Starting phenix.real_space_refine on Thu Mar 5 03:46:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.map" model { file = "/net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0w_14224/03_2026/7r0w_14224.cif" } resolution = 2.8 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= 0.005 sd= 0.036 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 Fe 12 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 11209 2.51 5 N 2586 2.21 5 O 2933 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16830 Number of models: 1 Model: "" Number of chains: 32 Chain: "X" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "I" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "J" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "K" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2115 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "M" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "N" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "O" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "P" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1769 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 212} Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1223 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2115 Classifications: {'peptide': 279} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 257} Chain breaks: 1 Chain: "D" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1256 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "E" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 238 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "F" Number of atoms: 248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 248 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "G" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "H" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 234 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 1256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1256 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 10, 'TRANS': 158} Chain breaks: 1 Chain: "V" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 500 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "I" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 209 Unusual residues: {'ECH': 1, 'HEM': 3, 'PGV': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 161 Unusual residues: {'CLA': 1, 'PGV': 1, 'PL9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 10 Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 55 Unusual residues: {'LMG': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'ECH': 1, 'HEM': 2, 'PL9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'2WA': 1, 'CLA': 1, 'HEM': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'HEC': 1, 'PGV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12395 SG CYS D 120 39.548 55.252 52.072 1.00132.65 S ATOM 12535 SG CYS D 138 40.960 50.958 51.417 1.00140.44 S ATOM 14613 SG CYS L 120 102.025 55.430 44.575 1.00143.08 S ATOM 14753 SG CYS L 138 100.229 57.365 42.020 1.00145.78 S Time building chain proxies: 4.12, per 1000 atoms: 0.24 Number of scatterers: 16830 At special positions: 0 Unit cell: (138.86, 125.08, 135.68, 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) Fe 12 26.01 S 82 16.00 P 6 15.00 Mg 2 11.99 O 2933 8.00 N 2586 7.00 C 11209 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 140 " distance=2.04 Simple disulfide: pdb=" SG CYS L 125 " - pdb=" SG CYS L 140 " distance=2.03 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 724.0 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 201 " pdb="FE2 FES D 201 " - pdb=" ND1 HIS D 141 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 138 " pdb="FE1 FES D 201 " - pdb=" SG CYS D 120 " pdb="FE2 FES D 201 " - pdb=" NE2 HIS D 122 " pdb=" FES L 202 " pdb="FE2 FES L 202 " - pdb=" ND1 HIS L 141 " pdb="FE1 FES L 202 " - pdb=" SG CYS L 120 " pdb="FE2 FES L 202 " - pdb=" NE2 HIS L 122 " pdb="FE1 FES L 202 " - pdb=" SG CYS L 138 " Number of angles added : 6 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3672 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 19 sheets defined 50.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'X' and resid 19 through 26 Processing helix chain 'X' and resid 38 through 42 removed outlier: 3.713A pdb=" N GLY X 42 " --> pdb=" O ASP X 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 9 through 20 Processing helix chain 'I' and resid 21 through 31 removed outlier: 3.948A pdb=" N LYS I 31 " --> pdb=" O ASP I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 38 through 40 No H-bonds generated for 'chain 'I' and resid 38 through 40' Processing helix chain 'I' and resid 41 through 63 removed outlier: 4.506A pdb=" N GLY I 45 " --> pdb=" O TYR I 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE I 63 " --> pdb=" O PHE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 81 Processing helix chain 'I' and resid 85 through 114 Processing helix chain 'I' and resid 121 through 145 removed outlier: 3.575A pdb=" N SER I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU I 145 " --> pdb=" O THR I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 161 Processing helix chain 'I' and resid 162 through 165 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.992A pdb=" N GLN I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 196 Processing helix chain 'I' and resid 196 through 217 Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 23 through 27 removed outlier: 3.816A pdb=" N TYR J 26 " --> pdb=" O GLY J 23 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N TYR J 27 " --> pdb=" O HIS J 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 23 through 27' Processing helix chain 'J' and resid 38 through 58 removed outlier: 3.748A pdb=" N ILE J 42 " --> pdb=" O TYR J 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS J 43 " --> pdb=" O MET J 39 " (cutoff:3.500A) Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 91 Processing helix chain 'J' and resid 93 through 116 Proline residue: J 105 - end of helix Proline residue: J 112 - end of helix Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 149 removed outlier: 3.949A pdb=" N THR J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 20 through 25 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 122 through 124 No H-bonds generated for 'chain 'K' and resid 122 through 124' Processing helix chain 'K' and resid 247 through 284 removed outlier: 3.556A pdb=" N ILE K 251 " --> pdb=" O ASN K 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 29 Processing helix chain 'N' and resid 3 through 6 Processing helix chain 'N' and resid 7 through 33 removed outlier: 3.537A pdb=" N LEU N 19 " --> pdb=" O ILE N 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 30 Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 20 through 31 removed outlier: 4.289A pdb=" N ILE A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 63 removed outlier: 4.522A pdb=" N GLY A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 63 " --> pdb=" O PHE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 81 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.525A pdb=" N SER A 98 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 