Starting phenix.real_space_refine on Sat Jul 4 06:22:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r0w_14224/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.map" model { file = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_2026/7r0w_14224.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r0w_14224/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 3.29, per 1000 atoms: 0.20 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: 1.83 Conformation dependent library (CDL) restraints added in 690.1 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: 0.42 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: 2.66 Time building geometry restraints manager: 2.21 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: 9394 34.13 - 68.25: 451 68.25 - 102.38: 64 102.38 - 136.50: 5 136.50 - 170.63: 1 Dihedral angle restraints: 9915 sinusoidal: 4161 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 9912 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: 0.580 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.550 Find NCS groups from input model: 0.510 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: 0.000 Load rotamer database and sin/cos tables:6.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 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 : 19.220 170.631 6237 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/Z covalent geometry : bond 0.00467 / 0.20 (17270) covalent geometry : angle 0.96277 / 0.45 (23519) SS BOND : bond 0.00644 / 0.34 ( 2) SS BOND : angle 2.35826 / 1.21 ( 4) hydrogen bonds : bond 0.13769 / 9.20 ( 831) hydrogen bonds : angle 7.49351 / 5.50 ( 2409) metal coordination : bond 0.54250 / 28.12 ( 8) metal coordination : angle 20.05180 / 8.57 ( 6) Misc. bond : bond 0.15649 / 11.28 ( 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 : 0.426 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: 0.5445 time to fit residues: 253.9680 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 : 0.468 ------------------------------------------------------------------------------- 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... 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 = 0.3694 r_free = 0.3694 target = 0.090001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.063211 restraints weight = 42164.832| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.30 r_work: 0.2930 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.326 17292 Z= 0.162 Angle : 0.792 18.798 23529 Z= 0.353 Chirality : 0.046 0.405 2557 Planarity : 0.005 0.049 2868 Dihedral : 16.806 167.999 2702 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.80 % Allowed : 20.72 % Favored : 75.48 % 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: 0.63 (0.15), residues: 949 sheet: -1.85 (0.33), residues: 214 loop : -0.74 (0.20), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 52 TYR 0.024 0.002 TYR X 12 PHE 0.020 0.002 PHE M 15 TRP 0.021 0.002 TRP N 24 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (17270) covalent geometry : angle 0.77465 / 0.35 (23519) SS BOND : bond 0.00504 / 0.25 ( 2) SS BOND : angle 1.71624 / 1.01 ( 4) hydrogen bonds : bond 0.04668 / 3.19 ( 831) hydrogen bonds : angle 5.23552 / 3.79 ( 2409) metal coordination : bond 0.02198 / 1.12 ( 8) metal coordination : angle 10.22124 / 5.19 ( 6) Misc. bond : bond 0.13678 / 6.92 ( 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 448 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 385 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 12 TYR cc_start: 0.8863 (p90) cc_final: 0.8594 (p90) REVERT: X 22 VAL cc_start: 0.9148 (t) cc_final: 0.8645 (t) REVERT: X 52 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7992 (tpm170) REVERT: I 82 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8704 (mp0) REVERT: J 3 ILE cc_start: 0.8501 (tp) cc_final: 0.8209 (pp) REVERT: J 11 ASP cc_start: 0.9177 (t0) cc_final: 0.8896 (t0) REVERT: A 4 LYS cc_start: 0.9308 (tppp) cc_final: 0.9086 (mmpt) REVERT: A 13 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8934 (mm-40) REVERT: B 11 ASP cc_start: 0.9195 (t0) cc_final: 0.8908 (t0) REVERT: B 15 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8390 (mtm110) REVERT: B 118 ASN cc_start: 0.9206 (t0) cc_final: 0.8928 (t0) REVERT: B 153 LYS cc_start: 0.9048 (mtmm) cc_final: 0.8782 (mtmm) REVERT: C 55 ASP cc_start: 0.8022 (t0) cc_final: 0.7727 (t0) REVERT: D 70 ASP cc_start: 0.7336 (t0) cc_final: 0.7037 (t0) REVERT: D 97 LYS cc_start: 0.7538 (tmmt) cc_final: 0.7297 (tmtt) REVERT: D 99 ASP cc_start: 0.7624 (m-30) cc_final: 0.6815 (m-30) REVERT: D 133 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8189 (mt-10) REVERT: D 144 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7146 (mp10) REVERT: D 150 LYS cc_start: 0.9280 (ptpp) cc_final: 0.9000 (ptpp) REVERT: D 187 GLU cc_start: 0.7117 (pm20) cc_final: 0.6806 (pm20) REVERT: F 1 MET cc_start: 0.7773 (ptp) cc_final: 0.7371 (ptm) REVERT: F 30 LYS cc_start: 0.9223 (tptt) cc_final: 0.8991 (tppt) REVERT: G 1 MET cc_start: 0.8082 (ptp) cc_final: 0.7683 (ptt) REVERT: L 69 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7324 (mmmm) REVERT: L 99 ASP cc_start: 0.7956 (m-30) cc_final: 