLN G 351 " --> pdb=" O LEU G 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 12 removed outlier: 4.047A pdb=" N LEU H 12 " --> pdb=" O PHE H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 30 Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 76 through 91 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 137 through 148 removed outlier: 3.947A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 165 removed outlier: 3.571A pdb=" N GLN H 154 " --> pdb=" O TYR H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 Proline residue: H 194 - end of helix Processing helix chain 'H' and resid 268 through 278 Processing helix chain 'I' and resid 40 through 42 No H-bonds generated for 'chain 'I' and resid 40 through 42' Processing helix chain 'I' and resid 43 through 52 Processing helix chain 'I' and resid 73 through 84 removed outlier: 3.572A pdb=" N ARG I 82 " --> pdb=" O ARG I 78 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.822A pdb=" N GLY I 95 " --> pdb=" O HIS I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 114 removed outlier: 4.811A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 117 through 132 Processing helix chain 'I' and resid 135 through 139 removed outlier: 3.732A pdb=" N ARG I 138 " --> pdb=" O PRO I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 146 Processing helix chain 'I' and resid 147 through 161 Processing helix chain 'I' and resid 177 through 195 Processing helix chain 'I' and resid 205 through 213 removed outlier: 3.923A pdb=" N ALA I 209 " --> pdb=" O ASP I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 239 through 250 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 85 removed outlier: 5.320A pdb=" N ILE A 49 " --> pdb=" O ALA A 62 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP A 64 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 47 " --> pdb=" O ASP A 64 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR A 66 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY A 45 " --> pdb=" O THR A 66 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR A 68 " --> pdb=" O GLU A 43 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU A 43 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N ALA A 70 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N ALA A 41 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL A 72 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ILE A 39 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU A 74 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU A 37 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N LEU C 88 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N LEU A 46 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N VAL C 90 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN A 48 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 116 through 117 removed outlier: 4.399A pdb=" N GLN C 116 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL A 139 " --> pdb=" O GLY G 7 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLY G 7 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N PHE A 141 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL G 3 " --> pdb=" O THR A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 removed outlier: 6.843A pdb=" N LEU B 123 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N THR B 177 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LEU B 125 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ALA B 95 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N GLN B 126 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N THR B 97 " --> pdb=" O GLN B 126 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N TRP B 63 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASP B 98 " --> pdb=" O TRP B 63 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 147 through 149 Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.444A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 222 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL C 256 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 246 " --> pdb=" O VAL C 232 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE C 234 " --> pdb=" O ASN C 244 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN C 244 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR C 270 " --> pdb=" O ASN C 257 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.457A pdb=" N ILE D 104 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N