144 removed outlier: 3.589A pdb=" N SER A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 168 through 178 Processing helix chain 'A' and resid 183 through 196 Processing helix chain 'A' and resid 196 through 217 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.724A pdb=" N TYR B 26 " --> pdb=" O GLY B 23 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR B 27 " --> pdb=" O HIS B 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 23 through 27' Processing helix chain 'B' and resid 38 through 58 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 91 Processing helix chain 'B' and resid 93 through 116 Proline residue: B 105 - end of helix removed outlier: 3.603A pdb=" N VAL B 111 " --> pdb=" O GLY B 107 " (cutoff:3.500A) Proline residue: B 112 - end of helix Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 148 removed outlier: 3.784A pdb=" N THR B 148 " --> pdb=" O GLY B 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 20 through 25 Processing helix chain 'C' and resid 91 through 99 Processing helix chain 'C' and resid 247 through 284 removed outlier: 3.544A pdb=" N ILE C 251 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 55 Proline residue: D 49 - end of helix Processing helix chain 'D' and resid 77 through 82 Processing helix chain 'D' and resid 96 through 98 No H-bonds generated for 'chain 'D' and resid 96 through 98' Processing helix chain 'E' and resid 2 through 29 Processing helix chain 'F' and resid 3 through 6 Processing helix chain 'F' and resid 7 through 32 Processing helix chain 'G' and resid 3 through 30 Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 26 Processing helix chain 'L' and resid 24 through 55 Proline residue: L 49 - end of helix Processing helix chain 'L' and resid 77 through 84 Processing helix chain 'L' and resid 96 through 98 No H-bonds generated for 'chain 'L' and resid 96 through 98' Processing helix chain 'V' and resid 19 through 26 removed outlier: 3.575A pdb=" N LEU V 26 " --> pdb=" O VAL V 22 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 54 through 57 removed outlier: 6.492A pdb=" N VAL X 46 " --> pdb=" O LYS X 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 32 through 33 Processing sheet with id=AA3, first strand: chain 'K' and resid 33 through 35 removed outlier: 3.641A pdb=" N VAL K 49 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS K 83 " --> pdb=" O LEU K 132 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 39 through 40 removed outlier: 6.318A pdb=" N ALA K 74 " --> pdb=" O GLY K 117 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY K 117 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU K 76 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N ILE K 115 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN K 104 " --> pdb=" O ILE K 115 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 60 through 61 Processing sheet with id=AA6, first strand: chain 'K' and resid 191 through 193 Processing sheet with id=AA7, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.639A pdb=" N VAL C 49 " --> pdb=" O GLU C 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 83 " --> pdb=" O LEU C 132 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 39 through 40 removed outlier: 6.450A pdb=" N ALA C 74 " --> pdb=" O GLY C 117 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLY C 117 " --> pdb=" O ALA C 74 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LEU C 76 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE C 115 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 39 through 40 Processing sheet with id=AB2, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AB3, first strand: chain 'C' and resid 191 through 193 Processing sheet with id=AB4, first strand: chain 'D' and resid 91 through 94 removed outlier: 4.024A pdb=" N VAL D 91 " --> pdb=" O ILE D 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 114 through 116 Processing sheet with id=AB6, first strand: chain 'D' and resid 129 through 130 removed outlier: 3.534A pdb=" N ASN D 130 " --> pdb=" O LYS D 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AB8, first strand: chain 'L' and resid 90 through 94 removed outlier: 3.873A pdb=" N VAL L 91 " --> pdb=" O ILE L 103 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 129 through 130 removed outlier: 3.662A pdb=" N ASN L 130 " --> pdb=" O LYS L 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 55 through 57 removed outlier: 3.965A pdb=" N ASP V 34 " --> pdb=" O VAL V 46 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N SER V 48 " --> pdb=" O VAL V 32 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N VAL V 32 " --> pdb=" O SER V 48 " (cutoff:3.500A) 838 hydrogen bonds defined for protein. 2409 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: 2.87 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6605 1.39 - 1.59: 10468 1.59 - 1.80: 97 1.80 - 2.00: 52 2.00 - 2.21: 48 Bond restraints: 17270 Sorted by residual: bond pdb=" C5 LMG N 101 " pdb=" O6 LMG N 101 " ideal model delta sigma weight residual 1.413 1.342 0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" CD LYS X 63 " pdb=" CE LYS X 63 " ideal model delta sigma weight residual 1.520 1.454 0.066 3.00e-02 1.11e+03 4.83e+00 bond pdb=" C4 LMG N 101 " pdb=" C5 LMG N 101 " ideal model delta sigma weight residual 1.531 1.491 0.040 2.00e-02 2.50e+03 4.08e+00 bond pdb=" C1 LMG N 101 " pdb=" C2 LMG N 101 " ideal model delta sigma weight residual 1.525 1.563 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C2 LMG N 101 " pdb=" C3 LMG N 101 " ideal model delta sigma weight residual 1.525 1.563 -0.038 2.00e-02 2.50e+03 3.57e+00 ... (remaining 17265 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 23109 3.10 - 6.21: 332 6.21 - 9.31: 56 9.31 - 12.41: 20 12.41 - 15.52: 2 Bond angle restraints: 23519 Sorted by residual: angle pdb=" CA LYS D 97 " pdb=" CB LYS D 97 " pdb=" CG LYS D 97 " ideal model delta sigma weight residual 114.10 125.34 -11.24 2.00e+00 2.50e-01 3.16e+01 angle pdb=" C10 CLA B 302 " pdb=" C8 CLA B 302 " pdb=" C9 CLA B 302 " ideal model delta sigma weight residual 110.21 125.73 -15.52 3.00e+00 1.11e-01 2.68e+01 angle pdb=" C1 6PL P 101 " pdb=" C2 6PL P 101 " pdb=" C3 6PL P 101 " ideal model delta sigma weight residual 114.77 127.74 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA ARG X 52 " pdb=" CB ARG X 52 " pdb=" CG ARG X 52 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" CB LYS X 63 " pdb=" CG LYS X 63 " pdb=" CD LYS X 63 " ideal model delta sigma weight residual 111.30 120.19 -8.89 2.30e+00 1.89e-01 1.49e+01 ... (remaining 23514 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.13: 9449 34.13 - 68.25: 485 68.25 - 102.38: 77 102.38 - 136.50: 9 136.50 - 170.63: 5 Dihedral angle restraints: 10025 sinusoidal: 4271 harmonic: 5754 Sorted by residual: dihedral pdb=" CB CYS D 125 " pdb=" SG CYS D 125 " pdb=" SG CYS D 140 " pdb=" CB CYS D 140 " ideal model delta sinusoidal sigma weight residual 93.00 18.01 74.99 1 1.00e+01 1.00e-02 7.11e+01 dihedral pdb=" C2C HEM B 301 " pdb=" C3C HEM B 301 " pdb=" CAC HEM B 301 " pdb=" CBC HEM B 301 " ideal model delta sinusoidal sigma weight residual -180.00 -102.88 -77.12 2 1.00e+01 1.00e-02 4.56e+01 dihedral pdb=" C2C HEC K 301 " pdb=" C3C HEC K 301 " pdb=" CAC HEC K 301 " pdb=" CBC HEC K 301 " ideal model delta sinusoidal sigma weight residual 240.00 169.44 70.56 2 1.00e+01 1.00e-02 4.27e+01 ... (remaining 10022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.631: 2551 0.631 - 1.261: 0 1.261 - 1.892: 0 1.892 - 2.522: 5 2.522 - 3.153: 1 Chirality restraints: 2557 Sorted by residual: chirality pdb=" C5 LMG N 101 " pdb=" C4 LMG N 101 " pdb=" C6 LMG N 101 " pdb=" O6 LMG N 101 " both_signs ideal model delta sigma weight residual False -2.46 0.69 -3.15 2.00e-01 2.50e+01 2.49e+02 chirality pdb=" C2 6PL H 101 " pdb=" C1 6PL H 101 " pdb=" C3 6PL H 101 " pdb=" O2 6PL H 101 " both_signs ideal model delta sigma weight residual False -2.33 0.11 -2.44 2.00e-01 2.50e+01 1.49e+02 chirality pdb=" C2 6PL P 101 " pdb=" C1 6PL P 101 " pdb=" C3 6PL P 101 " pdb=" O2 6PL P 101 " both_signs ideal model delta sigma weight residual False -2.33 -0.08 -2.25 2.00e-01 2.50e+01 1.27e+02 ... (remaining 2554 not shown) Planarity restraints: 2868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 301 " -0.018 2.00e-02 2.50e+03 5.53e-02 6.88e+01 pdb=" C2C HEC K 301 " 0.152 2.00e-02 2.50e+03 pdb=" C3C HEC K 301 " -0.028 2.00e-02 2.50e+03 pdb=" C4C HEC K 301 " -0.009 2.00e-02 2.50e+03 pdb=" CAC HEC K 301 " -0.026 2.00e-02 2.50e+03 pdb=" CHC HEC K 301 " -0.026 2.00e-02 2.50e+03 pdb=" CHD HEC K 301 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC K 301 " -0.043 2.00e-02 2.50e+03 pdb=" NC HEC K 301 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG X 52 " -0.021 2.00e-02 2.50e+03 4.20e-02 1.77e+01 pdb=" C ARG X 52 " 0.073 2.00e-02 2.50e+03 pdb=" O ARG X 52 " -0.027 2.00e-02 2.50e+03 pdb=" N THR X 53 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU N 22 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.47e+00 pdb=" C LEU N 22 " -0.053 2.00e-02 2.50e+03 pdb=" O LEU N 22 " 0.020 2.00e-02 2.50e+03 pdb=" N ALA N 23 " 0.018 2.00e-02 2.50e+03 ... (remaining 2865 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 184 2.62 - 3.19: 16026 3.19 - 3.76: 28333 3.76 - 4.33: 41174 4.33 - 4.90: 65089 Nonbonded interactions: 150806 Sorted by model distance: nonbonded pdb=" O ARG V 52 " pdb=" NH1 ARG V 52 " model vdw 2.048 3.120 nonbonded pdb=" N GLU A 180 " pdb=" OE1 GLU A 180 " model vdw 2.169 3.120 nonbonded pdb=" O ASN L 134 " pdb=" OD1 ASN L 134 " model vdw 2.184 3.040 nonbonded pdb=" OD1 ASP V 21 " pdb=" N VAL V 22 " model vdw 2.189 3.120 nonbonded pdb=" OD1 ASP D 70 " pdb=" N ALA D 71 " model vdw 2.198 3.120 ... (remaining 150801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 302) selection = (chain 'I' and resid 1 through 302) } ncs_group { reference = (chain 'B' and (resid 2 through 160 or resid 302)) selection = (chain 'J' and (resid 2 through 160 or resid 202)) } ncs_group { reference = (chain 'C' and resid 1 through 285) selection = (chain 'K' and resid 1 through 285) } ncs_group { reference = (chain 'D' and resid 21 through 192) selection = (chain 'L' and resid 21 through 192) } ncs_group { reference = (chain 'E' and resid 1 through 32) selection = chain 'M' } ncs_group { reference = chain 'F' selection = (chain 'N' and resid 1 through 34) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = (chain 'H' and (resid 1 through 29 or (resid 101 and (name N or name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C20 or name C21 or name C22 or name C23 o \ r name C24 or name C25 or name C26 or name C3 or name C31 or name C32 or name C3 \ 3 or name C34 or name C35 or name C36 or name C37 or name C38 or name C39 or nam \ e C4 or name C40 or name C41 or name C42 or name C43 or name C44 or name C45 or \ name C46 or name C47 or name C5 or name C6 or name C7 or name C8 or name O11 or \ name O1P or name O2 or name O2P or name O3 or name O31 or name O3P or name O4P o \ r name P )))) selection = chain 'P' } ncs_group { reference = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.710 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.950 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 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 : 0.013 1.129 17292 Z= 0.346 Angle : 1.015 37.261 23529 Z= 0.450 Chirality : 0.124 3.153 2557 Planarity : 0.006 0.055 2868 Dihedral : 20.394 170.631 6347 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.84 % Allowed : 22.89 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.64 (0.16), residues: 1996 helix: -1.54 (0.14), residues: 959 sheet: -2.80 (0.32), residues: 195 loop : -1.52 (0.18), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG X 52 TYR 0.032 0.002 TYR X 12 PHE 0.032 0.002 PHE I 138 TRP 0.033 0.003 TRP N 24 HIS 0.009 0.002 HIS I 209 Details of bonding type rmsd covalent geometry : bond 0.00467 (17270) covalent geometry : angle 0.96277 (23519) SS BOND : bond 0.00644 ( 2) SS BOND : angle 2.35826 ( 4) hydrogen bonds : bond 0.13769 ( 831) hydrogen bonds : angle 7.49351 ( 2409) metal coordination : bond 0.54250 ( 8) metal coordination : angle 20.05180 ( 6) Misc. bond : bond 0.15649 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 407 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 28 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7297 (tptm) REVERT: I 20 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7935 (tm-30) REVERT: D 81 PHE cc_start: 0.8954 (t80) cc_final: 0.8647 (t80) REVERT: D 99 ASP cc_start: 0.7776 (m-30) cc_final: 0.7419 (m-30) REVERT: D 187 GLU cc_start: 0.6650 (pm20) cc_final: 0.6369 (pm20) REVERT: E 1 MET cc_start: 0.7039 (mmm) cc_final: 0.6686 (mmm) REVERT: G 1 MET cc_start: 0.7693 (ptp) cc_final: 0.7480 (ptt) REVERT: L 135 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8329 (ttpp) REVERT: V 33 LYS cc_start: 0.9215 (ptmm) cc_final: 0.8905 (ptpp) outliers start: 14 outliers final: 8 residues processed: 416 average time/residue: 0.5991 time to fit residues: 278.0907 Evaluate side-chains 360 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 352 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 98 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 155 ARG Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 60 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.0770 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 50.0000 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 238 GLN N 9 ASN C 154 ASN D 86 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.065887 restraints weight = 42161.337| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.45 r_work: 0.2894 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.341 17292 Z= 0.164 Angle : 0.798 18.936 23529 Z= 0.355 Chirality : 0.046 0.408 2557 Planarity : 0.005 0.050 2868 Dihedral : 18.413 178.778 2812 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.73 % Allowed : 20.90 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.17), residues: 1996 helix: 0.64 (0.15), residues: 949 sheet: -1.92 (0.33), residues: 220 loop : -0.71 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 13 TYR 0.027 0.002 TYR X 12 PHE 0.020 0.002 PHE I 138 TRP 0.021 0.002 TRP N 24 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00373 (17270) covalent geometry : angle 