0.7263 (m-30) REVERT: L 144 GLN cc_start: 0.8823 (mt0) cc_final: 0.8337 (mm-40) REVERT: L 150 LYS cc_start: 0.8914 (tppt) cc_final: 0.8398 (mmtt) REVERT: V 13 ARG cc_start: 0.8233 (ptm-80) cc_final: 0.7730 (ptm-80) REVERT: V 19 SER cc_start: 0.8745 (p) cc_final: 0.8446 (p) REVERT: V 33 LYS cc_start: 0.9191 (ptmm) cc_final: 0.8872 (ptpp) REVERT: V 51 ASP cc_start: 0.8606 (p0) cc_final: 0.8396 (p0) REVERT: V 60 ASP cc_start: 0.8816 (t0) cc_final: 0.8361 (t0) outliers start: 63 outliers final: 22 residues processed: 411 average time/residue: 0.5237 time to fit residues: 241.7750 Evaluate side-chains 384 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 357 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 31 VAL Chi-restraints excluded: chain X residue 52 ARG 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 144 GLN 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: 0.9990 chunk 108 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 100 optimal weight: 0.0980 chunk 78 optimal weight: 5.9990 chunk 128 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 169 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN C 154 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.088537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063893 restraints weight = 42495.170| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.00 r_work: 0.2870 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.423 17292 Z= 0.196 Angle : 0.770 18.803 23529 Z= 0.338 Chirality : 0.046 0.371 2557 Planarity : 0.004 0.046 2868 Dihedral : 16.178 167.922 2693 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.52 % Allowed : 20.90 % 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: 0.36 (0.18), residues: 1996 helix: 1.37 (0.16), residues: 945 sheet: -1.59 (0.33), residues: 220 loop : -0.46 (0.21), residues: 831 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 0.025 0.002 TRP D 190 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (17270) covalent geometry : angle 0.75536 / 0.34 (23519) SS BOND : bond 0.00310 / 0.15 ( 2) SS BOND : angle 1.58520 / 0.89 ( 4) hydrogen bonds : bond 0.04602 / 3.13 ( 831) hydrogen bonds : angle 4.84901 / 3.50 ( 2409) metal coordination : bond 0.00829 / 0.51 ( 8) metal coordination : angle 9.30932 / 4.73 ( 6) Misc. bond : bond 0.17750 / 9.13 ( 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 439 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 364 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.7878 (tm-30) cc_final: 0.7596 (tm130) REVERT: X 12 TYR cc_start: 0.8855 (p90) cc_final: 0.8615 (p90) REVERT: I 24 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8932 (mp) REVERT: I 82 GLU cc_start: 0.9313 (OUTLIER) cc_final: 0.8728 (mp0) REVERT: J 3 ILE cc_start: 0.8471 (tp) cc_final: 0.8181 (pp) REVERT: J 11 ASP cc_start: 0.9220 (t0) cc_final: 0.8862 (t0) REVERT: K 238 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8559 (pt0) REVERT: A 8 GLU cc_start: 0.8755 (pp20) cc_final: 0.8400 (pp20) REVERT: B 15 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.8611 (mtm110) REVERT: B 93 ASN cc_start: 0.9035 (t0) cc_final: 0.8688 (t0) REVERT: B 153 LYS cc_start: 0.9124 (mtmm) cc_final: 0.8891 (ptpp) REVERT: C 55 ASP cc_start: 0.8042 (t0) cc_final: 0.7648 (t0) REVERT: C 284 ASN cc_start: 0.8379 (m-40) cc_final: 0.8025 (t0) REVERT: D 69 LYS cc_start: 0.7225 (mtpp) cc_final: 0.6899 (mmmm) REVERT: D 70 ASP cc_start: 0.7664 (t0) cc_final: 0.7305 (t0) REVERT: D 99 ASP cc_start: 0.7560 (m-30) cc_final: 0.6742 (m-30) REVERT: D 137 MET cc_start: 0.8622 (mmm) cc_final: 0.8408 (mmm) REVERT: D 150 LYS cc_start: 0.9413 (ptpp) cc_final: 0.9164 (ptpp) REVERT: D 187 GLU cc_start: 0.7316 (pm20) cc_final: 0.7034 (pm20) REVERT: F 30 LYS cc_start: 0.9273 (tptt) cc_final: 0.9024 (tppt) REVERT: G 1 MET cc_start: 0.8175 (ptp) cc_final: 0.7803 (ptt) REVERT: L 69 LYS cc_start: 0.8137 (mtmm) cc_final: 0.7780 (mmmt) REVERT: L 90 ARG cc_start: 0.8771 (mmt-90) cc_final: 0.7586 (mpt-90) REVERT: L 99 ASP cc_start: 0.8125 (m-30) cc_final: 0.7884 (m-30) REVERT: V 13 ARG cc_start: 0.8183 (ptm-80) cc_final: 0.7488 (ptm-80) REVERT: V 19 SER cc_start: 0.8841 (p) cc_final: 0.8573 (p) REVERT: V 33 LYS cc_start: 0.9160 (ptmm) cc_final: 0.8834 (ptpp) REVERT: V 60 ASP cc_start: 0.8774 (t0) cc_final: 0.8144 (t0) outliers start: 75 outliers final: 28 residues processed: 400 average time/residue: 0.5083 time to fit residues: 229.1910 Evaluate side-chains 383 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 351 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 96 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 161 VAL 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 176 SER Chi-restraints excluded: chain G residue 2 ILE 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 43 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 8 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 123 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 174 optimal weight: 0.9990 chunk 104 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 9 ASN A 13 GLN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.089712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.062935 restraints