GLN D 124 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N THR D 106 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N VAL D 65 " --> pdb=" O VAL D 103 " (cutoff:3.500A) removed outlier: 7.565A pdb=" N GLN D 105 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LYS D 67 " --> pdb=" O GLN D 105 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ARG D 107 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 69 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 181 through 183 removed outlier: 3.556A pdb=" N TYR D 181 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 251 through 255 Processing sheet with id=AB1, first strand: chain 'E' and resid 79 through 84 removed outlier: 5.311A pdb=" N PHE E 61 " --> pdb=" O ALA E 51 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ALA E 51 " --> pdb=" O PHE E 61 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLY E 63 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N ALA E 71 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA E 41 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ARG E 73 " --> pdb=" O ILE E 39 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE E 39 " --> pdb=" O ARG E 73 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU G 88 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N LEU E 46 " --> pdb=" O LEU G 88 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL G 90 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLN E 48 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 138 through 139 removed outlier: 4.328A pdb=" N GLN G 116 " --> pdb=" O VAL E 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 32 through 33 removed outlier: 6.696A pdb=" N LEU F 123 " --> pdb=" O ILE F 175 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N THR F 177 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU F 125 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA F 95 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N GLN F 126 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR F 97 " --> pdb=" O GLN F 126 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP F 63 " --> pdb=" O VAL F 96 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASP F 98 " --> pdb=" O TRP F 63 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 147 through 149 Processing sheet with id=AB5, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.465A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ALA G 222 " --> pdb=" O VAL G 256 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL G 256 " --> pdb=" O ALA G 222 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 246 " --> pdb=" O VAL G 232 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE G 234 " --> pdb=" O ASN G 244 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASN G 244 " --> pdb=" O ILE G 234 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR G 270 " --> pdb=" O ASN G 257 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 35 through 36 removed outlier: 6.462A pdb=" N ILE H 104 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N GLN H 124 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR H 106 " --> pdb=" O GLN H 124 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 181 through 183 Processing sheet with id=AB8, first strand: chain 'H' and resid 251 through 255 Processing sheet with id=AB9, first strand: chain 'I' and resid 21 through 26 removed outlier: 5.615A pdb=" N LEU I 11 " --> pdb=" O ASP I 23 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N SER I 25 " --> pdb=" O ASN I 9 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN I 9 " --> pdb=" O SER I 25 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL I 8 " --> pdb=" O HIS I 63 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N HIS I 63 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASN I 10 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU I 61 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 85 through 88 removed outlier: 6.249A pdb=" N GLY I 86 " --> pdb=" O PHE I 168 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N ASP I 170 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL I 88 " --> pdb=" O ASP I 170 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL I 167 " --> pdb=" O VAL I 200 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL I 202 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N MET I 169 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY I 38 " --> pdb=" O THR I 203 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 2181 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 16705 1.03 - 1.23: 83 1.23 - 1.42: 7024 1.42 - 1.62: 10003 1.62 - 1.81: 142 Bond restraints: 33957 Sorted by residual: bond pdb=" C ARG H 107 " pdb=" O ARG H 107 " ideal model delta sigma weight residual 1.234 1.141 0.093 1.17e-02 7.31e+03 6.38e+01 bond pdb=" C HIS G 333 " pdb=" O HIS G 333 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.26e-02 6.30e+03 2.52e+01 bond pdb=" C GLU B 192 " pdb=" O GLU B 192 " ideal model delta sigma weight residual 1.235 1.188 0.047 1.18e-02 7.18e+03 1.58e+01 bond pdb=" C HIS C 333 " pdb=" O HIS C 333 " ideal model delta sigma weight residual 1.235 1.192 0.043 1.12e-02 7.97e+03 1.49e+01 bond pdb=" C ARG D 107 " pdb=" O ARG D 107 " ideal model delta sigma weight residual 1.236 1.194 0.042 1.14e-02 7.69e+03 1.38e+01 ... (remaining 33952 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 60976 2.41 - 4.82: 380 4.82 - 7.23: 20 7.23 - 9.64: 3 9.64 - 12.04: 2 Bond angle restraints: 61381 Sorted by residual: angle pdb=" CA ARG H 107 " pdb=" C ARG H 107 " pdb=" N HIS H 108 " ideal model delta sigma weight residual 117.34 125.68 -8.34 1.22e+00 6.72e-01 4.67e+01 angle pdb=" CA ARG H 107 " pdb=" C ARG H 107 " pdb=" O ARG H 107 " ideal model delta sigma weight residual 120.42 110.65 9.77 1.48e+00 4.57e-01 4.36e+01 angle pdb=" CB GLN G 351 " pdb=" CG GLN G 351 " pdb=" CD GLN G 351 " ideal model delta sigma weight residual 112.60 103.81 8.79 1.70e+00 3.46e-01 2.67e+01 angle pdb=" N HIS G 333 " pdb=" CA HIS G 333 " pdb=" C HIS G 333 " ideal model delta sigma weight residual 111.71 104.87 6.84 1.34e+00 5.57e-01 2.61e+01 angle pdb=" CA ARG D 107 " pdb=" C ARG D 107 " pdb=" O ARG D 107 " ideal model delta sigma weight residual 120.40 115.39 5.01 1.05e+00 9.07e-01 2.28e+01 ... (remaining 61376 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 14620 17.82 - 35.64: 963 35.64 - 53.45: 274 53.45 - 71.27: 87 71.27 - 89.09: 52 Dihedral angle restraints: 15996 sinusoidal: 8858 harmonic: 7138 Sorted by residual: dihedral pdb=" CA LEU G 101 " pdb=" C LEU G 101 " pdb=" N GLU G 102 " pdb=" CA GLU G 102 " ideal model delta harmonic sigma weight residual 180.00 158.65 21.35 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA MET C 255 " pdb=" C MET C 255 " pdb=" N VAL C 256 " pdb=" CA VAL C 256 " ideal model delta harmonic sigma weight residual 180.00 163.70 16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA HIS I 239 " pdb=" C HIS I 239 " pdb=" N PRO I 240 " pdb=" CA PRO I 240 " ideal model delta harmonic sigma weight residual 180.00 -164.09 -15.91 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 15993 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2174 0.048 - 0.097: 334 0.097 - 0.145: 138 0.145 - 0.194: 8 0.194 - 0.242: 2 Chirality restraints: 2656 Sorted by residual: chirality pdb=" CA VAL B 191 " pdb=" N VAL B 191 " pdb=" C VAL B 191 " pdb=" CB VAL B 191 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA ARG I 67 " pdb=" N ARG I 67 " pdb=" C ARG I 67 " pdb=" CB ARG I 67 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CB VAL B 191 " pdb=" CA VAL B 191 " pdb=" CG1 VAL B 191 " pdb=" CG2 VAL B 191 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.00e-01 ... (remaining 2653 not shown) Planarity restraints: 5143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN G 352 " 0.019 2.00e-02 2.50e+03 4.42e-01 2.93e+03 pdb=" CG ASN G 352 " -0.003 2.00e-02 2.50e+03 pdb=" OD1 ASN G 352 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN G 352 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN G 352 " -0.763 2.00e-02 2.50e+03 pdb="HD22 ASN G 352 " 0.766 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 349 " -0.072 2.00e-02 2.50e+03 4.39e-01 2.89e+03 pdb=" CD GLN G 349 " 0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN G 349 " 0.071 2.00e-02 2.50e+03 pdb=" NE2 GLN G 349 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN G 349 " -0.757 2.00e-02 2.50e+03 pdb="HE22 GLN G 349 " 0.757 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 348 " -0.233 2.00e-02 2.50e+03 3.92e-01 2.31e+03 pdb=" CD GLN G 348 " 0.022 2.00e-02 2.50e+03 pdb=" OE1 GLN G 348 " 0.223 2.00e-02 2.50e+03 pdb=" NE2 GLN G 348 " 0.003 2.00e-02 2.50e+03 pdb="HE21 GLN G 348 " 0.633 2.00e-02 2.50e+03 pdb="HE22 GLN G 348 " -0.647 2.00e-02 2.50e+03 ... (remaining 5140 