0.78192 (23519) SS BOND : bond 0.00584 ( 2) SS BOND : angle 1.72993 ( 4) hydrogen bonds : bond 0.04603 ( 831) hydrogen bonds : angle 5.18199 ( 2409) metal coordination : bond 0.01910 ( 8) metal coordination : angle 9.88835 ( 6) Misc. bond : bond 0.14148 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 384 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8901 (p90) cc_final: 0.8681 (p90) REVERT: X 22 VAL cc_start: 0.9145 (t) cc_final: 0.8632 (t) REVERT: I 82 GLU cc_start: 0.9334 (OUTLIER) cc_final: 0.8796 (mp0) REVERT: J 3 ILE cc_start: 0.8556 (tp) cc_final: 0.8247 (pp) REVERT: J 11 ASP cc_start: 0.9219 (t0) cc_final: 0.8959 (t0) REVERT: A 4 LYS cc_start: 0.9334 (tppp) cc_final: 0.9111 (mmpt) REVERT: A 13 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.8968 (mm-40) REVERT: B 11 ASP cc_start: 0.9218 (t0) cc_final: 0.8908 (t0) REVERT: B 15 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8446 (mtm110) REVERT: B 118 ASN cc_start: 0.9223 (t0) cc_final: 0.8935 (t0) REVERT: B 153 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8809 (mtmm) REVERT: C 55 ASP cc_start: 0.8072 (t0) cc_final: 0.7786 (t0) REVERT: D 70 ASP cc_start: 0.7436 (t0) cc_final: 0.7195 (t0) REVERT: D 81 PHE cc_start: 0.9249 (t80) cc_final: 0.9044 (t80) REVERT: D 97 LYS cc_start: 0.7547 (tmmt) cc_final: 0.7276 (tmtt) REVERT: D 99 ASP cc_start: 0.7675 (m-30) cc_final: 0.6858 (m-30) REVERT: D 133 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8206 (mt-10) REVERT: D 137 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8222 (mmm) REVERT: D 150 LYS cc_start: 0.9279 (ptpp) cc_final: 0.9041 (ptpp) REVERT: D 187 GLU cc_start: 0.7092 (pm20) cc_final: 0.6783 (pm20) REVERT: F 1 MET cc_start: 0.7849 (ptp) cc_final: 0.7386 (ptm) REVERT: F 30 LYS cc_start: 0.9261 (tptt) cc_final: 0.9034 (tppt) REVERT: G 1 MET cc_start: 0.8173 (ptp) cc_final: 0.7798 (ptt) REVERT: L 69 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7425 (mmmt) REVERT: L 99 ASP cc_start: 0.8058 (m-30) cc_final: 0.7351 (m-30) REVERT: L 144 GLN cc_start: 0.8823 (mt0) cc_final: 0.8337 (mm-40) REVERT: L 150 LYS cc_start: 0.8890 (tppt) cc_final: 0.8354 (mmtt) REVERT: V 13 ARG cc_start: 0.8278 (ptm-80) cc_final: 0.7761 (ptm-80) REVERT: V 19 SER cc_start: 0.8751 (p) cc_final: 0.8447 (p) REVERT: V 33 LYS cc_start: 0.9194 (ptmm) cc_final: 0.8882 (ptpp) REVERT: V 51 ASP cc_start: 0.8616 (p0) cc_final: 0.8375 (p0) REVERT: V 60 ASP cc_start: 0.8860 (t0) cc_final: 0.8397 (t0) outliers start: 62 outliers final: 22 residues processed: 409 average time/residue: 0.5344 time to fit residues: 244.9751 Evaluate side-chains 384 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 358 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 65 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 2 ILE Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 11 VAL Chi-restraints excluded: chain V residue 48 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 178 optimal weight: 30.0000 chunk 161 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 100 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN C 284 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.088352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064175 restraints weight = 42514.140| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.01 r_work: 0.2867 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.434 17292 Z= 0.203 Angle : 0.775 18.783 23529 Z= 0.339 Chirality : 0.046 0.385 2557 Planarity : 0.005 0.047 2868 Dihedral : 17.460 176.603 2803 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.64 % Allowed : 20.96 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.18), residues: 1996 helix: 1.39 (0.16), residues: 945 sheet: -1.47 (0.34), residues: 210 loop : -0.48 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 27 TYR 0.020 0.002 TYR C 54 PHE 0.026 0.002 PHE J 85 TRP 0.024 0.002 TRP N 24 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00489 (17270) covalent geometry : angle 0.76014 (23519) SS BOND : bond 0.00381 ( 2) SS BOND : angle 1.51454 ( 4) hydrogen bonds : bond 0.04599 ( 831) hydrogen bonds : angle 4.82778 ( 2409) metal coordination : bond 0.00985 ( 8) metal coordination : angle 9.36321 ( 6) Misc. bond : bond 0.18352 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 365 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7612 (tm130) REVERT: X 12 TYR cc_start: 0.8849 (p90) cc_final: 0.8623 (p90) REVERT: I 24 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8940 (mp) REVERT: I 82 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: J 3 ILE cc_start: 0.8464 (tp) cc_final: 0.8178 (pp) REVERT: J 11 ASP cc_start: 0.9252 (t0) cc_final: 0.8898 (t0) REVERT: K 238 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: A 8 GLU cc_start: 0.8759 (pp20) cc_final: 0.8385 (pp20) REVERT: A 13 GLN cc_start: 0.9232 (OUTLIER) cc_final: 0.9011 (mm-40) REVERT: A 171 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8914 (mm-40) REVERT: B 15 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8610 (mtm110) REVERT: B 93 ASN cc_start: 0.9030 (t0) cc_final: 0.8682 (t0) REVERT: B 94 LYS cc_start: 0.8965 (tptt) cc_final: 0.8671 (tttt) REVERT: B 153 LYS cc_start: 0.9128 (mtmm) cc_final: 0.8901 (ptpp) REVERT: C 55 ASP cc_start: 0.8079 (t0) cc_final: 0.7665 (t0) REVERT: C 284 ASN cc_start: 0.8366 (m-40) cc_final: 0.8037 (t0) REVERT: D 70 ASP cc_start: 0.7941 (t0) cc_final: 0.7525 (t0) REVERT: D 99 ASP cc_start: 0.7601 (m-30) cc_final: 0.6769 (m-30) REVERT: D 137 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8486 (mpp) REVERT: D 150 LYS cc_start: 0.9408 (ptpp) cc_final: 0.9165 (ptpp) REVERT: D 187 GLU cc_start: 0.7269 (pm20) cc_final: 0.6993 (pm20) REVERT: F 30 LYS cc_start: 0.9270 (tptt) cc_final: 0.9008 (tppt) REVERT: G 1 MET cc_start: 0.8195 (ptp) cc_final: 0.7829 (ptt) REVERT: L 69 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7790 (mmmt) REVERT: L 90 ARG cc_start: 0.8768 (mmt-90) cc_final: 0.7590 (mpt-90) REVERT: L 99 ASP cc_start: 0.8097 (m-30) cc_final: 0.7869 (m-30) REVERT: V 13 ARG cc_start: 0.8206 (ptm-80) cc_final: 0.7526 (ptm-80) REVERT: V 19 SER cc_start: 0.8872 (p) cc_final: 0.8597 (p) REVERT: V 33 LYS cc_start: 0.9141 (ptmm) cc_final: 0.8830 (ptpp) REVERT: V 60 ASP cc_start: 0.8779 (t0) cc_final: 0.8182 (t0) outliers start: 77 outliers final: 27 residues processed: 402 average time/residue: 0.5614 time to fit residues: 253.1873 Evaluate side-chains 383 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 349 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 123 LEU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 156 THR Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain G residue 3 GLU Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 8 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 123 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 61 optimal weight: 0.0470 chunk 174 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 GLN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 117 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.090310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.065762 restraints weight = 42625.513| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.10 