weight = 42396.798| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.29 r_work: 0.2925 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.404 17292 Z= 0.141 Angle : 0.733 17.875 23529 Z= 0.323 Chirality : 0.045 0.332 2557 Planarity : 0.004 0.051 2868 Dihedral : 15.665 166.880 2693 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.55 % Allowed : 21.81 % Favored : 74.64 % 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: 0.70 (0.18), residues: 1996 helix: 1.64 (0.16), residues: 949 sheet: -1.22 (0.34), residues: 210 loop : -0.37 (0.21), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.020 0.001 TYR C 54 PHE 0.024 0.002 PHE V 49 TRP 0.024 0.002 TRP D 190 HIS 0.007 0.001 HIS D 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (17270) covalent geometry : angle 0.72080 / 0.32 (23519) SS BOND : bond 0.00634 / 0.33 ( 2) SS BOND : angle 1.34637 / 0.75 ( 4) hydrogen bonds : bond 0.04232 / 2.90 ( 831) hydrogen bonds : angle 4.61790 / 3.31 ( 2409) metal coordination : bond 0.01138 / 0.52 ( 8) metal coordination : angle 8.36234 / 4.27 ( 6) Misc. bond : bond 0.15464 / 7.03 ( 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 436 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 377 time to evaluate : 0.612 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: 0.8006 (tm-30) cc_final: 0.7710 (tm130) REVERT: X 12 TYR cc_start: 0.8922 (p90) cc_final: 0.8573 (p90) REVERT: X 28 LYS cc_start: 0.8459 (mmmm) cc_final: 0.7714 (tttt) REVERT: X 49 PHE cc_start: 0.8247 (m-80) cc_final: 0.7648 (m-80) REVERT: I 24 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8911 (mp) REVERT: J 11 ASP cc_start: 0.9217 (t0) cc_final: 0.8832 (t0) REVERT: K 55 ASP cc_start: 0.8386 (t0) cc_final: 0.8026 (t0) REVERT: K 238 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: A 8 GLU cc_start: 0.8778 (pp20) cc_final: 0.8568 (pp20) REVERT: A 13 GLN cc_start: 0.9098 (mm110) cc_final: 0.8880 (mm-40) REVERT: B 11 ASP cc_start: 0.9121 (t0) cc_final: 0.8897 (t0) REVERT: B 15 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8483 (mtm110) REVERT: B 93 ASN cc_start: 0.9009 (t0) cc_final: 0.8773 (t0) REVERT: B 135 PHE cc_start: 0.9035 (t80) cc_final: 0.8833 (t80) REVERT: C 55 ASP cc_start: 0.8072 (t0) cc_final: 0.7614 (t0) REVERT: C 186 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8110 (tt) REVERT: C 284 ASN cc_start: 0.8343 (m-40) cc_final: 0.8018 (t0) REVERT: D 69 LYS cc_start: 0.7289 (mtpp) cc_final: 0.6997 (mmmm) REVERT: D 70 ASP cc_start: 0.7800 (t0) cc_final: 0.7440 (t0) REVERT: D 97 LYS cc_start: 0.7449 (tmtt) cc_final: 0.7230 (tmtt) REVERT: D 99 ASP cc_start: 0.7565 (m-30) cc_final: 0.6809 (m-30) REVERT: D 150 LYS cc_start: 0.9443 (ptpp) cc_final: 0.9203 (ptpp) REVERT: D 187 GLU cc_start: 0.7242 (pm20) cc_final: 0.6707 (pm20) REVERT: F 30 LYS cc_start: 0.9307 (tptt) cc_final: 0.9076 (tppt) REVERT: G 1 MET cc_start: 0.8244 (ptp) cc_final: 0.7848 (ptt) REVERT: L 69 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7714 (mmmm) REVERT: L 144 GLN cc_start: 0.8791 (mt0) cc_final: 0.8485 (mm-40) REVERT: V 13 ARG cc_start: 0.8120 (ptm-80) cc_final: 0.7625 (ptm-80) REVERT: V 19 SER cc_start: 0.8881 (p) cc_final: 0.8563 (p) REVERT: V 33 LYS cc_start: 0.9172 (ptmm) cc_final: 0.8839 (ptpp) REVERT: V 51 ASP cc_start: 0.8555 (p0) cc_final: 0.8296 (p0) outliers start: 59 outliers final: 23 residues processed: 400 average time/residue: 0.5051 time to fit residues: 227.0754 Evaluate side-chains 380 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 353 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 172 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 75 VAL 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 79 THR 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: 0.0370 chunk 73 optimal weight: 0.7980 chunk 171 optimal weight: 5.9990 chunk 158 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 10.0000 chunk 149 optimal weight: 50.0000 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.065507 restraints weight = 42607.789| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.23 r_work: 0.2902 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8972 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.385 17292 Z= 0.139 Angle : 0.728 17.114 23529 Z= 0.322 Chirality : 0.044 0.279 2557 Planarity : 0.004 0.046 2868 Dihedral : 15.119 168.182 2692 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.07 % Allowed : 23.31 % Favored : 73.61 % 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: 1.80 (0.16), residues: 948 sheet: -1.22 (0.34), residues: 201 loop : -0.31 (0.21), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 27 TYR 0.016 0.001 TYR G 29 PHE 0.020 0.001 PHE J 85 TRP 0.021 0.001 TRP L 190 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (17270) covalent geometry : angle 0.71867 / 0.32 (23519) SS BOND : bond 0.00516 / 0.27 ( 2) SS BOND : angle 1.36278 / 0.72 ( 4) hydrogen bonds : bond 0.04078 / 2.80 ( 831) hydrogen bonds : angle 4.48739 / 3.21 ( 2409) metal coordination : bond 0.01125 / 0.55 ( 8) metal coordination : angle 7.18292 / 3.76 ( 6) Misc. bond : bond 0.14280 / 6.32 ( 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 420 