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2630 2.21 - 2.81: 72793 2.81 - 3.40: 99282 3.40 - 4.00: 136687 4.00 - 4.60: 209848 Nonbonded interactions: 521240 Sorted by model distance: nonbonded pdb=" O PHE H 86 " pdb=" HG1 THR H 90 " model vdw 1.609 2.450 nonbonded pdb=" O ASN A 31 " pdb="HD21 ASN A 31 " model vdw 1.612 2.450 nonbonded pdb=" OD1 ASP C 177 " pdb=" HG1 THR C 179 " model vdw 1.618 2.450 nonbonded pdb=" H CYS C 187 " pdb=" OE2 GLU C 310 " model vdw 1.621 2.450 nonbonded pdb="HH11 ARG F 137 " pdb=" OE1 GLU F 146 " model vdw 1.622 2.450 ... (remaining 521235 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' and resid 3 through 144) } ncs_group { reference = (chain 'B' and resid 3 through 194) selection = (chain 'F' and (resid 3 through 43 or resid 45 through 194)) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 4 through 302) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.230 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 41.340 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.070 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 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 : 0.006 0.222 17252 Z= 0.291 Angle : 0.677 25.813 23438 Z= 0.374 Chirality : 0.043 0.242 2656 Planarity : 0.004 0.050 3102 Dihedral : 13.359 89.040 6412 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.28 % Allowed : 0.55 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.19), residues: 2154 helix: 1.95 (0.19), residues: 842 sheet: -0.09 (0.28), residues: 360 loop : 0.11 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 180 TYR 0.021 0.001 TYR H 181 PHE 0.040 0.002 PHE C 156 TRP 0.064 0.003 TRP A 11 HIS 0.019 0.002 HIS H 108 Details of bonding type rmsd covalent geometry : bond 0.00514 (17240) covalent geometry : angle 0.61675 (23426) hydrogen bonds : bond 0.12599 ( 782) hydrogen bonds : angle 5.97066 ( 2181) metal coordination : bond 0.13326 ( 12) metal coordination : angle 12.38113 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 200 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.8066 (ptt) cc_final: 0.7833 (ptm) REVERT: E 122 ASP cc_start: 0.8187 (m-30) cc_final: 0.7948 (m-30) REVERT: I 84 GLU cc_start: 0.8292 (tt0) cc_final: 0.8080 (tt0) REVERT: I 127 LYS cc_start: 0.8867 (tmmt) cc_final: 0.8427 (tttm) REVERT: I 216 LEU cc_start: 0.8334 (tp) cc_final: 0.8109 (tm) outliers start: 5 outliers final: 1 residues processed: 203 average time/residue: 1.5497 time to fit residues: 349.0161 Evaluate side-chains 151 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 150 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN D 261 ASN G 319 ASN H 15 GLN ** I 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.077133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.061095 restraints weight = 95793.027| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.12 r_work: 0.2686 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2582 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17252 Z= 0.163 Angle : 0.527 6.991 23438 Z= 0.272 Chirality : 0.041 0.146 2656 Planarity : 0.004 0.050 3102 Dihedral : 4.191 57.779 2380 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.55 % Allowed : 5.38 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 2154 helix: 1.98 (0.18), residues: 848 sheet: -0.25 (0.28), residues: 359 loop : 0.09 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 22 TYR 0.014 0.001 TYR H 214 PHE 0.014 0.001 PHE D 86 TRP 0.034 0.001 TRP A 11 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00363 (17240) covalent geometry : angle 0.51835 (23426) hydrogen bonds : bond 0.04589 ( 782) hydrogen bonds : angle 5.09893 ( 2181) metal coordination : bond 0.01063 ( 12) metal coordination : angle 4.28328 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7857 (ptt) cc_final: 0.7584 (ptm) REVERT: E 122 ASP cc_start: 0.8584 (m-30) cc_final: 0.8260 (m-30) REVERT: G 180 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8466 (mtp85) REVERT: I 216 LEU cc_start: 0.8436 (tp) cc_final: 0.8214 (tm) outliers start: 10 outliers final: 2 residues processed: 161 average time/residue: 1.3012 time to fit residues: 236.5470 Evaluate side-chains 147 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 13 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 173 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN G 212 GLN G 319 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.075174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.059121 restraints weight = 95824.806| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.13 r_work: 0.2698 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 17252 Z= 0.235 Angle : 0.533 6.863 23438 Z= 0.274 Chirality : 0.042 0.143 2656 Planarity : 0.004 0.047 3102 Dihedral : 4.145 44.025 2378 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.78 % Allowed : 5.77 % Favored : 93.