r_work: 0.2919 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.393 17292 Z= 0.135 Angle : 0.723 17.527 23529 Z= 0.318 Chirality : 0.045 0.320 2557 Planarity : 0.004 0.051 2868 Dihedral : 16.558 172.071 2803 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.80 % Allowed : 21.63 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.18), residues: 1996 helix: 1.67 (0.16), residues: 949 sheet: -1.19 (0.34), residues: 209 loop : -0.36 (0.21), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 90 TYR 0.020 0.001 TYR C 54 PHE 0.024 0.002 PHE V 49 TRP 0.023 0.002 TRP D 190 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00314 (17270) covalent geometry : angle 0.71029 (23519) SS BOND : bond 0.00520 ( 2) SS BOND : angle 1.37704 ( 4) hydrogen bonds : bond 0.04161 ( 831) hydrogen bonds : angle 4.57569 ( 2409) metal coordination : bond 0.01050 ( 8) metal coordination : angle 8.45755 ( 6) Misc. bond : bond 0.14899 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 378 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7621 (tm130) REVERT: X 12 TYR cc_start: 0.8914 (p90) cc_final: 0.8512 (p90) REVERT: X 28 LYS cc_start: 0.8419 (mmmm) cc_final: 0.7796 (ttpp) REVERT: I 24 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8910 (mp) REVERT: J 11 ASP cc_start: 0.9253 (t0) cc_final: 0.8936 (t0) REVERT: K 55 ASP cc_start: 0.8401 (t0) cc_final: 0.8028 (t0) REVERT: K 238 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8526 (pt0) REVERT: N 4 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8693 (tp30) REVERT: A 13 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.9003 (mm-40) REVERT: A 171 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8928 (mm-40) REVERT: B 11 ASP cc_start: 0.9153 (t0) cc_final: 0.8927 (t0) REVERT: B 15 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8494 (mtm110) REVERT: B 93 ASN cc_start: 0.9030 (t0) cc_final: 0.8790 (t0) REVERT: C 55 ASP cc_start: 0.8100 (t0) cc_final: 0.7626 (t0) REVERT: C 186 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8142 (tt) REVERT: C 284 ASN cc_start: 0.8352 (m-40) cc_final: 0.8031 (t0) REVERT: D 70 ASP cc_start: 0.7641 (t0) cc_final: 0.7187 (t0) REVERT: D 97 LYS cc_start: 0.7460 (tmtt) cc_final: 0.7257 (tmtt) REVERT: D 99 ASP cc_start: 0.7593 (m-30) cc_final: 0.6880 (m-30) REVERT: D 150 LYS cc_start: 0.9456 (ptpp) cc_final: 0.9207 (ptpp) REVERT: D 187 GLU cc_start: 0.7292 (pm20) cc_final: 0.6757 (pm20) REVERT: F 30 LYS cc_start: 0.9301 (tptt) cc_final: 0.9069 (tppt) REVERT: G 1 MET cc_start: 0.8266 (ptp) cc_final: 0.7859 (ptt) REVERT: L 69 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7713 (mmmm) REVERT: V 13 ARG cc_start: 0.8114 (ptm-80) cc_final: 0.7676 (ptm-80) REVERT: V 19 SER cc_start: 0.8881 (p) cc_final: 0.8562 (p) REVERT: V 33 LYS cc_start: 0.9160 (ptmm) cc_final: 0.8824 (ptpp) outliers start: 63 outliers final: 20 residues processed: 402 average time/residue: 0.5931 time to fit residues: 266.7572 Evaluate side-chains 379 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 353 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain X residue 19 SER Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 13 GLN Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain F residue 7 LEU Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 120 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 161 optimal weight: 0.0970 chunk 73 optimal weight: 8.9990 chunk 171 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 149 optimal weight: 50.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 118 ASN N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.089425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.064251 restraints weight = 42580.815| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.57 r_work: 0.2887 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8908 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.426 17292 Z= 0.161 Angle : 0.735 17.971 23529 Z= 0.322 Chirality : 0.045 0.285 2557 Planarity : 0.004 0.047 2868 Dihedral : 16.078 166.736 2802 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.67 % Allowed : 22.95 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.18), residues: 1996 helix: 1.79 (0.16), residues: 949 sheet: -1.27 (0.33), residues: 213 loop : -0.28 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 27 TYR 0.019 0.001 TYR L 102 PHE 0.019 0.001 PHE J 85 TRP 0.020 0.002 TRP L 190 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00390 (17270) covalent geometry : angle 0.72490 (23519) SS BOND : bond 0.00549 ( 2) SS BOND : angle 1.29244 ( 4) hydrogen bonds : bond 0.04221 ( 831) hydrogen bonds : angle 4.53082 ( 2409) metal coordination : bond 0.00863 ( 8) metal coordination : angle 7.64772 ( 6) Misc. bond : bond 0.16987 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 361 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7589 (tm130) REVERT: X 12 TYR cc_start: 0.8853 (p90) cc_final: 0.8532 (p90) REVERT: X 28 LYS cc_start: 0.8474 (mmmm) cc_final: 0.7688 (tttt) REVERT: I 17 ASP cc_start: 0.8848 (m-30) cc_final: 0.8623 (t0) REVERT: I 24 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8905 (mp) REVERT: I 180 GLU cc_start: 0.7760 (pm20) cc_final: 0.7456 (pm20) REVERT: J 11 ASP cc_start: 0.9258 (t0) cc_final: 0.8873 (t0) REVERT: J 153 LYS cc_start: 0.9040 (mtmm) cc_final: 0.8591 (ptmt) REVERT: K 55 ASP cc_start: 0.8516 (t0) cc_final: 0.8091 (t0) REVERT: K 238 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8549 (pt0) REVERT: A 171 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8971 (mm-40) REVERT: B 11 ASP cc_start: 0.9207 (t0) cc_final: 0.8987 (t0) REVERT: B 93 ASN cc_start: 0.9070 (t0) cc_final: 0.8823 (t0) REVERT: C 11 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8907 (tm) REVERT: C 55 ASP cc_start: 0.8131 (t0) cc_final: 0.7667 (t0) REVERT: C 284 ASN cc_start: 0.8357 (m-40) cc_final: 0.7985 (t0) REVERT: D 70 ASP cc_start: 0.7694 (t0) cc_final: 0.7446 (t0) REVERT: D 97 LYS cc_start: 0.7298 (tmtt) cc_final: 0.7047 (tmmt) REVERT: D 99 ASP cc_start: 0.7517 (m-30) cc_final: 0.6820 (m-30) REVERT: D 150 LYS cc_start: 0.9494 (ptpp) cc_final: 0.9222 (ptpp) REVERT: D 187 GLU cc_start: 0.7396 (pm20) cc_final: 0.7048 (pm20) REVERT: F 30 LYS cc_start: 0.9334 (tptt) cc_final: 0.9130 (tppt) REVERT: G 1 MET cc_start: 0.8219 (ptp) cc_final: 0.7840 (ptt) REVERT: L 69 LYS cc_start: 0.8144 (mtmm) cc_final: 0.7705 (mmmm) REVERT: L 144 GLN cc_start: 0.8751 (mt0) cc_final: 0.8462 (mm-40) REVERT: V 19 SER cc_start: 0.8844 (p) cc_final: 0.8515 (p) REVERT: V 51 ASP cc_start: 0.8610 (p0) cc_final: 0.8340 (p0) REVERT: V 60 ASP cc_start: 0.8531 (p0) cc_final: 0.7936 (p0) outliers start: 61 outliers final: 23 residues processed: 388 average time/residue: 0.5987 time to fit residues: 260.0076 Evaluate side-chains 381 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain K residue 77 MET Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 120 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 147 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 0.0980 chunk 163 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 191 optimal weight: 6.