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 369 time to evaluate : 0.579 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: 0.8032 (tm-30) cc_final: 0.7633 (tm130) REVERT: X 12 TYR cc_start: 0.8846 (p90) cc_final: 0.8519 (p90) REVERT: X 28 LYS cc_start: 0.8459 (mmmm) cc_final: 0.7696 (tmtt) REVERT: X 49 PHE cc_start: 0.8108 (m-80) cc_final: 0.7219 (m-80) REVERT: I 24 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8895 (mp) REVERT: I 180 GLU cc_start: 0.7829 (pm20) cc_final: 0.7567 (pm20) REVERT: J 11 ASP cc_start: 0.9238 (t0) cc_final: 0.8864 (t0) REVERT: J 93 ASN cc_start: 0.8877 (t0) cc_final: 0.8614 (p0) REVERT: J 153 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8582 (ptmt) REVERT: K 55 ASP cc_start: 0.8480 (t0) cc_final: 0.8051 (t0) REVERT: K 238 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8508 (pt0) REVERT: N 4 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8619 (tp30) REVERT: B 11 ASP cc_start: 0.9215 (t0) cc_final: 0.8899 (t0) REVERT: B 15 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8519 (mtm110) REVERT: B 93 ASN cc_start: 0.9015 (t0) cc_final: 0.8731 (t0) REVERT: B 135 PHE cc_start: 0.9090 (t80) cc_final: 0.8864 (t80) REVERT: C 11 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9059 (tm) REVERT: C 55 ASP cc_start: 0.8125 (t0) cc_final: 0.7672 (t0) REVERT: C 284 ASN cc_start: 0.8350 (m-40) cc_final: 0.7988 (t0) REVERT: D 69 LYS cc_start: 0.7227 (mtpp) cc_final: 0.6964 (mmmm) REVERT: D 70 ASP cc_start: 0.7949 (t0) cc_final: 0.7652 (t0) REVERT: D 94 GLN cc_start: 0.7880 (tp-100) cc_final: 0.7666 (tp-100) REVERT: D 99 ASP cc_start: 0.7650 (m-30) cc_final: 0.7045 (m-30) REVERT: D 137 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.8379 (mmt) REVERT: D 144 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7600 (mp-120) REVERT: D 150 LYS cc_start: 0.9489 (ptpp) cc_final: 0.9222 (ptpp) REVERT: D 187 GLU cc_start: 0.7234 (pm20) cc_final: 0.6872 (pm20) REVERT: G 1 MET cc_start: 0.8271 (ptp) cc_final: 0.7817 (ptt) REVERT: L 21 ASP cc_start: 0.7247 (t0) cc_final: 0.6956 (t0) REVERT: L 69 LYS cc_start: 0.8096 (mtmm) cc_final: 0.7813 (mmmt) REVERT: L 144 GLN cc_start: 0.8747 (mt0) cc_final: 0.8491 (mm-40) REVERT: V 19 SER cc_start: 0.8868 (p) cc_final: 0.8537 (p) REVERT: V 25 LYS cc_start: 0.8986 (mmpt) cc_final: 0.8732 (mmtt) REVERT: V 33 LYS cc_start: 0.9188 (ptmm) cc_final: 0.8834 (ptpp) REVERT: V 60 ASP cc_start: 0.8588 (p0) cc_final: 0.7965 (p0) outliers start: 51 outliers final: 20 residues processed: 388 average time/residue: 0.5162 time to fit residues: 225.5116 Evaluate side-chains 382 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 356 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 11 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 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 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 137 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 96 optimal weight: 0.9990 chunk 161 optimal weight: 5.9990 chunk 22 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 163 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 overall best weight: 1.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 118 ASN N 9 ASN A 13 GLN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 130 ASN ** 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 = 0.3667 r_free = 0.3667 target = 0.088981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063957 restraints weight = 42521.840| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.41 r_work: 0.2868 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.430 17292 Z= 0.167 Angle : 0.744 17.915 23529 Z= 0.328 Chirality : 0.044 0.272 2557 Planarity : 0.004 0.047 2868 Dihedral : 14.914 172.165 2692 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.04 % Allowed : 23.13 % Favored : 72.83 % 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 (0.18), residues: 1996 helix: 1.84 (0.16), residues: 948 sheet: -1.07 (0.34), residues: 204 loop : -0.27 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.016 0.001 TYR G 29 PHE 0.017 0.001 PHE J 85 TRP 0.034 0.002 TRP D 190 HIS 0.008 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.16 (17270) covalent geometry : angle 0.73477 / 0.33 (23519) SS BOND : bond 0.00187 / 0.09 ( 2) SS BOND : angle 1.09017 / 0.60 ( 4) hydrogen bonds : bond 0.04206 / 2.88 ( 831) hydrogen bonds : angle 4.47679 / 3.20 ( 2409) metal coordination : bond 0.01147 / 0.70 ( 8) metal coordination : angle 7.21605 / 3.80 ( 6) Misc. bond : bond 0.17378 / 8.52 ( 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 426 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 359 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7621 (tm130) REVERT: I 17 ASP cc_start: 0.8849 (m-30) cc_final: 0.8613 (t0) REVERT: I 24 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8877 (mp) REVERT: I 180 GLU cc_start: 0.7858 (pm20) cc_final: 0.7596 (pm20) REVERT: J 11 ASP cc_start: 0.9230 (t0) cc_final: 0.8834 (t0) REVERT: J 93 ASN cc_start: 0.8925 (t0) cc_final: 0.8669 (p0) REVERT: K 55 ASP cc_start: 0.8508 (t0) cc_final: 0.8042 (t0) REVERT: K 238 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8571 (pt0) REVERT: A 8 GLU cc_start: 0.8832 (pp20) cc_final: 0.8598 (pp20) REVERT: A 13 GLN cc_start: 0.9115 (mm110) cc_final: 0.8855 (mm-40) REVERT: B 11 ASP cc_start: 0.9217 (t0) cc_final: 0.8961 (t0) REVERT: B 15 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8602 (mtm110) REVERT: B 93 ASN cc_start: 0.9035 (t0) cc_final: 0.8696 (t0) REVERT: B 119 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8975 (pptt) REVERT: C 11 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9031 (tm) REVERT: C 55 ASP cc_start: 0.8197 (t0) cc_final: 0.7747 (t0) REVERT: C 282 GLU cc_start: 0.8804 (tt0) cc_final: 0.8597 (mp0) REVERT: C 284 ASN cc_start: 0.8367 (m-40) cc_final: 0.7993 (t0) REVERT: D 69 LYS cc_start: 0.7280 (mtpp) cc_final: 0.7020 (mmmm) REVERT: D 70 ASP cc_start: 0.7950 (t0) cc_final: 0.7606 (t0) REVERT: D 94 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7618 (tp-100) REVERT: D 97 LYS cc_start: 0.7411 (tmtt) cc_final: 0.7065 (tmtt) REVERT: D 99 ASP cc_start: 0.7813 (m-30) cc_final: 0.7253 (m-30) REVERT: D 144 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7556 (mp-120) REVERT: D 150 LYS cc_start: 0.9517 (ptpp) cc_final: 0.9181 (ptpp) REVERT: D 187 GLU cc_start: 0.7342 (pm20) cc_final: 0.6996 (pm20) REVERT: G 1 MET cc_start: 0.8270 (ptp) cc_final: 0.7849 (ptt) REVERT: L 21 ASP cc_start: 0.7124 (t0) cc_final: 0.6770 (t0) REVERT: L 69 LYS cc_start: 0.8072 (mtmm) cc_final: 0.7709 (mmmm) REVERT: L 144 GLN cc_start: 0.8710 (mt0) cc_final: 0.8438 (mm-40) REVERT: V 13 ARG cc_start: 0.8260 (ptm-80) cc_final: 0.6998 (ptm-80) REVERT: V 19 SER cc_start: 0.8820 (p) cc_final: 0.8474 (p) REVERT: V 28 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8822 (mtmm) REVERT: V 33 LYS cc_start: 0.9227 (ptmm) cc_final: 0.8855 (ptpp) REVERT: V 57 PHE cc_start: 0.9495 (m-80) cc_final: 0.9291 (m-80) outliers start: 67 outliers final: 25 residues processed: 393 average time/residue: 0.5307 time to fit residues: 234.1096 Evaluate side-chains 384 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 353 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 2 ILE 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 15 ARG Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 119 LYS 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 45 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 80 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 151 optimal weight: 40.0000 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** H 27 ASN L 144 GLN V 7 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.089938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.065510 restraints weight = 42092.757| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.33 r_work: 0.2901 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8983 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.401 17292 Z= 0.144 Angle : 0.737 17.056 23529 Z= 0.328 Chirality : 0.044 0.248 2557 Planarity : 0.004 0.047 2868 Dihedral : 14.665 174.051 2692 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.77 % Allowed : 24.70 % Favored : 72.53 % 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: 1.86 (0.16), residues: 948 sheet: -1.09 (0.34), residues: 222 loop : -0.25 (0.21), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 27 TYR 0.031 0.001 TYR X 12 PHE 0.017 0.001 PHE J 85 TRP 0.039 0.002 TRP D 190 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 (17270) covalent geometry : angle 0.73023 / 0.33 (23519) SS BOND : bond 0.00398 / 0.21 ( 2) SS BOND : angle 1.00362 / 0.54 ( 4) hydrogen bonds : bond 0.04097 / 2.80 ( 831) hydrogen bonds : angle 4.44452 / 3.17 ( 2409) metal coordination : bond 0.00889 / 0.51 ( 8) metal coordination : angle 6.46162 / 3.43 ( 6) Misc. bond : bond 0.15460 / 7.15 ( 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 417 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7739 (tm130) REVERT: I 24 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8848 (mp) REVERT: I 104 MET cc_start: 0.9065 (ttm) cc_final: 0.8840 (ttp) REVERT: J 11 ASP cc_start: 0.9211 (t0) cc_final: 0.8831 (t0) REVERT: J 153 LYS cc_start: 0.8851 (mtmm) cc_final: 0.8591 (pttt) REVERT: K 55 ASP cc_start: 0.8541 (t0) cc_final: 0.8065 (t0) REVERT: K 238 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: N 4 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8644 (tp30) REVERT: A 5 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8562 (mp0) REVERT: B 11 ASP cc_start: 0.9260 (t0) cc_final: 0.8997 (t0) REVERT: B 15 ARG cc_start: 0.8823 (OUTLIER) cc_final: 0.8609 (mtm110) REVERT: B 93 ASN cc_start: 0.8976 (t0) cc_final: 0.8648 (t0) REVERT: B 119 LYS cc_start: 0.9295 (OUTLIER) cc_final: 0.8960 (pptt) REVERT: C 11 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8968 (tm) REVERT: C 55 ASP cc_start: 0.8239 (t0) cc_final: 0.7754 (t0) REVERT: C 284 ASN cc_start: 0.8378 (m-40) cc_final: 0.8036 (t0) REVERT: D 69 LYS cc_start: 0.7241 (mtpp) cc_final: 0.6985 (mmmm) REVERT: D 70 ASP cc_start: 0.8039 (t0) cc_final: 0.7722 (t0) REVERT: D 94 GLN cc_start: 0.7856 (tp-100) cc_final: 0.7598 (tp-100) REVERT: D 97 LYS cc_start: 0.7431 (tmtt) cc_final: 0.7157 (tmtt) REVERT: D 99 ASP cc_start: 0.7805 (m-30) cc_final: 0.7308 (m-30) REVERT: D 144 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7485 (mp-120) REVERT: D 150 LYS cc_start: 0.9525 (ptpp) cc_final: 0.9199 (ptpp) REVERT: D 187 GLU cc_start: 0.7350 (pm20) cc_final: 0.7010 (pm20) REVERT: G 1 MET cc_start: 0.8233 (ptp) cc_final: 0.7839 (ptt) REVERT: L 21 ASP cc_start: 0.7139 (t0) cc_final: 0.6724 (t0) REVERT: L 69 LYS cc_start: 0.8008 (mtmm) cc_final: 0.7576 (mmmm) REVERT: L 133 GLU cc_start: 0.8597 (tt0) cc_final: 0.8309 (pt0) REVERT: V 13 ARG cc_start: 0.8239 (ptm-80) cc_final: 0.7519 (ptm-80) REVERT: V 19 SER cc_start: 0.8864 (p) cc_final: 0.8641 (p) REVERT: V 33 LYS cc_start: 0.9208 (ptmm) cc_final: 0.8839 (ptpp) REVERT: V 49 PHE cc_start: 0.8610 (m-80) cc_final: 0.8350 (m-80) REVERT: V 57 PHE cc_start: 0.9458 (m-80) cc_final: 0.9161 (m-80) outliers start: 46 outliers final: 25 residues processed: 395 average time/residue: 0.5511 time to fit residues: 245.2779 Evaluate side-chains 385 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 354 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 146 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 30.0000 chunk 99 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.0870 chunk 88 optimal weight: 2.9990 overall best weight: 0.9960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3689 r_free = 0.3689 target = 0.090214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.065557 restraints weight = 42522.285| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.48 r_work: 0.2897 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.400 17292 Z= 0.147 Angle : 0.760 16.771 23529 Z= 0.339 Chirality : 0.044 0.261 2557 Planarity : 0.004 0.047 2868 Dihedral : 14.388 176.570 2692 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.59 % Allowed : 25.78 % Favored : 71.63 % 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: 1.92 (0.16), residues: 946 sheet: -1.03 (0.34), residues: 222 loop : -0.28 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 27 TYR 0.017 0.001 TYR G 29 PHE 0.020 0.001 PHE M 28 TRP 0.041 0.002 TRP D 190 HIS 0.008 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.14 (17270) covalent geometry : angle 0.75174 / 0.34 (23519) SS BOND : bond 0.00429 / 0.22 ( 2) SS BOND : angle 0.91436 / 0.50 ( 4) hydrogen bonds : bond 0.04105 / 2.82 ( 831) hydrogen bonds : angle 4.43736 / 3.17 ( 2409) metal coordination : bond 0.00836 / 0.53 ( 8) metal coordination : angle 7.03220 / 3.69 ( 6) Misc. bond : bond 0.15394 / 7.02 ( 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: 43 poor density : 366 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8198 (tm-30) cc_final: 0.7960 (tm130) REVERT: X 10 LYS cc_start: 0.9033 (tppt) cc_final: 0.7790 (tppt) REVERT: X 46 VAL cc_start: 0.9455 (t) cc_final: 0.9234 (p) REVERT: I 24 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8842 (mp) REVERT: I 180 GLU cc_start: 0.7668 (pm20) cc_final: 0.7444 (pm20) REVERT: J 11 ASP cc_start: 0.9243 (t0) cc_final: 0.8848 (t0) REVERT: J 95 LEU cc_start: 0.9235 (tp) cc_final: 0.8982 (mt) REVERT: J 153 LYS cc_start: 0.8862 (mtmm) cc_final: 0.8658 (ptmm) REVERT: K 55 ASP cc_start: 0.8580 (t0) cc_final: 0.8111 (t0) REVERT: K 238 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (pt0) REVERT: A 5 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8618 (mp0) REVERT: B 11 ASP cc_start: 0.9271 (t0) cc_final: 0.8966 (t0) REVERT: B 15 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8617 (mtm110) REVERT: B 93 ASN cc_start: 0.8973 (t0) cc_final: 0.8706 (t0) REVERT: C 11 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.9006 (tm) REVERT: C 55 ASP cc_start: 0.8240 (t0) cc_final: 0.7748 (t0) REVERT: C 284 ASN cc_start: 0.8401 (m-40) cc_final: 0.8072 (t0) REVERT: D 69 LYS cc_start: 0.7286 (mtpp) cc_final: 0.7039 (mmmm) REVERT: D 70 ASP cc_start: 0.7945 (t0) cc_final: 0.7636 (t0) REVERT: D 94 GLN cc_start: 0.7830 (tp-100) cc_final: 0.7622 (tp-100) REVERT: D 97 LYS cc_start: 0.7413 (tmtt) cc_final: 0.7180 (tmmt) REVERT: D 99 ASP cc_start: 0.7839 (m-30) cc_final: 0.7380 (m-30) REVERT: D 144 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: D 150 LYS cc_start: 0.9519 (ptpp) cc_final: 0.9191 (ptpp) REVERT: D 187 GLU cc_start: 0.7330 (pm20) cc_final: 0.6970 (pm20) REVERT: G 1 MET cc_start: 0.8201 (ptp) cc_final: 0.7764 (ptt) REVERT: L 21 ASP cc_start: 0.7072 (t0) cc_final: 0.6647 (t0) REVERT: L 69 LYS cc_start: 0.8005 (mtmm) cc_final: 0.7573 (mmmm) REVERT: L 137 MET cc_start: 0.9057 (mtp) cc_final: 0.8680 (mmm) REVERT: L 150 LYS cc_start: 0.8894 (tppt) cc_final: 0.8549 (mptp) REVERT: V 13 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.7616 (ptm-80) REVERT: V 19 SER cc_start: 0.8901 (p) cc_final: 0.8667 (p) REVERT: V 33 LYS cc_start: 0.9272 (ptmm) cc_final: 0.9024 (ptpp) REVERT: V 46 VAL cc_start: 0.9385 (t) cc_final: 0.9176 (p) REVERT: V 55 THR cc_start: 0.9203 (m) cc_final: 0.8981 (m) REVERT: V 57 PHE cc_start: 0.9444 (m-80) cc_final: 0.9185 (m-80) REVERT: V 60 ASP cc_start: 0.8941 (p0) cc_final: 0.8413 (p0) outliers start: 43 outliers final: 23 residues processed: 386 average time/residue: 0.5465 time to fit residues: 236.5170 Evaluate side-chains 382 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 354 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 