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.18), residues: 2154 helix: 1.98 (0.18), residues: 854 sheet: -0.37 (0.27), residues: 360 loop : 0.06 (0.20), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 137 TYR 0.014 0.001 TYR D 214 PHE 0.015 0.001 PHE D 86 TRP 0.028 0.002 TRP A 11 HIS 0.006 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00534 (17240) covalent geometry : angle 0.52578 (23426) hydrogen bonds : bond 0.04370 ( 782) hydrogen bonds : angle 4.89835 ( 2181) metal coordination : bond 0.01095 ( 12) metal coordination : angle 3.91399 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7920 (ptt) cc_final: 0.7623 (ptm) REVERT: D 261 ASN cc_start: 0.8458 (m-40) cc_final: 0.8075 (m-40) REVERT: E 122 ASP cc_start: 0.8595 (m-30) cc_final: 0.8317 (m-30) REVERT: G 26 ASP cc_start: 0.8449 (t0) cc_final: 0.8139 (t0) REVERT: I 216 LEU cc_start: 0.8487 (tp) cc_final: 0.8268 (tm) outliers start: 14 outliers final: 3 residues processed: 156 average time/residue: 1.2599 time to fit residues: 222.9242 Evaluate side-chains 147 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 171 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 213 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 154 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.076388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.060322 restraints weight = 95108.181| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.14 r_work: 0.2709 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17252 Z= 0.130 Angle : 0.491 5.825 23438 Z= 0.251 Chirality : 0.040 0.144 2656 Planarity : 0.004 0.072 3102 Dihedral : 4.008 37.351 2378 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.55 % Allowed : 6.32 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.19), residues: 2154 helix: 2.06 (0.18), residues: 854 sheet: -0.38 (0.28), residues: 359 loop : 0.09 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 67 TYR 0.014 0.001 TYR H 214 PHE 0.012 0.001 PHE D 86 TRP 0.023 0.001 TRP A 11 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00285 (17240) covalent geometry : angle 0.48483 (23426) hydrogen bonds : bond 0.03791 ( 782) hydrogen bonds : angle 4.69177 ( 2181) metal coordination : bond 0.00842 ( 12) metal coordination : angle 3.50612 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7898 (ptt) cc_final: 0.7631 (ptm) REVERT: D 261 ASN cc_start: 0.8453 (m-40) cc_final: 0.8075 (m-40) REVERT: E 122 ASP cc_start: 0.8573 (m-30) cc_final: 0.8326 (m-30) REVERT: G 26 ASP cc_start: 0.8480 (t0) cc_final: 0.8198 (t0) REVERT: G 51 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8612 (mt-10) REVERT: G 180 ARG cc_start: 0.8746 (mmm-85) cc_final: 0.8481 (mtp85) REVERT: I 196 ASN cc_start: 0.8471 (t0) cc_final: 0.8211 (t0) REVERT: I 216 LEU cc_start: 0.8488 (tp) cc_final: 0.8258 (tm) outliers start: 10 outliers final: 3 residues processed: 166 average time/residue: 1.3098 time to fit residues: 245.8305 Evaluate side-chains 152 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 174 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 chunk 14 optimal weight: 0.0000 chunk 26 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** D 108 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 = 0.3071 r_free = 0.3071 target = 0.076166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060142 restraints weight = 95447.056| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 2.14 r_work: 0.2704 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 17252 Z= 0.159 Angle : 0.496 5.771 23438 Z= 0.253 Chirality : 0.040 0.144 2656 Planarity : 0.004 0.056 3102 Dihedral : 3.972 33.559 2378 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.67 % Allowed : 6.93 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 2154 helix: 2.11 (0.18), residues: 854 sheet: -0.40 (0.28), residues: 359 loop : 0.10 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 134 TYR 0.013 0.001 TYR H 214 PHE 0.012 0.001 PHE D 86 TRP 0.019 0.001 TRP A 11 HIS 0.004 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00362 (17240) covalent geometry : angle 0.49007 (23426) hydrogen bonds : bond 0.03770 ( 782) hydrogen bonds : angle 4.62377 ( 2181) metal coordination : bond 0.00651 ( 12) metal coordination : angle 3.41520 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8495 (pt0) REVERT: A 144 MET cc_start: 0.7827 (ptt) cc_final: 0.7564 (ptm) REVERT: D 261 ASN cc_start: 0.8453 (m-40) cc_final: 0.8072 (m-40) REVERT: E 122 ASP cc_start: 0.8540 (m-30) cc_final: 0.8300 (m-30) REVERT: G 26 ASP cc_start: 0.8479 (t0) cc_final: 0.8186 (t0) REVERT: G 51 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8599 (mt-10) REVERT: I 50 SER cc_start: 0.9441 (OUTLIER) cc_final: 0.8898 (p) REVERT: I 196 ASN cc_start: 0.8480 (t0) cc_final: 0.8202 (t0) REVERT: I 216 LEU cc_start: 0.8492 (tp) cc_final: 0.8266 (tm) outliers start: 12 outliers final: 2 residues processed: 153 average time/residue: 1.1916 time to fit residues: 208.4064 Evaluate side-chains 149 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 144 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Chi-restraints excluded: chain I residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 184 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 46 optimal weight: 0.4980 chunk 79 optimal weight: 0.8980 chunk 190 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.077087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.060989 restraints weight = 95002.698| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.14 r_work: 0.2716 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 17252 Z= 0.114 Angle : 0.477 5.636 23438 Z= 0.242 Chirality : 0.040 0.145 2656 Planarity : 0.004 0.073 3102 Dihedral : 3.885 30.985 2378 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.67 % Allowed : 6.88 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.19), residues: 2154 helix: 2.18 (0.18), residues: 854 sheet: -0.39 (0.28), residues: 359 loop : 0.14 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR H 214 PHE 0.011 0.001 PHE D 86 TRP 0.018 0.001 TRP A 11 HIS 0.004 0.001 HIS I 239 Details of bonding type rmsd covalent geometry : bond 0.00259 (17240) covalent geometry : angle 0.47116 (23426) hydrogen bonds : bond 0.03530 ( 782) hydrogen bonds : angle 4.52407 ( 2181) metal coordination : bond 0.00569 ( 12) metal coordination : angle 3.22114 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 155 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: A 144 MET cc_start: 0.7834 (ptt) cc_final: 0.7569 (ptm) REVERT: D 261 ASN cc_start: 0.8471 (m-40) cc_final: 0.8086 (m-40) REVERT: E 122 ASP cc_start: 0.8538 (m-30) cc_final: 0.8294 (m-30) REVERT: G 26 ASP cc_start: 0.8476 (t0) cc_final: 0.8189 (t0) REVERT: G 180 ARG cc_start: 0.8741 (mmm-85) cc_final: 0.8465 (mtp85) REVERT: I 50 SER cc_start: 0.9430 (m) cc_final: 0.8892 (p) REVERT: I 196 ASN cc_start: 0.8468 (t0) cc_final: 0.8159 (t0) REVERT: I 216 LEU cc_start: 0.8489 (tp) cc_final: 0.8263 (tm) outliers start: 12 outliers final: 2 residues processed: 162 average time/residue: 1.2460 time to fit residues: 229.7931 Evaluate side-chains 155 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 152 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 97 optimal weight: 0.7980 chunk 213 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN B 58 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 131 GLN F 82 ASN H 15 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.075973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.060033 restraints weight = 96028.732| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.13 r_work: 0.2690 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17252 Z= 0.215 Angle : 0.509 5.979 23438 Z= 0.260 Chirality : 0.041 0.142 2656 Planarity : 0.004 0.048 3102 Dihedral : 3.935 25.425 2378 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.72 % Allowed : 7.04 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 2154 helix: 2.16 (0.18), residues: 854 sheet: -0.42 (0.28), residues: 359 loop : 0.11 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.013 0.001 TYR D 214 PHE 0.012 0.001 PHE D 86 TRP 0.018 0.001 TRP A 11 HIS 0.005 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00492 (17240) covalent geometry : angle 0.50347 (23426) hydrogen bonds : bond 0.03850 ( 782) hydrogen bonds : angle 4.55591 ( 2181) metal coordination : bond 0.00833 ( 12) metal coordination : angle 3.36153 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8556 (pt0) REVERT: A 144 MET cc_start: 0.7862 (ptt) cc_final: 0.7606 (ptm) REVERT: D 261 ASN cc_start: 0.8447 (m-40) cc_final: 0.8068 (m-40) REVERT: E 122 ASP cc_start: 0.8536 (m-30) cc_final: 0.8317 (m-30) REVERT: G 26 ASP cc_start: 0.8507 (t0) cc_final: 0.8227 (t0) REVERT: G 51 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: G 180 ARG cc_start: 0.8770 (mmm-85) cc_final: 0.8535 (mtp85) REVERT: I 50 SER cc_start: 0.9447 (OUTLIER) cc_final: 0.8906 (p) REVERT: I 196 ASN cc_start: 0.8488 (t0) cc_final: 0.8182 (t0) REVERT: I 216 LEU cc_start: 0.8531 (tp) cc_final: 0.8302 (tm) outliers start: 13 outliers final: 3 residues processed: 155 average time/residue: 1.1923 time to fit residues: 211.2564 Evaluate side-chains 154 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 148 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain G residue 51 GLU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 130 GLU Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 97 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 209 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 105 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.2980 chunk 59 optimal weight: 0.0870 chunk 181 optimal weight: 0.0970 chunk 176 optimal weight: 1.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN G 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.062216 restraints weight = 94974.344| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.13 r_work: 0.2747 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17252 Z= 0.089 Angle : 0.468 5.183 23438 Z= 0.238 Chirality : 0.040 0.147 2656 Planarity : 0.004 0.049 3102 Dihedral : 3.792 25.830 2378 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.55 % Allowed : 7.32 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2154 helix: 2.25 (0.18), residues: 855 sheet: -0.44 (0.28), residues: 362 loop : 0.19 (0.20), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 67 TYR 0.018 0.001 TYR I 241 PHE 0.010 0.001 PHE B 18 TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00197 (17240) covalent geometry : angle 0.46315 (23426) hydrogen bonds : bond 0.03334 ( 782) hydrogen bonds : angle 4.42655 ( 2181) metal coordination : bond 0.00422 ( 12) metal coordination : angle 3.06301 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: A 144 MET cc_start: 0.7817 (ptt) cc_final: 0.7570 (ptm) REVERT: D 258 ASP cc_start: 0.8611 (p0) cc_final: 0.8308 (p0) REVERT: D 261 ASN cc_start: 0.8443 (m-40) cc_final: 0.8052 (m-40) REVERT: E 122 ASP cc_start: 0.8512 (m-30) cc_final: 0.8295 (m-30) REVERT: F 13 ASP cc_start: 0.8948 (m-30) cc_final: 0.8737 (m-30) REVERT: G 26 ASP cc_start: 0.8452 (t0) cc_final: 0.8167 (t0) REVERT: G 180 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.8481 (mtp85) REVERT: I 50 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.8919 (p) REVERT: I 196 ASN cc_start: 0.8421 (t0) cc_final: 0.8095 (t0) REVERT: I 216 LEU cc_start: 0.8493 (tp) cc_final: 0.8275 (tm) outliers start: 10 outliers final: 2 residues processed: 159 average time/residue: 1.2105 time to fit residues: 218.9784 Evaluate side-chains 154 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 150 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 22 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 109 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 131 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN D 3 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.076284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.060306 restraints weight = 95369.834| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.13 r_work: 0.2660 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2552 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2552 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 17252 Z= 0.175 Angle : 0.491 5.640 23438 Z= 0.250 Chirality : 0.040 0.143 2656 Planarity : 0.004 0.050 3102 Dihedral : 3.819 21.707 2378 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.50 % Allowed : 7.60 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.19), residues: 2154 helix: 2.29 (0.18), residues: 854 sheet: -0.41 (0.28), residues: 348 loop : 0.15 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 67 TYR 0.013 0.001 TYR D 214 PHE 0.011 0.001 PHE D 86 TRP 0.017 0.001 TRP A 11 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00403 (17240) covalent geometry : angle 0.48602 (23426) hydrogen bonds : bond 