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 86 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.065870 restraints weight = 42009.240| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.50 r_work: 0.2916 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.386 17292 Z= 0.133 Angle : 0.718 16.618 23529 Z= 0.317 Chirality : 0.044 0.298 2557 Planarity : 0.004 0.047 2868 Dihedral : 15.587 164.203 2802 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.49 % Allowed : 23.86 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.18), residues: 1996 helix: 1.89 (0.16), residues: 949 sheet: -1.17 (0.33), residues: 216 loop : -0.26 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.014 0.001 TYR V 12 PHE 0.019 0.001 PHE J 85 TRP 0.024 0.001 TRP L 190 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00314 (17270) covalent geometry : angle 0.70735 (23519) SS BOND : bond 0.00255 ( 2) SS BOND : angle 1.19849 ( 4) hydrogen bonds : bond 0.04035 ( 831) hydrogen bonds : angle 4.42198 ( 2409) metal coordination : bond 0.00891 ( 8) metal coordination : angle 7.52909 ( 6) Misc. bond : bond 0.14587 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 372 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8003 (tm-30) cc_final: 0.7617 (tm130) REVERT: X 10 LYS cc_start: 0.9220 (tmmm) cc_final: 0.8539 (tptp) REVERT: I 24 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8863 (mp) REVERT: I 61 MET cc_start: 0.9244 (mtm) cc_final: 0.9033 (mtm) REVERT: I 180 GLU cc_start: 0.7747 (pm20) cc_final: 0.7449 (pm20) REVERT: J 11 ASP cc_start: 0.9269 (t0) cc_final: 0.8925 (t0) REVERT: J 15 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8731 (mtm110) REVERT: J 153 LYS cc_start: 0.8932 (mtmm) cc_final: 0.8530 (ptmt) REVERT: K 19 ARG cc_start: 0.9096 (ttt-90) cc_final: 0.8513 (ttt-90) REVERT: K 55 ASP cc_start: 0.8514 (t0) cc_final: 0.8049 (t0) REVERT: K 238 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8548 (pt0) REVERT: N 4 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8782 (tp30) REVERT: A 171 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8988 (mm-40) REVERT: B 11 ASP cc_start: 0.9265 (t0) cc_final: 0.8894 (t0) REVERT: B 15 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8384 (mtm110) REVERT: B 93 ASN cc_start: 0.9012 (t0) cc_final: 0.8713 (t0) REVERT: B 94 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8560 (mttt) REVERT: B 119 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.8987 (pptt) REVERT: C 55 ASP cc_start: 0.8178 (t0) cc_final: 0.7719 (t0) REVERT: C 284 ASN cc_start: 0.8374 (m-40) cc_final: 0.8023 (t0) REVERT: D 69 LYS cc_start: 0.6879 (mmmm) cc_final: 0.6670 (tttp) REVERT: D 97 LYS cc_start: 0.7437 (tmtt) cc_final: 0.7225 (tmmt) REVERT: D 99 ASP cc_start: 0.7561 (m-30) cc_final: 0.6856 (m-30) REVERT: D 137 MET cc_start: 0.8476 (mmt) cc_final: 0.8181 (mmt) REVERT: D 150 LYS cc_start: 0.9507 (ptpp) cc_final: 0.9223 (ptpp) REVERT: D 187 GLU cc_start: 0.7275 (pm20) cc_final: 0.6935 (pm20) REVERT: F 30 LYS cc_start: 0.9326 (tptt) cc_final: 0.9110 (tppt) REVERT: G 1 MET cc_start: 0.8215 (ptp) cc_final: 0.7779 (ptt) REVERT: L 69 LYS cc_start: 0.8032 (mtmm) cc_final: 0.7684 (mmmm) REVERT: L 144 GLN cc_start: 0.8682 (mt0) cc_final: 0.8450 (mm-40) REVERT: V 13 ARG cc_start: 0.8317 (ptm-80) cc_final: 0.6975 (ptm-80) REVERT: V 19 SER cc_start: 0.8873 (p) cc_final: 0.8527 (p) REVERT: V 33 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.9013 (mtmm) REVERT: V 57 PHE cc_start: 0.9497 (m-80) cc_final: 0.9255 (m-80) outliers start: 58 outliers final: 21 residues processed: 399 average time/residue: 0.5938 time to fit residues: 264.4830 Evaluate side-chains 381 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 354 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 171 GLN Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 45 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 chunk 159 optimal weight: 30.0000 chunk 111 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 151 optimal weight: 40.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN A 13 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN L 144 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.089868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.064862 restraints weight = 42542.893| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.39 r_work: 0.2909 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.398 17292 Z= 0.143 Angle : 0.733 16.593 23529 Z= 0.325 Chirality : 0.044 0.275 2557 Planarity : 0.004 0.047 2868 Dihedral : 15.288 161.274 2800 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.89 % Allowed : 24.82 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.19), residues: 1996 helix: 1.95 (0.16), residues: 948 sheet: -1.28 (0.34), residues: 224 loop : -0.25 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.033 0.001 TYR X 12 PHE 0.019 0.001 PHE M 28 TRP 0.028 0.001 TRP L 190 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00345 (17270) covalent geometry : angle 0.72363 (23519) SS BOND : bond 0.00309 ( 2) SS BOND : angle 0.95520 ( 4) hydrogen bonds : bond 0.04064 ( 831) hydrogen bonds : angle 4.43943 ( 2409) metal coordination : bond 0.00935 ( 8) metal coordination : angle 7.27220 ( 6) Misc. bond : bond 0.15304 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 370 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8079 (tm-30) cc_final: 0.7852 (tm130) REVERT: I 24 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8875 (mp) REVERT: I 180 GLU cc_start: 0.7831 (pm20) cc_final: 0.7581 (pm20) REVERT: J 11 ASP cc_start: 0.9263 (t0) cc_final: 0.8940 (t0) REVERT: J 15 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8753 (mtm110) REVERT: K 19 ARG cc_start: 0.9076 (ttt-90) cc_final: 0.8495 (ttt-90) REVERT: K 55 ASP cc_start: 0.8531 (t0) cc_final: 0.8055 (t0) REVERT: K 238 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8535 (pt0) REVERT: A 8 GLU cc_start: 0.8768 (pp20) cc_final: 0.8546 (pp20) REVERT: A 13 GLN cc_start: 0.9107 (mm110) cc_final: 0.8848 (mm-40) REVERT: A 171 GLN cc_start: 0.9211 (mp10) cc_final: 0.8997 (mm-40) REVERT: B 11 ASP cc_start: 0.9261 (t0) cc_final: 0.8840 (t0) REVERT: B 15 ARG cc_start: 0.8827 (mtm110) cc_final: 0.8316 (mtm110) REVERT: B 93 ASN cc_start: 0.9056 (t0) cc_final: 0.8754 (t0) REVERT: B 119 LYS cc_start: 0.9322 (OUTLIER) cc_final: 0.8996 (pptt) REVERT: C 55 ASP cc_start: 0.8239 (t0) cc_final: 0.7753 (t0) REVERT: C 284 ASN cc_start: 0.8353 (m-40) cc_final: 0.8016 (t0) REVERT: D 99 ASP cc_start: 0.7476 (m-30) cc_final: 0.6620 (m-30) REVERT: D 150 LYS cc_start: 0.9523 (ptpp) cc_final: 0.9212 (ptpp) REVERT: D 187 GLU cc_start: 0.7341 (pm20) cc_final: 0.6991 (pm20) REVERT: F 30 LYS cc_start: 0.9337 (tptt) cc_final: 0.9123 (tppt) REVERT: G 1 MET cc_start: 0.8226 (ptp) cc_final: 0.7814 (ptt) REVERT: L 69 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7618 (mmmm) REVERT: L 133 GLU cc_start: 0.8518 (tt0) cc_final: 0.8116 (pt0) REVERT: V 13 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7739 (ptm-80) REVERT: V 19 SER cc_start: 0.8917 (p) cc_final: 0.8424 (p) REVERT: V 25 LYS cc_start: 0.8979 (mmtp) cc_final: 0.8775 (tptm) REVERT: V 33 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8981 (ptpp) REVERT: V 46 VAL