59 PHE Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 LEU 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 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: 0.9980 chunk 84 optimal weight: 6.9990 chunk 180 optimal weight: 9.9990 chunk 63 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 151 optimal weight: 30.0000 chunk 7 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 ASN ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN ** L 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.087580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.062428 restraints weight = 42551.161| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.10 r_work: 0.2841 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.508 17292 Z= 0.245 Angle : 0.840 18.825 23529 Z= 0.374 Chirality : 0.048 0.191 2557 Planarity : 0.004 0.048 2868 Dihedral : 14.547 174.638 2692 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.35 % Allowed : 26.02 % Favored : 71.63 % 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: 0.76 (0.18), residues: 1996 helix: 1.60 (0.16), residues: 958 sheet: -0.99 (0.34), residues: 222 loop : -0.29 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 27 TYR 0.025 0.002 TYR X 12 PHE 0.018 0.002 PHE A 51 TRP 0.034 0.002 TRP L 190 HIS 0.011 0.002 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.24 (17270) covalent geometry : angle 0.83318 / 0.37 (23519) SS BOND : bond 0.00366 / 0.19 ( 2) SS BOND : angle 0.85233 / 0.47 ( 4) hydrogen bonds : bond 0.04630 / 3.17 ( 831) hydrogen bonds : angle 4.60976 / 3.30 ( 2409) metal coordination : bond 0.02299 / 1.34 ( 8) metal coordination : angle 6.66868 / 3.40 ( 6) Misc. bond : bond 0.22576 / 12.23 ( 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 394 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 355 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7711 (tm-30) REVERT: I 24 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8874 (mp) REVERT: I 180 GLU cc_start: 0.7827 (pm20) cc_final: 0.7617 (pm20) REVERT: J 11 ASP cc_start: 0.9246 (t0) cc_final: 0.8877 (t0) REVERT: K 55 ASP cc_start: 0.8652 (t0) cc_final: 0.8209 (t0) REVERT: A 5 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8704 (mp0) REVERT: B 11 ASP cc_start: 0.9239 (t0) cc_final: 0.8990 (t0) REVERT: B 15 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8632 (mtm110) REVERT: B 93 ASN cc_start: 0.8917 (t0) cc_final: 0.8575 (t0) REVERT: B 119 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8947 (pptt) REVERT: C 11 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (tm) REVERT: C 55 ASP cc_start: 0.8254 (t0) cc_final: 0.7810 (t0) REVERT: C 284 ASN cc_start: 0.8503 (m-40) cc_final: 0.8163 (t0) REVERT: D 69 LYS cc_start: 0.7240 (mtpp) cc_final: 0.6964 (mmmm) REVERT: D 70 ASP cc_start: 0.8081 (t0) cc_final: 0.7745 (t0) REVERT: D 97 LYS cc_start: 0.7531 (tmtt) cc_final: 0.7270 (tmtt) REVERT: D 99 ASP cc_start: 0.7881 (m-30) cc_final: 0.7228 (m-30) REVERT: D 144 GLN cc_start: 0.8069 (OUTLIER) cc_final: 0.7540 (mm110) REVERT: D 150 LYS cc_start: 0.9508 (ptpp) cc_final: 0.9225 (ptpp) REVERT: D 187 GLU cc_start: 0.7239 (pm20) cc_final: 0.6869 (pm20) REVERT: L 21 ASP cc_start: 0.7241 (t0) cc_final: 0.6814 (t0) REVERT: L 69 LYS cc_start: 0.7974 (mtmm) cc_final: 0.7545 (mmmm) REVERT: V 13 ARG cc_start: 0.8374 (ptm-80) cc_final: 0.7785 (ptm-80) REVERT: V 19 SER cc_start: 0.8978 (p) cc_final: 0.8753 (p) REVERT: V 25 LYS cc_start: 0.9220 (tppp) cc_final: 0.9005 (tppp) REVERT: V 49 PHE cc_start: 0.8232 (m-80) cc_final: 0.7980 (m-80) REVERT: V 57 PHE cc_start: 0.9441 (m-80) cc_final: 0.9152 (m-80) REVERT: V 60 ASP cc_start: 0.9036 (p0) cc_final: 0.8609 (p0) outliers start: 39 outliers final: 24 residues processed: 373 average time/residue: 0.5688 time to fit residues: 238.5162 Evaluate side-chains 369 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 340 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 22 MET 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 172 LEU Chi-restraints excluded: chain B residue 15 ARG Chi-restraints excluded: chain B residue 110 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 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 105 VAL Chi-restraints excluded: chain L residue 120 CYS Chi-restraints excluded: chain V residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 189 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 238 GLN N 9 ASN ** B 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.063851 restraints weight = 42247.731| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.27 r_work: 0.2862 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.447 17292 Z= 0.172 Angle : 0.809 17.413 23529 Z= 0.362 Chirality : 0.046 0.208 2557 Planarity : 0.004 0.046 2868 Dihedral : 14.307 175.258 2692 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.23 % Allowed : 26.57 % Favored : 71.