0.03604 ( 782) hydrogen bonds : angle 4.44928 ( 2181) metal coordination : bond 0.00638 ( 12) metal coordination : angle 3.17631 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8479 (pt0) REVERT: A 144 MET cc_start: 0.7731 (ptt) cc_final: 0.7454 (ptm) REVERT: D 258 ASP cc_start: 0.8693 (p0) cc_final: 0.8383 (p0) REVERT: D 261 ASN cc_start: 0.8417 (m-40) cc_final: 0.8020 (m-40) REVERT: E 122 ASP cc_start: 0.8489 (m-30) cc_final: 0.8251 (m-30) REVERT: G 26 ASP cc_start: 0.8447 (t0) cc_final: 0.8142 (t0) REVERT: I 50 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.8930 (p) REVERT: I 196 ASN cc_start: 0.8477 (t0) cc_final: 0.8159 (t0) REVERT: I 216 LEU cc_start: 0.8493 (tp) cc_final: 0.8254 (tm) outliers start: 9 outliers final: 1 residues processed: 156 average time/residue: 1.2601 time to fit residues: 223.2919 Evaluate side-chains 152 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 149 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 109 optimal weight: 0.0870 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 189 optimal weight: 2.9990 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN G 319 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.077477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061501 restraints weight = 95607.758| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.13 r_work: 0.2707 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17252 Z= 0.124 Angle : 0.479 5.395 23438 Z= 0.243 Chirality : 0.040 0.145 2656 Planarity : 0.004 0.087 3102 Dihedral : 3.785 19.854 2378 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.33 % Allowed : 7.76 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 2154 helix: 2.31 (0.18), residues: 854 sheet: -0.54 (0.29), residues: 326 loop : 0.14 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 180 TYR 0.012 0.001 TYR H 214 PHE 0.011 0.001 PHE D 86 TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS C 333 Details of bonding type rmsd covalent geometry : bond 0.00284 (17240) covalent geometry : angle 0.47349 (23426) hydrogen bonds : bond 0.03448 ( 782) hydrogen bonds : angle 4.39985 ( 2181) metal coordination : bond 0.00544 ( 12) metal coordination : angle 3.11788 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8522 (pt0) REVERT: A 144 MET cc_start: 0.7803 (ptt) cc_final: 0.7544 (ptm) REVERT: D 258 ASP cc_start: 0.8639 (p0) cc_final: 0.8329 (p0) REVERT: D 261 ASN cc_start: 0.8434 (m-40) cc_final: 0.8038 (m-40) REVERT: E 122 ASP cc_start: 0.8514 (m-30) cc_final: 0.8281 (m-30) REVERT: G 26 ASP cc_start: 0.8472 (t0) cc_final: 0.8183 (t0) REVERT: G 180 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.8467 (mtp85) REVERT: I 50 SER cc_start: 0.9433 (OUTLIER) cc_final: 0.8910 (p) REVERT: I 196 ASN cc_start: 0.8437 (t0) cc_final: 0.8115 (t0) REVERT: I 216 LEU cc_start: 0.8511 (tp) cc_final: 0.8288 (tm) outliers start: 6 outliers final: 1 residues processed: 156 average time/residue: 1.2392 time to fit residues: 219.5851 Evaluate side-chains 153 residues out of total 1803 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 150 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 191 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 ASN D 3 ASN ** D 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 ASN G 319 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.077184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.061167 restraints weight = 95202.810| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.13 r_work: 0.2710 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17252 Z= 0.122 Angle : 0.475 5.349 23438 Z= 0.241 Chirality : 0.040 0.145 2656 Planarity : 0.004 0.070 3102 Dihedral : 3.739 17.800 2378 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.33 % Allowed : 7.99 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 2154 helix: 2.34 (0.18), residues: 854 sheet: -0.54 (0.29), residues: 328 loop : 0.18 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 67 TYR 0.013 0.001 TYR D 214 PHE 0.011 0.001 PHE D 86 TRP 0.018 0.001 TRP A 11 HIS 0.003 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00278 (17240) covalent geometry : angle 0.47033 (23426) hydrogen bonds : bond 0.03395 ( 782) hydrogen bonds : angle 4.36927 ( 2181) metal coordination : bond 0.00476 ( 12) metal coordination : angle 3.04705 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10498.80 seconds wall clock time: 178 minutes 6.75 seconds (10686.75 seconds total)