cc_start: 0.9408 (t) cc_final: 0.9184 (p) REVERT: V 55 THR cc_start: 0.9152 (m) cc_final: 0.8947 (m) REVERT: V 57 PHE cc_start: 0.9419 (m-80) cc_final: 0.9216 (m-80) outliers start: 48 outliers final: 23 residues processed: 397 average time/residue: 0.5871 time to fit residues: 260.9380 Evaluate side-chains 383 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 355 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 11 TYR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 33 LYS Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 146 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 131 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 99 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 88 optimal weight: 0.6980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.090570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.066140 restraints weight = 43072.825| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.33 r_work: 0.2918 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.386 17292 Z= 0.138 Angle : 0.760 16.479 23529 Z= 0.337 Chirality : 0.044 0.297 2557 Planarity : 0.004 0.047 2868 Dihedral : 14.896 159.121 2800 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.41 % Allowed : 25.90 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.19), residues: 1996 helix: 1.96 (0.16), residues: 948 sheet: -1.18 (0.34), residues: 223 loop : -0.27 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 27 TYR 0.029 0.001 TYR X 12 PHE 0.017 0.001 PHE J 85 TRP 0.032 0.001 TRP L 190 HIS 0.006 0.001 HIS D 122 Details of bonding type rmsd covalent geometry : bond 0.00331 (17270) covalent geometry : angle 0.74894 (23519) SS BOND : bond 0.00440 ( 2) SS BOND : angle 0.84284 ( 4) hydrogen bonds : bond 0.03972 ( 831) hydrogen bonds : angle 4.42128 ( 2409) metal coordination : bond 0.01049 ( 8) metal coordination : angle 8.14665 ( 6) Misc. bond : bond 0.14040 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7843 (tm-30) REVERT: I 24 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8857 (mp) REVERT: I 180 GLU cc_start: 0.7911 (pm20) cc_final: 0.7701 (pm20) REVERT: J 11 ASP cc_start: 0.9254 (t0) cc_final: 0.8939 (t0) REVERT: J 15 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8757 (mtm110) REVERT: J 93 ASN cc_start: 0.9126 (t0) cc_final: 0.8771 (p0) REVERT: J 153 LYS cc_start: 0.8900 (mtmm) cc_final: 0.8619 (ptmt) REVERT: K 19 ARG cc_start: 0.9069 (ttt-90) cc_final: 0.8497 (ttt-90) REVERT: K 55 ASP cc_start: 0.8563 (t0) cc_final: 0.8086 (t0) REVERT: K 238 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (pt0) REVERT: B 11 ASP cc_start: 0.9276 (t0) cc_final: 0.8871 (t0) REVERT: B 15 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8393 (mtm110) REVERT: B 93 ASN cc_start: 0.9001 (t0) cc_final: 0.8754 (t0) REVERT: B 119 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8987 (pptt) REVERT: C 55 ASP cc_start: 0.8222 (t0) cc_final: 0.7753 (t0) REVERT: C 284 ASN cc_start: 0.8340 (m-40) cc_final: 0.8040 (t0) REVERT: D 97 LYS cc_start: 0.7185 (tmtt) cc_final: 0.6923 (tmmt) REVERT: D 99 ASP cc_start: 0.7568 (m-30) cc_final: 0.7223 (m-30) REVERT: D 150 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9209 (ptpp) REVERT: D 187 GLU cc_start: 0.7386 (pm20) cc_final: 0.7045 (pm20) REVERT: F 30 LYS cc_start: 0.9304 (tptt) cc_final: 0.9053 (tppt) REVERT: G 1 MET cc_start: 0.8179 (ptp) cc_final: 0.7776 (ptt) REVERT: L 69 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7565 (mmmm) REVERT: L 133 GLU cc_start: 0.8421 (tt0) cc_final: 0.8216 (pt0) REVERT: L 137 MET cc_start: 0.9042 (mtp) cc_final: 0.8688 (mmm) REVERT: L 150 LYS cc_start: 0.8896 (tppt) cc_final: 0.8570 (mptp) REVERT: V 13 ARG cc_start: 0.8320 (ptm-80) cc_final: 0.7649 (ptm-80) REVERT: V 25 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8688 (tptm) REVERT: V 55 THR cc_start: 0.9151 (m) cc_final: 0.8943 (m) REVERT: V 57 PHE cc_start: 0.9419 (m-80) cc_final: 0.9217 (m-80) REVERT: V 60 ASP cc_start: 0.8896 (p0) cc_final: 0.8354 (p0) outliers start: 40 outliers final: 23 residues processed: 387 average time/residue: 0.6019 time to fit residues: 260.3492 Evaluate side-chains 387 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 360 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain J residue 20 LYS Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 32 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 180 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 151 optimal weight: 30.0000 chunk 7 optimal weight: 6.9990 chunk 127 optimal weight: 0.0670 chunk 72 optimal weight: 7.9990 chunk 103 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 overall best weight: 0.8838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** L 144 GLN ** 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 = 0.3700 r_free = 0.3700 target = 0.090719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.065825 restraints weight = 42864.194| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.27 r_work: 0.2931 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8872 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.391 17292 Z= 0.142 Angle : 0.769 16.226 23529 Z= 0.343 Chirality : 0.044 0.263 2557 Planarity : 0.004 0.048 2868 Dihedral : 14.622 156.872 2800 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 26.45 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.18), residues: 1996 helix: 1.93 (0.16), residues: 946 sheet: -1.07 (0.34), residues: 219 loop : -0.28 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.041 0.001 TYR X 12 PHE 0.015 0.001 PHE J 85 TRP 0.035 0.001 TRP L 190 HIS 0.007 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00344 (17270) covalent geometry : angle 0.75927 (23519) SS BOND : bond 0.00466 ( 2) SS BOND : angle 0.95011 ( 4) hydrogen bonds : bond 0.03992 ( 831) hydrogen bonds : angle 4.42569 ( 2409) metal coordination : bond 0.01085 ( 8) metal coordination : angle 7.84910 ( 6) Misc. bond : bond 0.14669 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 356 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8319 (tm-30) cc_final: 0.7983 (tm130) REVERT: I 24 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8832 (mp) REVERT: I 180 GLU cc_start: 0.7864 (pm20) cc_final: 0.7661 (pm20) REVERT: J 11 ASP cc_start: 0.9207 (t0) cc_final: 0.8907 (t0) REVERT: J 15 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8747 (mtm110) REVERT: J 93 ASN cc_start: 0.9102 (t0) cc_final: 0.8748 (p0) REVERT: J 153 LYS cc_start: 0.8881 (mtmm) cc_final: 0.8624 (ptmt) REVERT: K 19 ARG cc_start: 0.9059 (ttt-90) cc_final: 0.8494 (ttt-90) REVERT: K 55 ASP cc_start: 0.8556 (t0) cc_final: 0.8082 (t0) REVERT: K 238 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: A 5 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8636 (mp0) REVERT: B 11 ASP cc_start: 0.9272 (t0) cc_final: 0.8903 (t0) REVERT: B 15 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8413 (mtm110) REVERT: B 93 ASN cc_start: 0.8959 (t0) cc_final: 0.8737 (t0) REVERT: B 119 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.8989 (pptt) REVERT: C 11 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8855 (tm) REVERT: C 55 ASP cc_start: 0.8212 (t0) cc_final: 0.7741 (t0) REVERT: C 284 ASN cc_start: 0.8374 (m-40) cc_final: 0.8069 (t0) REVERT: D 97 LYS cc_start: 0.7167 (tmtt) cc_final: 0.6860 (tmmt) REVERT: D 99 ASP cc_start: 0.7578 (m-30) cc_final: 0.7207 (m-30) REVERT: D 150 LYS cc_start: 0.9517 (ptpp) cc_final: 0.9225 (ptpp) REVERT: D 187 GLU cc_start: 0.7363 (pm20) cc_final: 0.7009 (pm20) REVERT: F 30 LYS cc_start: 0.9347 (tptt) cc_final: 0.9079 (tppt) REVERT: L 28 ARG cc_start: 0.9336 (OUTLIER) cc_final: 0.9134 (mtm180) REVERT: L 69 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7565 (mmmm) REVERT: L 133 GLU cc_start: 0.8319 (tt0) cc_final: 0.8095 (pt0) REVERT: L 137 MET cc_start: 0.9041 (mtp) cc_final: 0.8752 (mmm) REVERT: L 150 LYS cc_start: 0.8883 (tppt) cc_final: 0.8557 (mptp) REVERT: V 13 ARG cc_start: 0.8285 (ptm-80) cc_final: 0.7861 (ptm-80) REVERT: V 25 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8791 (tptm) REVERT: V 60 ASP cc_start: 0.8941 (p0) cc_final: 0.8552 (p0) outliers start: 35 outliers final: 23 residues processed: 373 average time/residue: 0.5687 time to fit residues: 236.9981 Evaluate side-chains 380 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 351 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain G residue 2 ILE Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 28 ARG Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 56 optimal weight: 0.3980 chunk 109 optimal weight: 0.3980 chunk 167 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 189 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 71 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.091140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.066759 restraints weight = 42725.989| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 2.25 r_work: 0.2959 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.375 17292 Z= 0.136 Angle : 0.778 15.579 23529 Z= 0.349 Chirality : 0.044 0.251 2557 Planarity : 0.004 0.048 2868 Dihedral : 14.323 155.040 2800 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.11 % Allowed : 26.75 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1996 helix: 1.85 (0.16), residues: 958 sheet: -0.99 (0.35), residues: 219 loop : -0.30 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.065 0.002 TYR X 12 PHE 0.017 0.001 PHE D 81 TRP 0.044 0.002 TRP L 190 HIS 0.008 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00326 (17270) covalent geometry : angle 0.76940 (23519) SS BOND : bond 0.00325 ( 2) SS BOND : angle 0.81979 ( 4) hydrogen bonds : bond 0.03911 ( 831) hydrogen bonds : angle 4.38964 ( 2409) metal coordination : bond 0.01290 ( 8) metal coordination : angle 7.38155 ( 6) Misc. bond : bond 0.13757 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3992 Ramachandran restraints generated. 1996 Oldfield, 0 Emsley, 1996 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 360 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7845 (tm130) REVERT: I 24 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8795 (mp) REVERT: J 11 ASP cc_start: 0.9191 (t0) cc_final: 0.8903 (t0) REVERT: J 15 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8731 (mtm110) REVERT: J 93 ASN cc_start: 0.9112 (t0) cc_final: 0.8813 (p0) REVERT: J 153 LYS cc_start: 0.8855 (mtmm) cc_final: 0.8624 (ptmt) REVERT: K 19 ARG cc_start: 0.9032 (ttt-90) cc_final: 0.8480 (ttt-90) REVERT: K 55 ASP cc_start: 0.8550 (t0) cc_final: 0.8083 (t0) REVERT: K 238 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8499 (pt0) REVERT: A 5 GLU cc_start: 0.8958 (mm-30) cc_final: 0.8626 (mp0) REVERT: B 11 ASP cc_start: 0.9265 (t0) cc_final: 0.8886 (t0) REVERT: B 15 ARG cc_start: 0.8807 (mtm110) cc_final: 0.8372 (mtm110) REVERT: B 93 ASN cc_start: 0.8975 (t0) cc_final: 0.8749 (t0) REVERT: B 119 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8994 (pptt) REVERT: C 11 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8880 (tm) REVERT: C 55 ASP cc_start: 0.8184 (t0) cc_final: 0.7708 (t0) REVERT: C 284 ASN cc_start: 0.8501 (m-40) cc_final: 0.8157 (t0) REVERT: D 97 LYS cc_start: 0.7247 (tmtt) cc_final: 0.6934 (tmmt) REVERT: D 99 ASP cc_start: 0.7586 (m-30) cc_final: 0.7207 (m-30) REVERT: D 150 LYS cc_start: 0.9512 (ptpp) cc_final: 0.9220 (ptpp) REVERT: D 187 GLU cc_start: 0.7372 (pm20) cc_final: 0.6810 (pm20) REVERT: L 69 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7705 (mmmt) REVERT: L 133 GLU cc_start: 0.8245 (tt0) cc_final: 0.8031 (pt0) REVERT: L 137 MET cc_start: 0.9053 (mtp) cc_final: 0.8732 (mmm) REVERT: L 150 LYS cc_start: 0.8875 (tppt) cc_final: 0.8418 (mmtp) REVERT: V 13 ARG cc_start: 0.8200 (ptm-80) cc_final: 0.7813 (ptm-80) REVERT: V 25 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8750 (tptm) REVERT: V 60 ASP cc_start: 0.8944 (p0) cc_final: 0.8561 (p0) outliers start: 35 outliers final: 20 residues processed: 378 average time/residue: 0.5974 time to fit residues: 252.9486 Evaluate side-chains 378 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 353 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 11 VAL Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 15 ARG Chi-restraints excluded: chain K residue 238 GLN Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain N residue 31 LEU Chi-restraints excluded: chain O residue 27 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 152 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 25 CYS Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 75 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 144 GLN Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain H residue 29 PHE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 43 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 142 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 178 optimal weight: 50.0000 chunk 192 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 127 optimal weight: 0.1980 chunk 171 optimal weight: 1.9990 chunk 153 optimal weight: 0.4980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 171 GLN ** K 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 ASN ** D 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.066349 restraints weight = 42764.737| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 2.16 r_work: 0.2952 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.388 17292 Z= 0.145 Angle : 0.790 15.790 23529 Z= 0.355 Chirality : 0.045 0.250 2557 Planarity : 0.004 0.048 2868 Dihedral : 14.081 153.182 2800 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.75 % Allowed : 27.59 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1996 helix: 1.88 (0.16), residues: 960 sheet: -0.84 (0.34), residues: 226 loop : -0.22 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.057 0.001 TYR X 12 PHE 0.030 0.001 PHE A 59 TRP 0.049 0.001 TRP L 190 HIS 0.007 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00351 (17270) covalent geometry : angle 0.78209 (23519) SS BOND : bond 0.00301 ( 2) SS BOND : angle 0.75359 ( 4) hydrogen bonds : bond 0.03953 ( 831) hydrogen bonds : angle 4.39300 ( 2409) metal coordination : bond 0.01203 ( 8) metal coordination : angle 7.18702 ( 6) Misc. bond : bond 0.14343 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8684.73 seconds wall clock time: 148 minutes 14.06 seconds (8894.06 seconds total)