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.87 (0.18), residues: 1996 helix: 1.73 (0.16), residues: 946 sheet: -0.90 (0.34), residues: 222 loop : -0.28 (0.21), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 27 TYR 0.019 0.001 TYR L 102 PHE 0.022 0.001 PHE B 135 TRP 0.042 0.002 TRP L 190 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.17 (17270) covalent geometry : angle 0.80109 / 0.36 (23519) SS BOND : bond 0.00348 / 0.18 ( 2) SS BOND : angle 0.88139 / 0.51 ( 4) hydrogen bonds : bond 0.04313 / 2.94 ( 831) hydrogen bonds : angle 4.56787 / 3.26 ( 2409) metal coordination : bond 0.01314 / 0.71 ( 8) metal coordination : angle 6.94126 / 3.51 ( 6) Misc. bond : bond 0.18690 / 9.37 ( 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 389 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 352 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 7 GLN cc_start: 0.8157 (tm-30) cc_final: 0.7800 (tm130) REVERT: X 10 LYS cc_start: 0.8928 (tppt) cc_final: 0.8516 (tppt) REVERT: X 12 TYR cc_start: 0.9186 (p90) cc_final: 0.8619 (p90) REVERT: X 46 VAL cc_start: 0.9464 (t) cc_final: 0.9222 (p) REVERT: X 63 LYS cc_start: 0.8614 (pmtt) cc_final: 0.8279 (pmtt) REVERT: I 1 MET cc_start: 0.7844 (ttt) cc_final: 0.7586 (ttt) REVERT: I 19 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9301 (mm) REVERT: I 24 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8795 (mp) REVERT: I 180 GLU cc_start: 0.7805 (pm20) cc_final: 0.7565 (pm20) REVERT: J 11 ASP cc_start: 0.9248 (t0) cc_final: 0.8886 (t0) REVERT: J 153 LYS cc_start: 0.9077 (mtmm) cc_final: 0.8783 (ptmm) REVERT: K 55 ASP cc_start: 0.8629 (t0) cc_final: 0.8146 (t0) REVERT: K 284 ASN cc_start: 0.8735 (p0) cc_final: 0.8512 (p0) REVERT: B 11 ASP cc_start: 0.9248 (t0) cc_final: 0.8973 (t0) REVERT: B 15 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8639 (mtm110) REVERT: B 93 ASN cc_start: 0.8990 (t0) cc_final: 0.8660 (t0) REVERT: B 119 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8934 (pptt) REVERT: C 11 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8996 (tm) REVERT: C 55 ASP cc_start: 0.8335 (t0) cc_final: 0.7868 (t0) REVERT: C 284 ASN cc_start: 0.8555 (m-40) cc_final: 0.8187 (t0) REVERT: D 69 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7045 (mmmm) REVERT: D 70 ASP cc_start: 0.8099 (t0) cc_final: 0.7811 (t0) REVERT: D 97 LYS cc_start: 0.7414 (tmtt) cc_final: 0.7148 (tmmt) REVERT: D 99 ASP cc_start: 0.7919 (m-30) cc_final: 0.7369 (m-30) REVERT: D 150 LYS cc_start: 0.9513 (ptpp) cc_final: 0.9250 (ptpp) REVERT: D 187 GLU cc_start: 0.7362 (pm20) cc_final: 0.7058 (pm20) REVERT: L 21 ASP cc_start: 0.7126 (t0) cc_final: 0.6695 (t0) REVERT: L 69 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7542 (mmmm) REVERT: L 137 MET cc_start: 0.8614 (mpp) cc_final: 0.8194 (mpp) REVERT: L 150 LYS cc_start: 0.8937 (tppt) cc_final: 0.8553 (mptp) REVERT: V 13 ARG cc_start: 0.8310 (ptm-80) cc_final: 0.7692 (ptm-80) REVERT: V 19 SER cc_start: 0.8900 (p) cc_final: 0.8698 (p) REVERT: V 25 LYS cc_start: 0.9240 (tppp) cc_final: 0.9033 (tppp) REVERT: V 46 VAL cc_start: 0.9378 (t) cc_final: 0.9136 (p) REVERT: V 49 PHE cc_start: 0.8536 (m-80) cc_final: 0.8289 (m-80) REVERT: V 57 PHE cc_start: 0.9457 (m-80) cc_final: 0.9141 (m-80) REVERT: V 60 ASP cc_start: 0.9066 (p0) cc_final: 0.8619 (p0) outliers start: 37 outliers final: 21 residues processed: 371 average time/residue: 0.5651 time to fit residues: 236.1445 Evaluate side-chains 371 residues out of total 1660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 345 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 19 LEU Chi-restraints excluded: chain I residue 24 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 22 MET 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 172 LEU Chi-restraints excluded: chain B residue 15 ARG 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 142 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 178 optimal weight: 50.0000 chunk 192 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 171 optimal weight: 0.6980 chunk 153 optimal weight: 10.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3684 r_free = 0.3684 target = 0.089788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.063011 restraints weight = 42193.671| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.33 r_work: 0.2912 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.421 17292 Z= 0.153 Angle : 0.794 16.962 23529 Z= 0.358 Chirality : 0.045 0.186 2557 Planarity : 0.004 0.049 2868 Dihedral : 13.932 173.101 2692 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.99 % Allowed : 26.81 % Favored : 71.20 % 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: 0.87 (0.18), residues: 1996 helix: 1.73 (0.16), residues: 946 sheet: -0.89 (0.35), residues: 217 loop : -0.29 (0.21), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 27 TYR 0.020 0.001 TYR G 29 PHE 0.022 0.001 PHE D 81 TRP 0.051 0.002 TRP L 190 HIS 0.008 0.001 HIS D 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (17270) covalent geometry : angle 0.78632 / 0.36 (23519) SS BOND : bond 0.00328 / 0.17 ( 2) SS BOND : angle 0.74824 / 0.44 ( 4) hydrogen bonds : bond 0.04206 / 2.87 ( 831) hydrogen bonds : angle 4.55353 / 3.25 ( 2409) metal coordination : bond 0.01360 / 0.67 ( 8) metal coordination : angle 6.90418 / 3.52 ( 6) Misc. bond : bond 0.16849 / 8.04 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7701.94 seconds wall clock time: 131 minutes 42.73 seconds (7902.73 seconds total)